diff --git a/HTAN.dependencies.csv b/HTAN.dependencies.csv index 8c12b081..e02fb1ce 100644 --- a/HTAN.dependencies.csv +++ b/HTAN.dependencies.csv @@ -1,1692 +1,1692 @@ Unnamed: 0,Attribute,Label,Description,Required,Cond_Req,Valid Values,Conditional Requirements,Component Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Patient HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Patient -Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Italy', 'Lebanon', 'Canada', 'Macau', 'Israel', 'Malta', 'Curacao', 'Mauritius', 'Gabon', 'Samoa', 'Sao Tome and Principe', 'Wallis and Futuna', 'Finland', 'Iraq', 'Indonesia', 'Lesotho', 'Mali', 'Qatar', 'Solomon Islands', 'Niger', 'Hong Kong', 'Algeria', 'Pakistan', 'Holy See', 'Bermuda', 'Barbados', 'Croatia', 'Iceland', 'Saint Kitts and Nevis', 'Saint Vincent and the Grenadines', 'Virgin Islands U.S.', 'Equatorial Guinea', 'Guinea', 'Costa Rica', 'Romania', 'Switzerland', 'Albania', 'Guatemala', 'Senegal', 'Serbia', 'Cyprus', 'Uzbekistan', 'Kenya', 'Djibouti', 'Brazil', 'Papua New Guinea', 'Tajikistan', 'India', 'Congo', 'Aruba', 'Nepal', 'Togo', 'Guadeloupe', ""Cote d'Ivoire"", 'Czech Republic (Czechia)', 'Kuwait', 'Zambia', 'Madagascar', 'Fiji', 'Sri Lanka', 'New Zealand', 'Tanzania', 'Antigua and Barbuda', 'Monaco', 'Jamaica', 'Australia', 'Argentina', 'Luxembourg', 'Guinea-Bissau', 'United Arab Emirates', 'South Sudan', 'Benin', 'Burundi', 'Denmark', 'Jordan', 'Saint Helena Ascension and Tristan da Cunha', 'United Kingdom', 'Zimbabwe', 'Bolivia', 'Guernsey', 'Nigeria', 'Mexico', 'Guam', 'Honduras', 'Grenada', 'Palau', 'Yemen', 'Panama', 'Isle of Man', 'Gibraltar', 'Uruguay', 'Dominica', 'Laos', 'Anguilla', 'Kyrgyzstan', 'Venezuela', 'Cuba', 'Bhutan', 'El Salvador', 'Cambodia', 'Liechtenstein', 'Myanmar', 'Nauru', 'Portugal', 'Japan', 'Kiribati', 'Democratic Republic of the Congo', 'Sweden', 'Nicaragua', 'Guyana', 'Malaysia', 'Marshall Islands', 'Belize', 'Saint Lucia', 'Virgin Islands British', 'Mayotte', 'Seychelles', 'South Korea', 'Armenia', 'Philippines', 'Svalbard & Jan Mayen Islands', 'Kazakhstan', 'Slovenia', 'Greece', 'Northern Mariana Islands', 'Mongolia', 'Morocco', 'Saint Pierre and Miquelon', 'Slovakia', 'State of Palestine', 'Saudi Arabia', 'Tunisia', 'Spain', 'Oman', 'Comoros', 'French Guiana', 'Ireland', 'Western Sahara', 'Lithuania', 'Ukraine', 'Eritrea', 'Eswatini', 'Trinidad and Tobago', 'North Macedonia', 'Burkina Faso', 'Hungary', 'South Africa', 'Niue', 'Chad', 'Poland', 'Dominican Republic', 'Timor-Leste', 'Faroe Islands', 'Tokelau', 'Cook Islands', 'Turkmenistan', 'Tuvalu', 'Taiwan', 'China', 'Falkland Islands (Malvinas)', 'Cayman Islands', 'Montenegro', 'Libya', 'Colombia', 'Jersey', 'Paraguay', 'Vietnam', 'Bosnia and Herzegovina', 'Malawi', 'Gambia', 'Turkey', 'United States', 'French Polynesia', 'Sudan', 'Liberia', 'Belarus', 'Austria', 'Reunion', 'Central African Republic', 'Azerbaijan', 'Brunei', 'Norway', 'Cameroon', 'San Marino', 'Ghana', 'Moldova', 'Ethiopia', 'Bangladesh', 'North Korea', 'Singapore', 'Sierra Leone', 'Bahamas', 'Maldives', 'Bulgaria', 'Greenland', 'Netherlands', 'Rwanda', 'Suriname', 'Federated States of Micronesia', 'Somalia', 'Botswana', 'Georgia', 'Montserrat', 'Germany', 'Kosovo', 'Mozambique', 'Andorra', 'Puerto Rico', 'Haiti', 'Martinique', 'Afghanistan', 'Egypt', 'Namibia', 'Tonga', 'Uganda', 'Iran', 'Latvia', 'Peru', 'Bahrain', 'Cape Verde', 'Ecuador', 'Chile', 'Russia', 'Thailand', 'Angola', 'Syria', 'France', 'Belgium', 'Estonia', 'New Caledonia', 'Vanuatu', 'Mauritania', '']",,Demographics +Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['Unspecified', 'Male', 'Not Reported', 'Female', 'unknown']",,Demographics Occupation Duration Years,Occupation Duration Years,OccupationDurationYears,The number of years a patient worked in a specific occupation.,False,,,,Demographics +Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['unknown', 'Dead', 'Alive', 'Not Reported']",,Demographics Weeks Gestation at Birth,Weeks Gestation at Birth,WeeksGestationatBirth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,False,,,,Demographics -Premature At Birth,Premature At Birth,PrematureAtBirth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Demographics +Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['Not Reported', 'not allowed to collect', 'not hispanic or latino', 'hispanic or latino', 'unknown']",,Demographics +Age Is Obfuscated,Age Is Obfuscated,AgeIsObfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,False,,"['false', 'true', '']",,Demographics +Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['Not Reported', 'black or african american', 'not allowed to collect', 'white', 'american indian or alaska native', 'native hawaiian or other pacific islander', 'unknown', 'asian', 'Other']",,Demographics +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Demographics +Premature At Birth,Premature At Birth,PrematureAtBirth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Demographics Days to Birth,Days to Birth,DaystoBirth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable',False,,,,Demographics -Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['Unspecified', 'Not Reported', 'unknown', 'Female', 'Male']",,Demographics Year Of Birth,Year Of Birth,YearOfBirth,Numeric value to represent the calendar year in which an individual was born.,False,,,,Demographics -Age Is Obfuscated,Age Is Obfuscated,AgeIsObfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,False,,"['true', 'false', '']",,Demographics +Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Israel', 'Ethiopia', 'Solomon Islands', 'Dominica', 'Kenya', 'South Sudan', 'Tokelau', 'Burkina Faso', 'Mongolia', 'Jersey', 'Colombia', 'Antigua and Barbuda', 'Bahrain', 'Guinea-Bissau', 'Nigeria', 'Algeria', 'Austria', 'Laos', 'Bangladesh', 'Holy See', 'Kiribati', 'United States', 'Slovakia', 'Qatar', 'Seychelles', 'Germany', 'Northern Mariana Islands', 'Morocco', 'Malawi', 'Eritrea', 'Kosovo', 'Saint Vincent and the Grenadines', 'Faroe Islands', 'Czech Republic (Czechia)', 'Guadeloupe', 'Monaco', 'Cape Verde', 'Jamaica', 'French Guiana', 'Bahamas', 'Sri Lanka', 'Samoa', 'Georgia', 'Saint Lucia', 'Hong Kong', 'Saudi Arabia', 'South Africa', 'Mayotte', 'Reunion', 'Palau', 'Australia', 'Ukraine', 'Benin', 'Malaysia', 'Gambia', 'Lebanon', 'Sudan', 'Tonga', 'Albania', 'Cook Islands', 'Azerbaijan', 'Jordan', 'Venezuela', 'Zimbabwe', 'Nepal', 'Russia', 'Ecuador', 'Gibraltar', 'Peru', 'Iraq', 'New Zealand', 'Sweden', 'North Korea', 'Equatorial Guinea', 'Tajikistan', 'China', 'Malta', 'Mozambique', 'Cayman Islands', 'Moldova', 'Ireland', 'Andorra', 'Montenegro', 'Saint Kitts and Nevis', 'Zambia', 'Norway', 'France', 'Finland', 'Philippines', 'Chad', 'India', 'Guyana', 'Japan', 'Kyrgyzstan', 'Brazil', 'Marshall Islands', 'Costa Rica', 'Bhutan', 'Serbia', 'Central African Republic', 'Mauritania', 'Trinidad and Tobago', 'State of Palestine', 'United Kingdom', 'Isle of Man', 'Cambodia', 'Iran', 'Tunisia', 'Argentina', 'Congo', 'Hungary', 'Saint Helena Ascension and Tristan da Cunha', 'Egypt', 'Bulgaria', 'Kuwait', 'Libya', 'Panama', 'Guinea', 'Djibouti', 'Niue', 'Papua New Guinea', 'Greece', 'Haiti', 'Sierra Leone', 'El Salvador', 'Vietnam', 'Netherlands', 'French Polynesia', 'Guatemala', 'Turkey', 'Turkmenistan', 'Namibia', 'Indonesia', 'Mexico', ""Cote d'Ivoire"", 'Luxembourg', 'San Marino', 'Togo', 'Uzbekistan', 'Yemen', 'Estonia', 'Uruguay', 'Canada', 'Senegal', 'Wallis and Futuna', 'Botswana', 'Burundi', 'Denmark', 'Croatia', 'Poland', 'Montserrat', 'Guam', 'Syria', 'Belize', 'Belgium', 'Madagascar', 'Afghanistan', 'Dominican Republic', 'Oman', 'Switzerland', 'Comoros', 'Vanuatu', 'Cameroon', 'Macau', 'Falkland Islands (Malvinas)', 'Ghana', 'New Caledonia', 'Bolivia', 'Chile', 'Iceland', 'Western Sahara', 'Angola', 'Armenia', 'Bosnia and Herzegovina', 'Paraguay', 'Somalia', 'Slovenia', 'Mali', 'Eswatini', 'Pakistan', 'Liberia', 'Sao Tome and Principe', 'Honduras', 'Lithuania', 'Aruba', 'Federated States of Micronesia', 'Belarus', 'Anguilla', 'Bermuda', 'Maldives', 'Virgin Islands British', 'Grenada', 'Portugal', 'Tuvalu', 'Rwanda', 'United Arab Emirates', 'Fiji', 'Singapore', 'Brunei', 'Tanzania', 'Lesotho', 'Taiwan', 'Guernsey', 'Puerto Rico', 'Timor-Leste', 'Spain', 'Suriname', 'Saint Pierre and Miquelon', 'South Korea', 'Kazakhstan', 'Cuba', 'Latvia', 'Nicaragua', 'Romania', 'Uganda', 'Svalbard & Jan Mayen Islands', 'Democratic Republic of the Congo', 'Gabon', 'Martinique', 'Mauritius', 'Thailand', 'Liechtenstein', 'Greenland', 'Myanmar', 'Virgin Islands U.S.', 'Niger', 'Curacao', 'Cyprus', 'Barbados', 'Nauru', 'North Macedonia', 'Italy', '']",,Demographics Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Demographics -Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Not Reported', 'Alive', 'unknown', 'Dead']",,Demographics -Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['Not Reported', 'hispanic or latino', 'not allowed to collect', 'unknown', 'not hispanic or latino']",,Demographics -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Demographics -Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['Not Reported', 'Other', 'black or african american', 'asian', 'not allowed to collect', 'american indian or alaska native', 'unknown', 'white', 'native hawaiian or other pacific islander']",,Demographics -Days to Vital Status Reference,Days to Vital Status Reference,DaystoVitalStatusReference,Number of days between the date used for index and the reference date for designation of vital status,False,True,,"['Vital Status is ""Alive""']",Demographics -Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Not Reported', 'Cancer Related', 'End-stage Renal Disease', 'Cardiovascular Disorder NOS', 'Not Applicable', 'Surgical Complications', 'Toxicity', 'Infection', 'Renal Disorder NOS', 'Not Cancer Related', 'unknown', 'Spinal Muscular Atrophy', '']","['Vital Status is ""Dead""']",Demographics -Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Not Reported', 'Death Certificate', 'Obituary', 'Medical Record', 'unknown', 'Social Security Death Index', 'Autopsy', '']","['Vital Status is ""Dead""']",Demographics Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,,"['Vital Status is ""Dead""']",Demographics +Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Death Certificate', 'Social Security Death Index', 'Not Reported', 'Autopsy', 'Medical Record', 'unknown', 'Obituary', '']","['Vital Status is ""Dead""']",Demographics +Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Toxicity', 'Renal Disorder NOS', 'Not Reported', 'Spinal Muscular Atrophy', 'Cardiovascular Disorder NOS', 'Cancer Related', 'Not Cancer Related', 'Surgical Complications', 'End-stage Renal Disease', 'Infection', 'unknown', 'Not Applicable', '']","['Vital Status is ""Dead""']",Demographics Days to Death,Days to Death,DaystoDeath,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days. If not applicable please enter 'Not Applicable',False,True,,"['Vital Status is ""Dead""']",Demographics +Days to Vital Status Reference,Days to Vital Status Reference,DaystoVitalStatusReference,Number of days between the date used for index and the reference date for designation of vital status,False,True,,"['Vital Status is ""Alive""']",Demographics Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FamilyHistory +Relative with Cancer History,Relative with Cancer History,RelativewithCancerHistory,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,False,,"['unknown', 'Yes - Cancer History Relative', 'None', 'Not Reported', '']",,FamilyHistory HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FamilyHistory -Relative with Cancer History,Relative with Cancer History,RelativewithCancerHistory,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,False,,"['Not Reported', 'None', 'unknown', 'Yes - Cancer History Relative', '']",,FamilyHistory Relationship Age at Diagnosis,Relationship Age at Diagnosis,RelationshipAgeatDiagnosis,The age (in years) when the patient's relative was first diagnosed.,False,True,,"['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Relationship Gender,Relationship Gender,RelationshipGender,The text term used to describe the gender of the patient's relative with a history of cancer.,False,True,"['Unspecified', 'Not Reported', 'unknown', 'Female', 'Male', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Relationship Type,Relationship Type,RelationshipType,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,False,True,"['Half Brother', 'Paternal Grandmother', 'Aunt', 'Natural Son', 'Identical Twin Sister', 'Maternal Half Sibling', 'Natural Grandchild', 'Natural Mother', 'Paternal Uncle', 'Spouse', 'Foster Daughter', 'Maternal Great Uncle', 'Adoptive Sister', 'Maternal Great Aunt', 'Natural Grandmother', 'Adoptive Mother', 'Adopted Daughter', 'Maternal Grandparent', 'Paternal First Cousin Once Removed', 'Natural Child', 'Wife', 'Daughter-in-law', 'Adoptive Brother', 'Stepfather', 'Natural Father', 'Cousin', 'Paternal Great Aunt', 'Grandmother', 'Niece Second Degree Relative', 'Natural Brother', 'Natural Sibling', 'Natural Grandfather', 'Sister', 'Stepsister', 'Refused', 'Fraternal Twin Sister', 'Grandfather', 'Natural Sister', 'Foster Brother', 'Identical Twin Sibling', 'Maternal Half Sister', 'Mother-in-law', 'Paternal Half Brother', 'Step Sibling', 'Identical Twin Brother', 'Maternal Grandmother', 'Sister-in-law', 'Grandchild', 'Female Cousin', 'Uncle', 'Paternal Aunt', 'Natural Daughter', 'Son-in-law', 'First Cousin', 'Stepbrother', 'Twin Sibling', 'Adopted Son', 'Full Sister', 'Paternal Grandparent', 'Step Child', 'Father', 'Maternal Uncle', 'Foster Sister', 'Foster Son', 'Granddaughter', 'Full Brother', 'Male Cousin', 'Natural Parent', 'Foster Father', 'Other', 'Foster Mother', 'Paternal Half Sister', 'Natural Grandparent', 'Paternal Great Grandparent', 'Son', 'First Cousin Once Removed', 'Fraternal Twin Sibling', 'Nephew', 'Maternal Grandfather', 'Unrelated', 'Sibling', 'Fraternal Twin Brother', 'Brother-in-law', 'Niece', 'Maternal First Cousin', 'Paternal Grandfather', 'Not Reported', 'Grand Niece', 'Grandson', 'Mother', 'Stepson', 'Stepdaughter', 'Adoptive Father', 'Maternal First Cousin Once Removed', 'Parent', 'Maternal Half Brother', 'unknown', 'Child', 'Grandparent', 'Daughter', 'Paternal Half Sibling', 'Brother', 'Half Sibling', 'Stepmother', 'Half Sister', 'Grand Nephew', 'Husband', 'Paternal Great Uncle', 'Maternal Aunt', 'Great Grandchild', 'Ward', 'Maternal Great Grandparent', 'Paternal First Cousin', 'Domestic Partner', 'Father-in-law', 'Legal Guardian', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory +Relationship Type,Relationship Type,RelationshipType,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,False,True,"['Grandfather', 'Paternal Grandparent', 'Stepsister', 'Sibling', 'Adopted Daughter', 'Grandchild', 'Natural Grandparent', 'Natural Father', 'Maternal Uncle', 'Maternal First Cousin Once Removed', 'Mother-in-law', 'Uncle', 'Paternal Uncle', 'Brother', 'Foster Daughter', 'Foster Brother', 'Nephew', 'Identical Twin Sister', 'Son-in-law', 'Aunt', 'Sister-in-law', 'Grandson', 'Natural Brother', 'Half Sister', 'Full Sister', 'Fraternal Twin Sibling', 'Half Brother', 'Legal Guardian', 'Paternal Great Aunt', 'Foster Mother', 'Not Reported', 'Identical Twin Brother', 'Half Sibling', 'Great Grandchild', 'Fraternal Twin Brother', 'Natural Sister', 'Maternal Aunt', 'Natural Grandfather', 'Niece Second Degree Relative', 'Grandmother', 'Paternal Half Brother', 'Natural Parent', 'unknown', 'Adoptive Father', 'Grandparent', 'Female Cousin', 'Wife', 'Parent', 'Daughter', 'Stepdaughter', 'Male Cousin', 'Sister', 'Natural Grandchild', 'Natural Grandmother', 'Natural Mother', 'Son', 'Mother', 'Maternal Half Sibling', 'Maternal Half Brother', 'Natural Son', 'Maternal Great Uncle', 'Spouse', 'Adoptive Sister', 'Foster Father', 'Niece', 'Ward', 'Maternal Grandmother', 'Maternal Great Aunt', 'Stepfather', 'Maternal Half Sister', 'Paternal First Cousin', 'Foster Sister', 'Full Brother', 'Identical Twin Sibling', 'Maternal Great Grandparent', 'Adoptive Brother', 'Brother-in-law', 'Paternal First Cousin Once Removed', 'Paternal Grandfather', 'First Cousin Once Removed', 'Step Child', 'Maternal Grandparent', 'Paternal Half Sibling', 'Maternal Grandfather', 'Daughter-in-law', 'Paternal Great Grandparent', 'First Cousin', 'Paternal Aunt', 'Father', 'Stepson', 'Natural Sibling', 'Grand Nephew', 'Granddaughter', 'Paternal Great Uncle', 'Foster Son', 'Father-in-law', 'Stepbrother', 'Fraternal Twin Sister', 'Grand Niece', 'Husband', 'Natural Daughter', 'Cousin', 'Unrelated', 'Other', 'Child', 'Paternal Half Sister', 'Adoptive Mother', 'Step Sibling', 'Paternal Grandmother', 'Natural Child', 'Stepmother', 'Refused', 'Maternal First Cousin', 'Domestic Partner', 'Adopted Son', 'Twin Sibling', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory +Relationship Gender,Relationship Gender,RelationshipGender,The text term used to describe the gender of the patient's relative with a history of cancer.,False,True,"['Unspecified', 'Male', 'Not Reported', 'Female', 'unknown', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory Relatives with Cancer History Count,Relatives with Cancer History Count,RelativeswithCancerHistoryCount,The number of relatives the patient has with a known history of cancer.,False,True,,"['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Relationship Primary Diagnosis,Relationship Primary Diagnosis,RelationshipPrimaryDiagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,False,True,"['Not Reported', 'Blood Cancer', 'Osteosarcoma', 'Head and Neck Cancer', 'Rectal Cancer', 'Mesothelioma', 'Wilms Tumor', 'Ewing Sarcoma', 'Leukemia', 'Lymphoma', 'Melanoma', 'Bone Cancer', 'unknown', 'Bile Duct Cancer', 'Adrenal Gland Cancer', 'Laryngeal Cancer', 'Lung Cancer', 'Tonsillar Cancer', 'Glioblastoma', 'Breast Cancer', 'Esophageal Cancer', 'Basal Cell Cancer', 'Colorectal Cancer', 'CNS Cancer', 'Chondrosarcoma', 'Cervical Cancer', 'Gastric Cancer', 'Prostate Cancer', 'Uterine Cancer', 'Skin Cancer', 'Throat Cancer', 'Kidney Cancer', 'Thyroid Cancer', 'Bladder Cancer', 'Cancer', 'Kaposi Sarcoma', 'Multiple Myeloma', 'Tongue Cancer', 'Gallbladder Cancer', 'Hematologic Cancer', 'Liver Cancer', 'Lymph Node Cancer', 'Pancreas Cancer', 'Testicular Cancer', 'Spleen Cancer', 'Sarcoma', 'Neuroblastoma', 'Ovarian Cancer', 'Rhabdomyosarcoma', 'Gynecologic Cancer', 'Brain Cancer', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Coal Dust Exposure,Coal Dust Exposure,CoalDustExposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,False,,"['no', 'unknown', 'yes', '']",,Exposure -Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Exposure -Environmental Tobacco Smoke Exposure,Environmental Tobacco Smoke Exposure,EnvironmentalTobaccoSmokeExposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.",False,,"['no', 'unknown', 'yes', '']",,Exposure -Respirable Crystalline Silica Exposure,Respirable Crystalline Silica Exposure,RespirableCrystallineSilicaExposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.",False,,"['no', 'unknown', 'yes', '']",,Exposure -Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Exposure -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Exposure -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,Exposure -Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Not Reported', 'Yes - Alcohol Exposure', 'No - Alcohol Exposure']",,Exposure -Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['Not Reported', 'No - Smoking Exposure', 'Yes - Smoking Exposure']",,Exposure +Relationship Primary Diagnosis,Relationship Primary Diagnosis,RelationshipPrimaryDiagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,False,True,"['Ewing Sarcoma', 'Brain Cancer', 'Adrenal Gland Cancer', 'Not Reported', 'Lymphoma', 'Osteosarcoma', 'Bile Duct Cancer', 'Hematologic Cancer', 'Ovarian Cancer', 'Chondrosarcoma', 'Rhabdomyosarcoma', 'Bladder Cancer', 'Gallbladder Cancer', 'Glioblastoma', 'Cervical Cancer', 'Kidney Cancer', 'CNS Cancer', 'Pancreas Cancer', 'Prostate Cancer', 'Lung Cancer', 'Uterine Cancer', 'Mesothelioma', 'Throat Cancer', 'Liver Cancer', 'Head and Neck Cancer', 'Tonsillar Cancer', 'Testicular Cancer', 'unknown', 'Laryngeal Cancer', 'Bone Cancer', 'Breast Cancer', 'Neuroblastoma', 'Thyroid Cancer', 'Colorectal Cancer', 'Kaposi Sarcoma', 'Sarcoma', 'Wilms Tumor', 'Leukemia', 'Melanoma', 'Blood Cancer', 'Esophageal Cancer', 'Cancer', 'Lymph Node Cancer', 'Tongue Cancer', 'Basal Cell Cancer', 'Skin Cancer', 'Spleen Cancer', 'Multiple Myeloma', 'Rectal Cancer', 'Gastric Cancer', 'Gynecologic Cancer', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory +Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Yes - Alcohol Exposure', 'No - Alcohol Exposure', 'Not Reported']",,Exposure +Coal Dust Exposure,Coal Dust Exposure,CoalDustExposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,False,,"['unknown', 'no', 'yes', '']",,Exposure +Environmental Tobacco Smoke Exposure,Environmental Tobacco Smoke Exposure,EnvironmentalTobaccoSmokeExposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.",False,,"['unknown', 'no', 'yes', '']",,Exposure +Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['No - Smoking Exposure', 'Yes - Smoking Exposure', 'Not Reported']",,Exposure +Respirable Crystalline Silica Exposure,Respirable Crystalline Silica Exposure,RespirableCrystallineSilicaExposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.",False,,"['unknown', 'no', 'yes', '']",,Exposure HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Exposure -Alcohol Intensity,Alcohol Intensity,AlcoholIntensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,False,True,"['Not Reported', 'Lifelong Non-Drinker', 'Drinker', 'Heavy Drinker', 'Occasional Drinker', 'Non-Drinker', 'unknown', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure -Alcohol History,Alcohol History,AlcoholHistory,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,False,True,"['Not Reported', 'no', 'unknown', 'yes', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Exposure +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,Exposure +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Exposure +Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Exposure +Alcohol Intensity,Alcohol Intensity,AlcoholIntensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,False,True,"['Drinker', 'Non-Drinker', 'Heavy Drinker', 'Not Reported', 'Occasional Drinker', 'Lifelong Non-Drinker', 'unknown', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +Alcohol History,Alcohol History,AlcoholHistory,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,False,True,"['unknown', 'no', 'yes', 'Not Reported', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure Alcohol Days Per Week,Alcohol Days Per Week,AlcoholDaysPerWeek,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,False,True,,"['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +Alcohol Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Not Reported', 'Liquor', 'Wine', 'unknown', 'Other', 'Beer', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure Alcohol Drinks Per Day,Alcohol Drinks Per Day,AlcoholDrinksPerDay,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,False,True,,"['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure -Alcohol Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Not Reported', 'Other', 'Liquor', 'Wine', 'unknown', 'Beer', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure -Time between Waking and First Smoke,Time between Waking and First Smoke,TimebetweenWakingandFirstSmoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,False,True,"['6-30 Minutes', 'Within 5 Minutes', '31-60 Minutes', 'unknown', 'After 60 Minutes', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Type of Tobacco Used,Type of Tobacco Used,TypeofTobaccoUsed,The text term used to describe the specific type of tobacco used by the patient.,False,True,"['Not Reported', 'Pipe', 'Other', 'Electronic Cigarette', 'Cigarettes', 'Cigar', 'Smokeless Tobacco', 'unknown', 'Marijuana', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Smoke Exposure Duration,Smoke Exposure Duration,SmokeExposureDuration,Text term used to describe the length of time the patient was exposed to an environmental factor.,False,True,"['Not Reported', 'Six Weeks or More', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Smokeless Tobacco Quit Age,Smokeless Tobacco Quit Age,SmokelessTobaccoQuitAge,Smokeless tobacco quit age,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Tobacco Smoking Status,Tobacco Smoking Status,TobaccoSmokingStatus,Category describing current smoking status and smoking history as self-reported by a patient,False,True,"['Not Reported', 'Lifelong Non-Smoker', 'Smoking history not documented', 'Duration Not Specified', 'Current Smoker', 'unknown', 'Current Reformed Smoker for < or = 15 yrs', 'Current Reformed Smoker', 'Current Reformed Smoker for > 15 yrs', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Tobacco Smoking Quit Year,Tobacco Smoking Quit Year,TobaccoSmokingQuitYear,The year in which the participant quit smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Time between Waking and First Smoke,Time between Waking and First Smoke,TimebetweenWakingandFirstSmoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,False,True,"['Within 5 Minutes', '31-60 Minutes', 'unknown', '6-30 Minutes', 'After 60 Minutes', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Tobacco Smoking Onset Year,Tobacco Smoking Onset Year,TobaccoSmokingOnsetYear,The year in which the participant began smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Type of Smoke Exposure,Type of Smoke Exposure,TypeofSmokeExposure,The text term used to describe the patient's specific type of smoke exposure.,False,True,"['Volcanic smoke', 'Wood burning smoke factory', 'Workrelated smoke generators', 'Workrelated smoke NOS', 'Workrelated smoke paint baking', 'Workrelated smoke plumbing', 'Grilling smoke', 'Workrelated smoke fire fighting', 'unknown', 'Wood burning smoke NOS', 'Accidental building fire smoke', 'Accidental forest fire smoke', 'Accidental fire smoke NOS', 'Indoor coal burning stove or fireplace smoke', 'Workrelated smoke soldering/welding', 'Hashish smoke', 'Indoor stove or fireplace smoke NOS', 'Fire smoke NOS', 'Electrical fire smoke', 'Environmental tobacco smoke', 'Workrelated smoke military', 'Accidental vehicle fire smoke', 'Oil burning smoke Kerosene', 'Oil burning smoke NOS', 'Burning tree smoke', 'Smoke exposure NOS', 'Furnace or boiler smoke', 'Workrelated smoke foundry', 'Smokehouse smoke', 'Marijuana smoke', 'Workrelated smoke plastics factory', 'Cooking related smoke NOS', 'Gas burning smoke propane', 'Tobacco smoke cigarettes', 'Factory smokestack smoke', 'Workrelated smoke artificial smoke machines', 'Field burning smoke', 'Electronic cigarette smoke NOS', 'Coal smoke NOS', 'Aircraft smoke', 'Recreational fire smoke', 'Waste burning smoke', 'Machine smoke', 'Tobacco smoke cigar', 'No Smoke Exposure', 'Indoor wood burning stove or fireplace smoke', 'Accidental grass fire smoke', 'Tobacco smoke pipe', 'Grease fire smoke', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Secondhand Smoke as Child,Secondhand Smoke as Child,SecondhandSmokeasChild,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,False,True,"['Not Reported', 'no', 'unknown', 'yes', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Tobacco Use per Day,Tobacco Use per Day,TobaccoUseperDay,Numeric value that represents the number of times the patient uses tobacco each day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Cigarettes per Day,Cigarettes per Day,CigarettesperDay,The average number of cigarettes smoked per day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['Every day', 'unknown', 'Some days', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Tobacco Smoking Quit Year,Tobacco Smoking Quit Year,TobaccoSmokingQuitYear,The year in which the participant quit smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Smoke Exposure Duration,Smoke Exposure Duration,SmokeExposureDuration,Text term used to describe the length of time the patient was exposed to an environmental factor.,False,True,"['Six Weeks or More', 'unknown', 'Not Reported', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Type of Smoke Exposure,Type of Smoke Exposure,TypeofSmokeExposure,The text term used to describe the patient's specific type of smoke exposure.,False,True,"['Electrical fire smoke', 'Workrelated smoke artificial smoke machines', 'Workrelated smoke plumbing', 'Smoke exposure NOS', 'Workrelated smoke fire fighting', 'Accidental grass fire smoke', 'Indoor wood burning stove or fireplace smoke', 'Tobacco smoke cigarettes', 'Marijuana smoke', 'Oil burning smoke NOS', 'Volcanic smoke', 'Coal smoke NOS', 'Hashish smoke', 'Workrelated smoke generators', 'Accidental vehicle fire smoke', 'Recreational fire smoke', 'Workrelated smoke foundry', 'Furnace or boiler smoke', 'Workrelated smoke plastics factory', 'Oil burning smoke Kerosene', 'Wood burning smoke NOS', 'Electronic cigarette smoke NOS', 'Smokehouse smoke', 'Accidental building fire smoke', 'Indoor coal burning stove or fireplace smoke', 'Grease fire smoke', 'Waste burning smoke', 'unknown', 'Workrelated smoke NOS', 'Indoor stove or fireplace smoke NOS', 'Factory smokestack smoke', 'No Smoke Exposure', 'Burning tree smoke', 'Wood burning smoke factory', 'Aircraft smoke', 'Tobacco smoke pipe', 'Environmental tobacco smoke', 'Cooking related smoke NOS', 'Workrelated smoke soldering/welding', 'Grilling smoke', 'Machine smoke', 'Workrelated smoke military', 'Fire smoke NOS', 'Workrelated smoke paint baking', 'Gas burning smoke propane', 'Accidental fire smoke NOS', 'Tobacco smoke cigar', 'Accidental forest fire smoke', 'Field burning smoke', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['unknown', 'Every day', 'Some days', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Smokeless Tobacco Quit Age,Smokeless Tobacco Quit Age,SmokelessTobaccoQuitAge,Smokeless tobacco quit age,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Tobacco Use per Day,Tobacco Use per Day,TobaccoUseperDay,Numeric value that represents the number of times the patient uses tobacco each day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Secondhand Smoke as Child,Secondhand Smoke as Child,SecondhandSmokeasChild,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,False,True,"['unknown', 'no', 'yes', 'Not Reported', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Type of Tobacco Used,Type of Tobacco Used,TypeofTobaccoUsed,The text term used to describe the specific type of tobacco used by the patient.,False,True,"['Cigarettes', 'Not Reported', 'Electronic Cigarette', 'Cigar', 'Marijuana', 'unknown', 'Pipe', 'Other', 'Smokeless Tobacco', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Tobacco Smoking Status,Tobacco Smoking Status,TobaccoSmokingStatus,Category describing current smoking status and smoking history as self-reported by a patient,False,True,"['Lifelong Non-Smoker', 'Not Reported', 'Smoking history not documented', 'Current Reformed Smoker for > 15 yrs', 'Current Reformed Smoker for < or = 15 yrs', 'Duration Not Specified', 'Current Reformed Smoker', 'Current Smoker', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Marijuana Use Per Week,Marijuana Use Per Week,MarijuanaUsePerWeek,Numeric value that represents the number of times the patient uses marijuana each day.,False,True,,"['Type is ""Marijuana smoke""']",Exposure -HIV Viral Load,HIV Viral Load,HIVViralLoad,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",False,,,,FollowUp -Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'unknown', 'no']",,FollowUp -Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['MRI', '99mTc Bone Scintigraphy', 'PET', 'CT Scan', '']",,FollowUp +Reflux Treatment Type,Reflux Treatment Type,RefluxTreatmentType,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,False,,"['No Treatment', 'Not Reported', 'H2 Blockers', 'Surgically Treated', 'Medically Treated', 'Proton Pump Inhibitors', 'unknown', 'Not Applicable', 'Antacids', '']",,FollowUp +AIDS Risk Factors,AIDS Risk Factors,AIDSRiskFactors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,False,,"['Coccidioidomycosis', 'Isosporiasis', 'Mycobacterium', 'Cryptococcosis', 'Salmonella Septicemia', 'Pneumocystis Pneumonia', 'Wasting Syndrome', 'Toxoplasmosis', 'NOS', 'Mycobacterium avium Complex', 'pneumonia', 'Histoplasmosis', 'Mycobacterium tuberculosis', 'Candidiasis', 'Progressive Multifocal Leukoencephalopathy', 'Cytomegalovirus', 'Encephalopathy', 'Nocardiosis', 'Herpes Simplex Virus', '']",,FollowUp +Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Postmenopausal', 'Perimenopausal', 'Premenopausal', 'Not Reported', 'unknown', '']",,FollowUp +Adverse Event,Adverse Event,AdverseEvent,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,False,,"['Seroma', 'INR Increased', 'Jejunal Obstruction', 'Recurrent Laryngeal Nerve Palsy', 'Vestibular Disorder', 'Fetal Death', 'Heart Failure', 'Blood Antidiuretic Hormone Abnormal', 'Toxic Epidermal Necrolysis', 'Tumor Pain', 'Wrist Fracture', 'Blood Gonadotrophin Abnormal', 'Confusion', 'Acoustic Nerve Disorder NOS', 'Pleural Infection', 'Bone Marrow Hypocellular', 'Vaginal Inflammation', 'Breast Atrophy', 'Rectal Necrosis', 'Stomal Ulcer', 'Accessory Nerve Disorder', 'Flashing Lights', 'Typhlitis', 'Acute Coronary Syndrome', 'Extrapyramidal Disorder', 'Aphonia', 'Jejunal Perforation', 'Vaginal Anastomotic Leak', 'Hydrocephalus', 'Unequal Limb Length', 'Scrotal Infection', 'Abdominal Pain', 'Cheilitis', 'Female Genital Tract Fistula', 'Mediastinal Infection', 'Gastric Fistula', 'Death NOS', 'Encephalopathy', 'Esophageal Obstruction', 'Perforation Bile Duct', 'Skin Hyperpigmentation', 'Telangiectasia', 'Anorexia', 'Sinus Bradycardia', 'Surgical and Medical Procedures Other', 'Venous Injury', 'Colonic Stenosis', 'Ataxia', 'Keratitis', 'Ileal Stenosis', 'Immune System Disorders Other', 'Stenosis of Gastrointestinal Stoma', 'Vulval Infection', 'Gallbladder Infection', 'Akathisia', 'Small Intestinal Obstruction', 'Gastrointestinal Fistula', 'Fall', 'Virilization', 'Breast Infection', 'Tooth Infection', 'Hypoglycemia', 'Cranial Nerve Infection', 'Intestinal Stoma Obstruction', 'Anal Necrosis', 'Blurred Vision', 'Allergic Rhinitis', 'Colitis', 'Activated Partial Thromboplastin Time Prolonged', 'Peripheral Sensory Neuropathy', 'Restlessness', 'Vomiting', 'Productive Cough', 'Chylothorax', 'Postoperative Hemorrhage', 'Thoracic and Mediastinal Disorders Other', 'Fallopian Tube Obstruction', 'Tracheal Fistula', 'Sepsis', 'Skin Induration', 'Renal Colic', 'Chronic Kidney Disease', 'Familial and Genetic Disorders Other', 'Penile Infection', 'Renal and Urinary Disorders Other', 'Dysphasia', 'Edema Cerebral', 'Pharyngeal Stenosis', 'Urinary Frequency', 'Vaginal Pain', 'Myelitis', 'Weight Gain', 'Rash Pustular', 'Death Neonatal', 'Intraoperative Venous Injury', 'Colonic Obstruction', 'Pregnancy', 'Erythroderma', 'Joint Infection', 'Oral Pain', 'Laryngeal Mucositis', 'Pancreatic Hemorrhage', 'Postoperative Thoracic Procedure Complication', 'Urinary Retention', 'Bone Infection', 'Buttock Pain', 'Ejaculation Disorder', 'Ileal Ulcer', 'Myocardial Infarction', 'Vaginal Fistula', 'Pericarditis', 'Atrioventricular Block First Degree', 'Jejunal Ulcer', 'Sinus Pain', 'Social Circumstances Other', 'Tracheal Hemorrhage', 'Peripheral Motor Neuropathy', 'Corneal Infection', 'Myalgia', 'Photophobia', 'Hyperglycemia', 'Oral Cavity Fistula', 'Spermatic Cord Hemorrhage', 'Vagus Nerve Disorder', 'Electrocardiogram QT Corrected Interval Prolonged', 'Lymphocyte Count Decreased', 'Mediastinal Hemorrhage', 'Flu Like Symptoms', 'Gallbladder Obstruction', 'Superficial Soft Tissue Fibrosis', 'Dry Skin', 'Enterovesical Fistula', 'Restrictive Cardiomyopathy', 'Phlebitis Infective', 'Dry Mouth', 'Middle Ear Inflammation', 'Lymph Leakage', 'Anemia', 'Intra-Abdominal Hemorrhage', 'Esophageal Pain', 'Kyphosis', 'Intraoperative Urinary Injury', 'Small Intestinal Mucositis', 'Periodontal Disease', 'Flank Pain', 'Hypoparathyroidism', 'Pruritus', 'Esophageal Varices Hemorrhage', 'General Disorders and Administration Site Conditions Other', 'Rectal Mucositis', 'Vaginal Perforation', 'Pharyngeal Hemorrhage', 'Hepatic Pain', 'Irregular Menstruation', 'Optic Nerve Disorder', 'Hepatic Infection', 'Amnesia', 'Alkaline Phosphatase Increased', 'Blood Corticotrophin Decreased', 'Toothache', 'Trismus', 'Musculoskeletal Deformity', 'Vaginal Discharge', 'Myelodysplastic Syndrome', 'Hypoalbuminemia', 'Cerebrospinal Fluid Leakage', 'Genital Edema', 'Musculoskeletal and Connective Tissue Disorders Other', 'Intraoperative Reproductive Tract Injury', 'Respiratory Failure', 'Paronychia', 'Gallbladder Necrosis', 'Vital Capacity Abnormal', 'Duodenal Perforation', 'Uterine Fistula', 'Platelet Count Decreased', 'Urostomy Leak', 'Apnea', 'dysphagia', 'Gastric Hemorrhage', 'Lymphocyte Count Increased', 'Ileus', 'Pancreatic Fistula', 'Soft Tissue Necrosis Upper Limb', 'Eye Pain', 'Lactation Disorder', 'Hypertrichosis', 'Soft Tissue Necrosis Lower Limb', 'Uterine Infection', 'Neuralgia', 'Depressed Level of Consciousness', 'Forced Expiratory Volume Decreased', 'Hypertriglyceridemia', 'Leukoencephalopathy', 'Salivary Gland Infection', 'Hot Flashes', 'Palpitations', 'Bloating', 'Hemolysis', 'Lip Pain', 'Ventricular Fibrillation', 'Extraocular Muscle Paresis', 'Prostatic Pain', 'Rectal Pain', 'Ureteric Anastomotic Leak', 'Tinnitus', 'Poisoning and Procedural Complications Other', 'Hyperuricemia', 'Myocarditis', 'Vitreous Hemorrhage', 'Phlebitis', 'Flushing', 'Rectal Perforation', 'Sinusitis', 'Spasticity', 'Nystagmus', 'Tooth Discoloration', 'Bronchial Fistula', 'Postnasal Drip', 'Colonic Hemorrhage', 'Capillary Leak Syndrome', 'Joint Range of Motion Decreased Lumbar Spine', 'Pharyngitis', 'Pulmonary Fistula', 'Enterocolitis', 'Kidney Infection', 'Uterine Hemorrhage', 'Muscle Weakness Upper Limb', 'Esophageal Stenosis', 'Asystole', 'Cardiac Troponin I Increased', 'Premature Menopause', 'Upper Gastrointestinal Hemorrhage', 'Ovarian Rupture', 'Aortic Valve Disease', 'Growth Hormone Abnormal', 'Jejunal Hemorrhage', 'Periorbital Infection', 'Alopecia', 'Facial Muscle Weakness', 'Blood and Lymphatic System Disorders Other', 'Hypocalcemia', 'Large Intestinal Anastomotic Leak', 'Pharyngeal Anastomotic Leak', 'Skin Infection', 'Atrial Flutter', 'Gastroesophageal Reflux Disease', 'Vertigo', 'Cardiac Disorders Other', 'Hallucinations', 'Prostatic Hemorrhage', 'Dysgeusia', 'Adrenal Insufficiency', 'Gastritis', 'Sinus Tachycardia', 'Abdominal Soft Tissue Necrosis', 'Renal Hemorrhage', 'Erectile Dysfunction', 'Nervous System Disorders Other', 'Floaters', 'Glucose Intolerance', 'Autoimmune Disorder', 'Anal Fistula', 'Premature Delivery', 'Gallbladder Pain', 'Gastric Stenosis', 'Anaphylaxis', 'Pneumonitis', 'Hypersomnia', 'Periorbital Edema', 'Urethral Anastomotic Leak', 'Obstruction Gastric', 'Hypomagnesemia', 'Ejection Fraction Decreased', 'Serum Amylase Increased', 'Jejunal Stenosis', 'Wound Complication', 'Blood Prolactin Abnormal', 'Oligospermia', 'Dermatitis Radiation', 'Urticaria', 'Corneal Ulcer', 'Hiccups', 'Kidney Anastomotic Leak', 'Meningismus', 'Salivary Duct Inflammation', 'Aspartate Aminotransferase Increased', 'Rash Maculo-Papular', 'dyspnea', 'Bronchospasm', 'Proteinuria', 'Intraoperative Renal Injury', 'Anal Hemorrhage', 'Dysarthria', 'Metabolism and Nutrition Disorders Other', 'Personality Change', 'Feminization Acquired', 'CPK Increased', 'Esophageal Infection', 'Joint Effusion', 'Spleen Disorder', 'Aspiration', 'Neck Soft Tissue Necrosis', 'Serum Sickness', 'Conduction Disorder', 'Anorectal Infection', 'Stroke', 'Ventricular Arrhythmia', 'Radiation Recall Reaction (Dermatologic)', 'Facial Pain', 'Memory Impairment', 'Hypokalemia', 'Pulmonary Valve Disease', 'Dizziness', 'Trigeminal Nerve Disorder', 'Wolff-Parkinson-White Syndrome', 'Ovarian Hemorrhage', 'Suicidal Ideation', 'Generalized Muscle Weakness', 'Hirsutism', 'Ankle Fracture', 'Muscle Weakness Right-Sided', 'Constrictive Pericarditis', 'Hepatic Failure', 'Bronchopulmonary Hemorrhage', 'Hypernatremia', 'Mucosal Infection', 'Spinal Fracture', 'Urine Discoloration', 'Bronchial Obstruction', 'White Blood Cell Decreased', 'Endocrine Disorders Other', 'Carbon Monoxide Diffusing Capacity Decreased', 'Night Blindness', 'Tumor Lysis Syndrome', 'Suicide Attempt', 'Neoplasms Benign', 'Esophageal Anastomotic Leak', 'Pleural Effusion', 'Creatinine Increased', 'Bullous Dermatitis', 'Hypotension', 'Laryngeal Edema', 'Presyncope', 'Gait Disturbance', 'Papilledema', 'Oral Dysesthesia', 'Headache', 'Delusions', 'Libido Increased', 'Intraoperative Endocrine Injury', 'Hypercalcemia', 'Intraoperative Ear Injury', 'Pulmonary Edema', 'Photosensitivity', 'Rectal Anastomotic Leak', 'Urostomy Site Bleeding', 'Vascular Disorders Other', 'Purpura', 'Uterine Obstruction', 'Fever', 'Oculomotor Nerve Disorder', 'Injury to Jugular Vein', 'Arthralgia', 'Urinary Incontinence', 'Intraoperative Cardiac Injury', 'Urinary Urgency', 'Osteonecrosis of Jaw', 'Pancreatic Duct Stenosis', 'Lordosis', 'Injection Site Reaction', 'Sudden Death NOS', 'Non-Cardiac Chest Pain', 'Fallopian Tube Stenosis', 'Retinal Vascular Disorder', 'Sleep Apnea', 'Dehydration', 'Biliary Anastomotic Leak', 'Cholecystitis', 'Rectal Ulcer', 'Pleuritic Pain', 'Bronchial Stricture', 'Anal Pain', 'Tracheostomy Site Bleeding', 'Hepatobiliary Disorders Other', 'Investigations Other', 'Cardiac Arrest', 'Conjunctivitis Infective', 'Breast Pain', 'Lymph Gland Infection', 'Cough', 'Intraoperative Head and Neck Injury', 'Oral Hemorrhage', 'Pharyngeal Necrosis', 'Allergic Reaction', 'Seizure', 'Scoliosis', 'Upper Respiratory Infection', 'Arterial Injury', 'Malaise', 'Gastrointestinal Pain', 'Dental Caries', 'Tricuspid Valve Disease', 'Pelvic Infection', 'Pleural Hemorrhage', 'Stevens-Johnson Syndrome', 'Pain in Extremity', 'Bladder Anastomotic Leak', 'Intraoperative Respiratory Injury', 'Thromboembolic Event', 'Urostomy Obstruction', 'Pharyngeal Mucositis', 'Gingival Pain', 'Abdominal Infection', 'Delayed Orgasm', 'Chills', 'Agitation', 'Pyramidal Tract Syndrome', 'Weight Loss', 'Cystitis Noninfective', 'Vaginal Hemorrhage', 'Small Intestinal Stenosis', 'Pancreas Infection', 'Hematuria', 'Hypophosphatemia', 'Hemoglobinuria', 'Dysmenorrhea', 'Duodenal Infection', 'Pharyngolaryngeal Pain', 'Biliary Tract Infection', 'Fecal Incontinence', 'Alcohol Intolerance', 'CD4 Lymphocytes Decreased', 'Endocarditis Infective', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Pelvic Floor Muscle Weakness', 'Hypermagnesemia', 'Ear Pain', 'Duodenal Hemorrhage', 'Esophageal Perforation', 'Gastric Ulcer', 'Glaucoma', 'Intraoperative Hemorrhage', 'Psychosis', 'Adult Respiratory Distress Syndrome', 'Endophthalmitis', 'Hyperhidrosis', 'Irritability', 'Malabsorption', 'Laryngospasm', 'Acute Kidney Injury', 'Laryngitis', 'Retinopathy', 'Pericardial Effusion', 'Pancreatic Necrosis', 'Small Intestinal Anastomotic Leak', 'Scleral Disorder', 'Intraoperative Arterial Injury', 'Treatment Related Secondary Malignancy', 'Acidosis', 'Papulopustular Rash', 'Injury', 'Muscle Weakness Trunk', 'Fallopian Tube Anastomotic Leak', 'Peritoneal Necrosis', 'Joint Range of Motion Decreased Cervical Spine', 'Nausea', 'Cecal Hemorrhage', 'Aortic Injury', 'Bone Pain', 'Tremor', 'Libido Decreased', 'Splenic Infection', 'External Ear Inflammation', 'Lethargy', 'Uterine Perforation', 'Esophageal Ulcer', 'Psychiatric Disorders Other', 'Dyspareunia', 'Bile Duct Stenosis', 'Phantom Pain', 'Vaginal Obstruction', 'Gastrointestinal Disorders Other', 'Intraoperative Gastrointestinal Injury', 'Pancreatic Enzymes Decreased', 'Atrial Fibrillation', 'Rectal Fistula', 'Chest Pain Cardiac', 'Gallbladder Fistula', 'Superior Vena Cava Syndrome', 'Cognitive Disturbance', 'Urinary Tract Infection', 'Salivary Gland Fistula', 'Nail Ridging', 'Fetal Growth Retardation', 'Constipation', 'Diarrhea', 'Delirium', 'Chest Wall Pain', 'Pancreatic Anastomotic Leak', 'Intraoperative Musculoskeletal Injury', 'Esophageal Hemorrhage', 'IVth Nerve Disorder', 'Catheter Related Infection', 'Gastric Perforation', 'Tracheal Stenosis', 'Hoarseness', 'Febrile Neutropenia', 'Eye Infection', 'Jejunal Fistula', 'Ventricular Tachycardia', 'Rhinitis Infective', 'Exostosis', 'Back Pain', 'Anal Ulcer', 'Spermatic Cord Obstruction', 'Renal Calculi', 'Visceral Arterial Ischemia', 'Sneezing', 'Otitis Externa', 'Ileal Fistula', 'Uterine Pain', 'Ileal Obstruction', 'Edema Limbs', 'wheezing', 'Lip Infection', 'Wound Dehiscence', 'Colonic Ulcer', 'Intraoperative Splenic Injury', 'Hypothyroidism', 'Rash Acneiform', 'Sinus Disorder', 'Anorgasmia', 'Prolapse of Urostomy', 'Intestinal Stoma Leak', 'Pneumothorax', 'Gum Infection', 'Tracheal Mucositis', 'Encephalitis Infection', 'Hemoglobin Increased', 'Lymph Node Pain', 'Proctitis', 'Mitral Valve Disease', 'Fibrinogen Decreased', 'Neck Pain', 'Laryngopharyngeal Dysesthesia', 'Neck Edema', 'Colonic Fistula', 'Atelectasis', 'Urethral Infection', 'Sore Throat', 'Hyperkalemia', 'Stomach Pain', 'Hypertension', 'Central Nervous System Necrosis', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Eye Disorders Other', 'Duodenal Ulcer', 'Hematoma', 'Small Intestine Infection', 'Cholesterol High', 'Mobitz (Type) II Atrioventricular Block', 'Lower Gastrointestinal Hemorrhage', 'Cytokine Release Syndrome', 'Conjunctivitis', 'Brachial Plexopathy', 'Tooth Development Disorder', 'Stoma Site Infection', 'Lymphedema', 'Scrotal Pain', 'Lung Infection', 'Nipple Deformity', 'Testicular Hemorrhage', 'Laryngeal Obstruction', 'Laryngeal Stenosis', 'Joint Range of Motion Decreased', 'Intraoperative Skin Injury', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Hearing Impaired', 'Ascites', 'Paresthesia', 'Portal Hypertension', 'Olfactory Nerve Disorder', 'Bladder Infection', 'Flatulence', 'Vasovagal Reaction', 'Eyelid Function Disorder', 'Enterocolitis Infectious', 'Nasal Congestion', 'Cecal Infection', 'Facial Nerve Disorder', 'Gallbladder Perforation', 'Burn', 'Hemolytic Uremic Syndrome', 'Testicular Disorder', 'Iron Overload', 'Laryngeal Inflammation', 'Ileal Hemorrhage', 'Perineal Pain', 'Fatigue', 'Ovulation Pain', 'Pulmonary Hypertension', 'Uterine Anastomotic Leak', 'Localized Edema', 'Gastric Necrosis', 'Gastric Anastomotic Leak', 'Cataract', 'Menorrhagia', 'Vascular Access Complication', 'Hepatitis Viral', 'Ear and Labyrinth Disorders Other', 'Fat Atrophy', 'Hip Fracture', 'Lipase Increased', 'Prostate Infection', 'Syncope', 'Blood Bilirubin Increased', 'Hyperthyroidism', 'Left Ventricular Systolic Dysfunction', 'Edema Trunk', 'Glossopharyngeal Nerve Disorder', 'Ischemia Cerebrovascular', 'Depression', 'Otitis Media', 'Rectal Hemorrhage', 'Transient Ischemic Attacks', 'Watering Eyes', 'Haptoglobin Decreased', 'Hypohidrosis', 'Sick Sinus Syndrome', 'Intraoperative Hepatobiliary Injury', 'Respiratory', 'Cushingoid', 'Alanine Aminotransferase Increased', 'Esophagitis', 'Supraventricular Tachycardia', 'Vasculitis', 'GGT Increased', 'Urostomy Stenosis', 'Retroperitoneal Hemorrhage', 'Leukemia Secondary to Oncology Chemotherapy', 'Urinary Tract Pain', 'Peripheral Nerve Infection', 'Prostatic Obstruction', 'Anxiety', 'Intestinal Stoma Site Bleeding', 'Fracture', 'Infective Myositis', 'Skin Hypopigmentation', 'Esophageal Necrosis', 'Nail Discoloration', 'Hypoxia', 'Small Intestine Ulcer', 'Hepatic Necrosis', 'Rectal Stenosis', 'Body Odor', 'External Ear Pain', 'Arteritis Infective', 'Penile Pain', 'Precocious Puberty', 'Duodenal Obstruction', 'Pancreatitis', 'Anal Mucositis', 'Reproductive System and Breast Disorders Other', 'Encephalomyelitis Infection', 'Atrioventricular Block Complete', 'Congenital', 'Ovarian Infection', 'Cardiac Troponin T Increased', 'Meningitis', 'Urinary Tract Obstruction', 'Mania', 'Uveitis', 'Hyponatremia', 'Concentration Impairment', 'Skin Atrophy', 'Dyspepsia', 'Intraoperative Ocular Injury', 'Neutrophil Count Decreased', 'Bladder Spasm', 'Vaginismus', 'Gastrointestinal Stoma Necrosis', 'Anal Stenosis', 'Head Soft Tissue Necrosis', 'Euphoria', 'Pulmonary Fibrosis', 'Bruising', 'Abdominal Distension', 'Biliary Fistula', 'Retinal Detachment', 'Cervicitis Infection', 'Soft Tissue Infection', 'Right Ventricular Dysfunction', 'Pericardial Tamponade', 'Appendicitis', 'Infections and Infestations Other', 'Vaginal Infection', 'Insomnia', 'Delayed Puberty', 'Device Related Infection', 'Azoospermia', 'Hypoglossal Nerve Disorder', 'Hemorrhoidal Hemorrhage', 'Pharyngeal Fistula', 'Rectal Obstruction', 'Arthritis', 'Injury to Carotid Artery', 'Peripheral Ischemia', 'Disseminated Intravascular Coagulation', 'Gynecomastia', 'Skin Ulceration', 'Multi-Organ Failure', 'Pelvic Soft Tissue Necrosis', 'Arachnoiditis', 'Avascular Necrosis', 'Injury to Superior Vena Cava', 'Skin and Subcutaneous Tissue Disorders Other', 'Somnolence', 'Edema Face', 'Voice Alteration', 'Ileal Perforation', 'Alkalosis', 'Hemorrhoids', 'Intracranial Hemorrhage', 'Menopause', 'Dry Eye', 'Retinal Tear', 'Movements Involuntary', 'Infusion Site Extravasation', 'Gastrointestinal Anastomotic Leak', 'Small Intestinal Perforation', 'Unintended Pregnancy', 'Vaginal Dryness', 'Prolapse of Intestinal Stoma', 'Myositis', 'Tracheal Obstruction', 'Injury to Inferior Vena Cava', 'Mobitz Type I', 'Intraoperative Neurological Injury', 'Retinoic Acid Syndrome', 'Esophageal Fistula', 'Scalp Pain', 'Growth Accelerated', 'Hepatic Hemorrhage', 'Hyperparathyroidism', 'Duodenal Stenosis', 'Testicular Pain', 'Erythema Multiforme', 'Appendicitis Perforated', 'Superficial Thrombophlebitis', 'Wound Infection', 'Mucositis Oral', 'Osteoporosis', 'Radiculitis', 'Abducens Nerve Disorder', 'Bronchial Infection', 'Vaginal Stricture', 'Growth Suppression', 'Dysesthesia', 'Pain', 'Infusion Related Reaction', 'Fibrosis Deep Connective Tissue', 'Nail Infection', 'Intraoperative Breast Injury', 'Muscle Weakness Left-Sided', 'Leukocytosis', 'Duodenal Fistula', 'Laryngeal Hemorrhage', 'Stridor', 'Urine Output Decreased', 'Nail Loss', 'Bladder Perforation', 'Lymphocele', 'Epistaxis', 'Colonic Perforation', 'Lipohypertrophy', 'Hypothermia', 'Hematosalpinx', 'Spermatic Cord Anastomotic Leak', 'Laryngeal Fistula', 'Thrombotic Thrombocytopenic Purpura', 'Tracheitis', 'Puerperium and Perinatal Conditions Other', 'Fallopian Tube Perforation', 'Paroxysmal Atrial Tachycardia', 'Pelvic Pain', 'Vas Deferens Anastomotic Leak', 'Bronchopleural Fistula', 'Pain of Skin', 'Muscle Weakness Lower Limb', 'Peritoneal Infection', 'Portal Vein Thrombosis', 'Urinary Fistula', 'Obesity', 'Gastroparesis', '']",,FollowUp +Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,Presence or absennce of Barretts esophagus goblet cells.,False,,"['no', 'yes', '']",,FollowUp +Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp +DLCO Ref Predictive Percent,DLCO Ref Predictive Percent,DLCORefPredictivePercent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",False,,,,FollowUp +HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['""52""', '""70""', 'Not Reported', '""51""', '""68""', '""56""', '""58""', '""26""', '""63""', '""18""', '""82""', 'unknown', 'Other', '""16""', '""31""', '""33""', '""35""', '""59""', '""53""', '""39""', '""45""', '""73""', '""66""', '']",,FollowUp +FEV 1 FVC Pre Bronch Percent,FEV 1 FVC Pre Bronch Percent,FEV1FVCPreBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,False,,,,FollowUp +Hormonal Contraceptive Use,Hormonal Contraceptive Use,HormonalContraceptiveUse,The text term used to indicate whether the patient used hormonal contraceptives.,False,,"['Never Used', 'Not Reported', 'unknown', 'Current User', 'Former User', '']",,FollowUp +Days to Adverse Event,Days to Adverse Event,DaystoAdverseEvent,Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable',False,,,,FollowUp +Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable',True,,,,FollowUp +Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,Date of onset of pancreatitis.,False,,,,FollowUp +Recist Targeted Regions Number,Recist Targeted Regions Number,RecistTargetedRegionsNumber,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",False,,,,FollowUp +Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['DU-Disease Unchanged', 'PSR-Pseudoresponse', 'TE-Too Early', 'AJ-Adjuvant Therapy', 'Not Reported', 'RD-Responsive Disease', 'PB-Palliative Benefit', 'PPD-Pseudoprogression', 'NPB-No Palliative Benefit', 'VGPR-Very Good Partial Response', 'SPD-Surgical Progression', 'PA-Palliative Therapy', 'WT-With Tumor', 'PD-Progressive Disease', 'unknown', 'Non-CR/Non-PD-Non-CR/Non-PD', 'NR-No Response', 'TF-Tumor Free', 'PDM-Persistent Distant Metastasis', 'MR-Minimal/Marginal response', 'sCR-Stringent Complete Response', 'MX-Mixed Response', 'PLD-Persistent Locoregional Disease', 'IPD-Immunoprogression', 'PR-Partial Response', 'CR-Complete Response', 'BED-Biochemical Evidence of Disease', 'RP-Response', 'CRU-Complete Response Unconfirmed', 'RPD-Radiographic Progressive Disease', 'SD-Stable Disease', 'CPD-Clinical Progression', 'IMR-Immunoresponse', '']",,FollowUp +Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Yes - Progression or Recurrence', 'unknown', 'no', 'Not Reported']",,FollowUp +FEV1 Ref Post Bronch Percent,FEV1 Ref Post Bronch Percent,FEV1RefPostBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,False,,,,FollowUp +FEV1 FVC Post Bronch Percent,FEV1 FVC Post Bronch Percent,FEV1FVCPostBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,False,,,,FollowUp +Evidence of Recurrence Type,Evidence of Recurrence Type,EvidenceofRecurrenceType,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,False,,"['Positive Biomarkers', 'Convincing Image Source', 'Biopsy with Histologic Confirmation', '']",,FollowUp +FEV1 Ref Pre Bronch Percent,FEV1 Ref Pre Bronch Percent,FEV1RefPreBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,False,,,,FollowUp +Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['CT Scan', '99mTc Bone Scintigraphy', 'MRI', 'PET', '']",,FollowUp +CDC HIV Risk Factors,CDC HIV Risk Factors,CDCHIVRiskFactors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.",False,,"['Heterosexual Contact', 'Not Reported', 'Homosexual Contact', 'Hemophiliac', 'Intravenous Drug User', 'Transfusion Recipient', 'unknown', 'None', '']",,FollowUp +Hepatitis Sustained Virological Response,Hepatitis Sustained Virological Response,HepatitisSustainedVirologicalResponse,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,FollowUp +Risk Factor,Risk Factor,RiskFactor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Allergy Eggs', 'Diabetes Type I', 'Nonalcoholic Fatty Liver Disease', 'Hypospadias', 'Endosalpingiosis', 'Allergy Cat', 'Epstein-Barr Virus', 'Reflux Disease', 'Sensory Changes', ""Gilbert's Syndrome"", 'HIV', 'Gorlin Syndrome', 'Tobacco NOS', 'Denys-Drash Syndrome', 'Tobacco Smoking', 'Primary Sclerosing Cholangitis', 'Undescended Testis', 'Cancer', 'Li-Fraumeni Syndrome', 'Hepatitis B Infection', 'Rubinstein-Taybi Syndrome', 'Allergy Dog', 'Allergy Meat', 'Allergy Food NOS', 'Myasthenia Gravis', 'Not Reported', 'Low Grade Dysplasia', 'Recurrent Pyogenic Cholangitis', 'Lynch Syndrome', 'Oral Contraceptives', 'Common variable immune deficiency (CVID)', 'Pancreatitis', 'Serous tubal intraepithelial carcinoma (STIC)', 'Thyroid Nodular Hyperplasia', 'Alcohol Consumption', 'unknown', 'Sarcoidosis', 'Allergy Mold or Dust', 'Allergy Seafood', 'Chronic Hepatitis', 'Allergy Processed Foods', 'Vision Changes', 'Fanconi Anemia', 'Allergy Nuts', 'Cirrhosis', 'Hepatitis C Infection', 'Endometriosis', 'Hemochromatosis', 'Gastric Polyp(s)', 'Helicobacter Pylori-Associated Gastritis', 'Lymphocytic Thyroiditis', 'Diabetes NOS', 'Allergy Bee', 'Parasitic Disease of Biliary Tract', 'Hematologic Disorder NOS', 'Hay Fever', 'High Grade Dysplasia', 'Autoimmune Atrophic Chronic Gastritis', 'Turcot Syndrome', 'Allergy Ant', 'Hemihypertrophy', 'Allergy Animal NOS', 'Allergy Dairy or Lactose', 'Rheumatoid Arthritis', 'Diet', 'Alcoholic Liver Disease', 'Human Papillomavirus Infection', 'Intestinal Metaplasia', ""Behcet's Disease"", 'Diverticulitis', 'Headache', 'Hepatitis NOS', 'Cholelithiasis', 'Alpha-1 Antitrypsin Deficiency', ""Hashimoto's Thyroiditis"", 'Allergy Fruit', 'Beckwith-Wiedemann', 'Tobacco Smokeless', 'Steatosis', 'Allergy Wasp', 'Diabetes Type II', 'Nonalcoholic Steatohepatitis', 'Fibrosis', ""Barrett's Esophagus"", 'Familial Adenomatous Polyposis', 'Colon Polyps', 'Hepatic Encephalopathy', 'Eczema', 'Wagr Syndrome', 'Tattoo', 'Iron Overload', 'Obesity', 'Seizure', '']",,FollowUp BMI,BMI,BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,False,,,,FollowUp -Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['Not Reported', 'BED-Biochemical Evidence of Disease', 'RP-Response', 'WT-With Tumor', 'CPD-Clinical Progression', 'DU-Disease Unchanged', 'sCR-Stringent Complete Response', 'unknown', 'PSR-Pseudoresponse', 'Non-CR/Non-PD-Non-CR/Non-PD', 'IPD-Immunoprogression', 'IMR-Immunoresponse', 'RPD-Radiographic Progressive Disease', 'SPD-Surgical Progression', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'MR-Minimal/Marginal response', 'CRU-Complete Response Unconfirmed', 'PDM-Persistent Distant Metastasis', 'RD-Responsive Disease', 'PR-Partial Response', 'MX-Mixed Response', 'SD-Stable Disease', 'PPD-Pseudoprogression', 'PB-Palliative Benefit', 'NPB-No Palliative Benefit', 'CR-Complete Response', 'PLD-Persistent Locoregional Disease', 'AJ-Adjuvant Therapy', 'NR-No Response', 'TF-Tumor Free', 'PD-Progressive Disease', 'TE-Too Early', '']",,FollowUp +Hysterectomy Margins Involved,Hysterectomy Margins Involved,HysterectomyMarginsInvolved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,False,,"['Bladder', 'Not Reported', 'Vagina', 'Macroscopic Parametrium', 'unknown', 'None', 'Microscopic Parametrium', '']",,FollowUp +HIV Viral Load,HIV Viral Load,HIVViralLoad,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",False,,,,FollowUp Cause of Response,Cause of Response,CauseofResponse,The text term used to describe the suspected cause or reason for the patient disease response.,False,,,,FollowUp -Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Not Reported', 'Radical Hysterectomy', 'Not performed', 'unknown', 'Hysterectomy NOS', 'Simple Hysterectomy', '']",,FollowUp -Adverse Event,Adverse Event,AdverseEvent,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,False,,"['Ureteric Anastomotic Leak', 'Salivary Duct Inflammation', 'Voice Alteration', 'Cecal Hemorrhage', 'Stoma Site Infection', 'Hyperglycemia', 'IVth Nerve Disorder', 'Osteonecrosis of Jaw', 'Middle Ear Inflammation', 'Vital Capacity Abnormal', 'Postoperative Thoracic Procedure Complication', 'Vaginal Inflammation', 'Alopecia', 'Photophobia', 'Myalgia', 'Feminization Acquired', 'Chronic Kidney Disease', 'Accessory Nerve Disorder', 'Rash Acneiform', 'Pancreatic Duct Stenosis', 'Stridor', 'Bladder Spasm', 'Endocrine Disorders Other', 'Lymphocele', 'Pancreatic Hemorrhage', 'Nipple Deformity', 'Pulmonary Hypertension', 'Pleural Infection', 'Laryngeal Obstruction', 'Glossopharyngeal Nerve Disorder', 'Buttock Pain', 'Growth Hormone Abnormal', 'Colonic Hemorrhage', 'Delirium', 'Small Intestinal Mucositis', 'Hypocalcemia', 'Vaginal Hemorrhage', 'Encephalitis Infection', 'Abducens Nerve Disorder', 'Alanine Aminotransferase Increased', 'External Ear Inflammation', 'Hemolysis', 'Bloating', 'Hemoglobinuria', 'Sudden Death NOS', 'Electrocardiogram QT Corrected Interval Prolonged', 'Myelodysplastic Syndrome', 'Rectal Necrosis', 'Intraoperative Hepatobiliary Injury', 'Bladder Anastomotic Leak', 'Anaphylaxis', 'Hypothermia', 'Cardiac Troponin T Increased', 'Dental Caries', 'Mediastinal Hemorrhage', 'Vaginal Dryness', 'Gastrointestinal Anastomotic Leak', 'Supraventricular Tachycardia', 'Investigations Other', 'Anal Necrosis', 'Scalp Pain', 'Otitis Media', 'Bullous Dermatitis', 'Retinal Detachment', 'Spermatic Cord Hemorrhage', 'Vaginal Anastomotic Leak', 'Prostate Infection', 'Mucosal Infection', 'Localized Edema', 'Flashing Lights', 'Nausea', 'Intraoperative Head and Neck Injury', 'Platelet Count Decreased', 'Ileus', 'Pruritus', 'Tracheitis', 'Hepatic Pain', 'Skin Infection', 'Virilization', 'Laryngeal Edema', 'Corneal Ulcer', 'Laryngopharyngeal Dysesthesia', 'Myositis', 'Azoospermia', 'Hemorrhoids', 'Conjunctivitis Infective', 'Ileal Stenosis', 'Rash Maculo-Papular', 'Peripheral Sensory Neuropathy', 'Lactation Disorder', 'Pregnancy', 'Lung Infection', 'Pelvic Floor Muscle Weakness', 'Biliary Fistula', 'Intraoperative Gastrointestinal Injury', 'Colonic Obstruction', 'Eye Disorders Other', 'Serum Sickness', 'Pelvic Infection', 'Confusion', 'Urinary Tract Infection', 'Haptoglobin Decreased', 'Insomnia', 'Skin Hyperpigmentation', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Gastric Stenosis', 'Sepsis', 'Back Pain', 'Prostatic Obstruction', 'Intraoperative Cardiac Injury', 'GGT Increased', 'Pleuritic Pain', 'Social Circumstances Other', 'Intraoperative Skin Injury', 'Intraoperative Arterial Injury', 'Osteoporosis', 'Anorgasmia', 'Ovarian Hemorrhage', 'Hypoparathyroidism', 'Paronychia', 'Heart Failure', 'Flushing', 'dyspnea', 'Pain of Skin', 'Malaise', 'Soft Tissue Necrosis Lower Limb', 'Ischemia Cerebrovascular', 'Conjunctivitis', 'Injury to Carotid Artery', 'Infective Myositis', 'Keratitis', 'Capillary Leak Syndrome', 'Gallbladder Fistula', 'Muscle Weakness Right-Sided', 'Head Soft Tissue Necrosis', 'Infections and Infestations Other', 'Body Odor', 'Lipase Increased', 'Mobitz (Type) II Atrioventricular Block', 'Skin Ulceration', 'Mediastinal Infection', 'Hypercalcemia', 'Vulval Infection', 'Visceral Arterial Ischemia', 'Watering Eyes', 'Esophageal Obstruction', 'Intestinal Stoma Site Bleeding', 'Hemolytic Uremic Syndrome', 'Arthralgia', 'Psychiatric Disorders Other', 'Vitreous Hemorrhage', 'Death Neonatal', 'Constrictive Pericarditis', 'Meningitis', 'Hepatic Necrosis', 'Retinal Vascular Disorder', 'Pneumothorax', 'Pancreatic Fistula', 'Photosensitivity', 'Edema Cerebral', 'Aortic Injury', 'Intraoperative Neurological Injury', 'Right Ventricular Dysfunction', 'Neck Pain', 'Hepatic Hemorrhage', 'Euphoria', 'Kyphosis', 'Glaucoma', 'Phlebitis', 'Joint Effusion', 'Laryngospasm', 'Hyperthyroidism', 'Ileal Obstruction', 'Uterine Anastomotic Leak', 'Hyperuricemia', 'Gastric Ulcer', 'Skin Hypopigmentation', 'Left Ventricular Systolic Dysfunction', 'Pharyngolaryngeal Pain', 'Vasovagal Reaction', 'Erythroderma', 'Intraoperative Musculoskeletal Injury', 'Aphonia', 'Tremor', 'Olfactory Nerve Disorder', 'Presyncope', 'Depression', 'Hyperhidrosis', 'Bronchospasm', 'Pulmonary Valve Disease', 'Neck Soft Tissue Necrosis', 'Irregular Menstruation', 'Intraoperative Endocrine Injury', 'Anal Mucositis', 'Libido Increased', 'Neutrophil Count Decreased', 'Constipation', 'Splenic Infection', 'Tricuspid Valve Disease', 'Laryngeal Hemorrhage', 'Hemorrhoidal Hemorrhage', 'Prolapse of Urostomy', 'Peripheral Motor Neuropathy', 'Gastritis', 'CPK Increased', 'Personality Change', 'Oral Pain', 'Depressed Level of Consciousness', 'Hip Fracture', 'Recurrent Laryngeal Nerve Palsy', 'Growth Suppression', 'Cecal Infection', 'External Ear Pain', 'Phlebitis Infective', 'Prostatic Pain', 'Aortic Valve Disease', 'CD4 Lymphocytes Decreased', 'Aspiration', 'Fatigue', 'Uterine Perforation', 'Reproductive System and Breast Disorders Other', 'Myelitis', 'Soft Tissue Infection', 'Forced Expiratory Volume Decreased', 'Penile Infection', 'Acute Coronary Syndrome', 'Portal Hypertension', 'Glucose Intolerance', 'Intracranial Hemorrhage', 'Mania', 'Lipohypertrophy', 'Atrioventricular Block First Degree', 'Treatment Related Secondary Malignancy', 'Familial and Genetic Disorders Other', 'Nervous System Disorders Other', 'Periorbital Infection', 'Cholesterol High', 'Arthritis', 'Arterial Injury', 'Flu Like Symptoms', 'Uterine Fistula', 'Erythema Multiforme', 'Musculoskeletal Deformity', 'Fibrinogen Decreased', 'Pyramidal Tract Syndrome', 'Cytokine Release Syndrome', 'Bone Marrow Hypocellular', 'Paroxysmal Atrial Tachycardia', 'Toxic Epidermal Necrolysis', 'Musculoskeletal and Connective Tissue Disorders Other', 'Corneal Infection', 'Hydrocephalus', 'Rectal Mucositis', 'Cough', 'Gastrointestinal Disorders Other', 'Hematosalpinx', 'Nystagmus', 'Bronchopulmonary Hemorrhage', 'Appendicitis Perforated', 'Enterocolitis', 'Esophageal Varices Hemorrhage', 'Intra-Abdominal Hemorrhage', 'Trismus', 'Optic Nerve Disorder', 'Urinary Tract Pain', 'Weight Loss', 'Perforation Bile Duct', 'Cushingoid', 'Fibrosis Deep Connective Tissue', 'Infusion Site Extravasation', 'Lethargy', 'Dry Mouth', 'Rectal Fistula', 'Duodenal Hemorrhage', 'Penile Pain', 'Portal Vein Thrombosis', 'Amnesia', 'Colonic Stenosis', 'Large Intestinal Anastomotic Leak', 'Mucositis Oral', 'Adult Respiratory Distress Syndrome', 'Alkalosis', 'Premature Menopause', 'Eye Infection', 'Urostomy Leak', 'Muscle Weakness Upper Limb', 'Pancreatic Anastomotic Leak', 'Asystole', 'Stevens-Johnson Syndrome', 'Bladder Infection', 'Epistaxis', 'Lordosis', 'Lymph Gland Infection', 'Leukocytosis', 'Pancreatitis', 'Hyponatremia', 'Hypertriglyceridemia', 'Small Intestinal Obstruction', 'Ventricular Fibrillation', 'Esophageal Stenosis', 'Skin Atrophy', 'Fever', 'Breast Pain', 'Enterocolitis Infectious', 'Memory Impairment', 'Blurred Vision', 'Ventricular Arrhythmia', 'Flank Pain', 'Perineal Pain', 'Fracture', 'Lymphocyte Count Decreased', 'Acoustic Nerve Disorder NOS', 'Hepatitis Viral', 'Spermatic Cord Anastomotic Leak', 'Pericarditis', 'Flatulence', 'Hypophosphatemia', 'Rhinitis Infective', 'Bone Pain', 'Retinopathy', 'Duodenal Fistula', 'Appendicitis', 'Laryngeal Mucositis', 'Gallbladder Infection', 'Biliary Anastomotic Leak', 'Intraoperative Venous Injury', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Allergic Rhinitis', 'Gastroparesis', 'Dehydration', 'Syncope', 'Suicide Attempt', 'Gait Disturbance', 'Esophageal Fistula', 'Hypomagnesemia', 'Periodontal Disease', 'Duodenal Ulcer', 'Nasal Congestion', 'Gum Infection', 'Pancreatic Necrosis', 'Jejunal Fistula', 'Vasculitis', 'Encephalopathy', 'Hoarseness', 'Atrial Fibrillation', 'Menorrhagia', 'Ventricular Tachycardia', 'Female Genital Tract Fistula', 'Hypermagnesemia', 'Wrist Fracture', 'Rectal Pain', 'Dyspepsia', 'Hyperparathyroidism', 'Postoperative Hemorrhage', 'Wound Dehiscence', 'Biliary Tract Infection', 'Dyspareunia', 'Hepatic Infection', 'Sinus Pain', 'Sick Sinus Syndrome', 'Tracheostomy Site Bleeding', 'Anal Pain', 'Ileal Ulcer', 'Hypokalemia', 'Pancreas Infection', 'Muscle Weakness Lower Limb', 'Breast Atrophy', 'Dry Skin', 'Palpitations', 'Paresthesia', 'Salivary Gland Fistula', 'Bruising', 'Puerperium and Perinatal Conditions Other', 'Proctitis', 'Brachial Plexopathy', 'Pharyngeal Anastomotic Leak', 'Laryngeal Inflammation', 'Leukemia Secondary to Oncology Chemotherapy', 'Neoplasms Benign', 'Hypertrichosis', 'Superior Vena Cava Syndrome', 'Urinary Retention', 'Cervicitis Infection', 'Vas Deferens Anastomotic Leak', 'Myocardial Infarction', 'Ileal Perforation', 'Urinary Urgency', 'Ovarian Rupture', 'Periorbital Edema', 'Gastrointestinal Fistula', 'Ear and Labyrinth Disorders Other', 'Hepatobiliary Disorders Other', 'Pleural Hemorrhage', 'Hypothyroidism', 'Radiation Recall Reaction (Dermatologic)', 'Acidosis', 'Arachnoiditis', 'Lymphedema', 'Agitation', 'Gastric Necrosis', 'Concentration Impairment', 'Febrile Neutropenia', 'Delusions', 'Sinus Disorder', 'Generalized Muscle Weakness', 'Trigeminal Nerve Disorder', 'Urinary Frequency', 'Productive Cough', 'Hiccups', 'Sinus Bradycardia', 'Obesity', 'Poisoning and Procedural Complications Other', 'Movements Involuntary', 'Intestinal Stoma Leak', 'Tooth Discoloration', 'Encephalomyelitis Infection', 'Vaginal Stricture', 'Thrombotic Thrombocytopenic Purpura', 'Pharyngeal Stenosis', 'Urine Discoloration', 'Vaginal Pain', 'Delayed Orgasm', 'Pharyngeal Mucositis', 'Conduction Disorder', 'Ankle Fracture', 'Fetal Growth Retardation', 'Hemoglobin Increased', 'Colonic Fistula', 'Mitral Valve Disease', 'Hepatic Failure', 'Jejunal Hemorrhage', 'Pericardial Tamponade', 'Spleen Disorder', 'Vaginal Infection', 'Spermatic Cord Obstruction', 'Hypotension', 'Urostomy Stenosis', 'Urine Output Decreased', 'Gallbladder Pain', 'Premature Delivery', 'Weight Gain', 'Lymph Node Pain', 'Soft Tissue Necrosis Upper Limb', 'Spasticity', 'Tinnitus', 'Vagus Nerve Disorder', 'Vaginal Perforation', 'Chest Pain Cardiac', 'Vaginismus', 'Respiratory', 'Hypoalbuminemia', 'Laryngeal Stenosis', 'Scrotal Infection', 'Purpura', 'Superficial Soft Tissue Fibrosis', 'Scrotal Pain', 'Small Intestine Infection', 'Lower Gastrointestinal Hemorrhage', 'Respiratory Failure', 'Gastric Hemorrhage', 'Edema Face', 'Otitis Externa', 'Anxiety', 'Papilledema', 'Sinusitis', 'Duodenal Infection', 'Tumor Lysis Syndrome', 'Anal Stenosis', 'Exostosis', 'Seizure', 'Retroperitoneal Hemorrhage', 'Gastric Anastomotic Leak', 'Injection Site Reaction', 'Bronchopleural Fistula', 'Uterine Pain', 'Cardiac Troponin I Increased', 'Gallbladder Necrosis', 'Genital Edema', 'Duodenal Stenosis', 'Pain', 'Thoracic and Mediastinal Disorders Other', 'Fallopian Tube Perforation', 'Rash Pustular', 'Intraoperative Urinary Injury', 'Serum Amylase Increased', 'Sneezing', 'Pain in Extremity', 'Endophthalmitis', 'Central Nervous System Necrosis', 'Esophageal Pain', 'Cardiac Disorders Other', 'Ovarian Infection', 'Rectal Ulcer', 'Testicular Pain', 'Testicular Disorder', 'Ear Pain', 'Lip Pain', 'Ovulation Pain', 'Unequal Limb Length', 'Allergic Reaction', 'Blood Corticotrophin Decreased', 'Joint Infection', 'Hypersomnia', 'Nail Discoloration', 'Gallbladder Perforation', 'Night Blindness', 'Anorexia', 'Peritoneal Infection', 'Dry Eye', 'Edema Limbs', 'Hypertension', 'Colonic Perforation', 'Ascites', 'Intraoperative Splenic Injury', 'Jejunal Ulcer', 'Abdominal Soft Tissue Necrosis', 'Small Intestinal Anastomotic Leak', 'Nail Loss', 'Jejunal Stenosis', 'Papulopustular Rash', 'Urethral Anastomotic Leak', 'Enterovesical Fistula', 'Uterine Obstruction', 'Mobitz Type I', 'Akathisia', 'Blood Antidiuretic Hormone Abnormal', 'Hot Flashes', 'Menopause', 'Pharyngeal Necrosis', 'Facial Nerve Disorder', 'Renal Calculi', 'Gastric Fistula', 'Salivary Gland Infection', 'Urinary Fistula', 'Gastric Perforation', 'Rectal Perforation', 'Tumor Pain', 'Peritoneal Necrosis', 'Pleural Effusion', 'Retinoic Acid Syndrome', 'Psychosis', 'Vaginal Fistula', 'Facial Muscle Weakness', 'Wolff-Parkinson-White Syndrome', 'Muscle Weakness Trunk', 'Superficial Thrombophlebitis', 'Anal Fistula', 'Pelvic Soft Tissue Necrosis', 'Uterine Infection', 'Intestinal Stoma Obstruction', 'Chylothorax', 'Ejaculation Disorder', 'Fallopian Tube Anastomotic Leak', 'Testicular Hemorrhage', 'Growth Accelerated', 'Dysphasia', 'Tooth Infection', 'Vaginal Discharge', 'Prolapse of Intestinal Stoma', 'Retinal Tear', 'Telangiectasia', 'Leukoencephalopathy', 'Injury to Superior Vena Cava', 'Irritability', 'Uterine Hemorrhage', 'Atrial Flutter', 'Venous Injury', 'Tooth Development Disorder', 'Hirsutism', 'Headache', 'Pulmonary Edema', 'Device Related Infection', 'Oral Dysesthesia', 'Urethral Infection', 'Intraoperative Ocular Injury', 'Abdominal Distension', 'Anorectal Infection', 'Renal Hemorrhage', 'Intraoperative Ear Injury', 'Pericardial Effusion', 'Sore Throat', 'Lip Infection', 'Stomach Pain', 'White Blood Cell Decreased', 'Cataract', 'Catheter Related Infection', 'Erectile Dysfunction', 'Renal Colic', 'Dysarthria', 'Fallopian Tube Stenosis', 'Injury to Jugular Vein', 'Abdominal Infection', 'Pelvic Pain', 'Eyelid Function Disorder', 'Laryngitis', 'Small Intestinal Perforation', 'Blood and Lymphatic System Disorders Other', 'Laryngeal Fistula', 'Anal Hemorrhage', 'Intraoperative Respiratory Injury', 'Dysesthesia', 'Dysmenorrhea', 'Jejunal Perforation', 'Peripheral Nerve Infection', 'Tracheal Fistula', 'Vomiting', 'Pulmonary Fibrosis', 'Precocious Puberty', 'Stroke', 'Bone Infection', 'Acute Kidney Injury', 'Eye Pain', 'Facial Pain', 'Gallbladder Obstruction', 'Malabsorption', 'Hearing Impaired', 'Bronchial Infection', 'Anal Ulcer', 'Gingival Pain', 'Gastrointestinal Stoma Necrosis', 'Injury to Inferior Vena Cava', 'Esophageal Ulcer', 'Bronchial Stricture', 'Oral Hemorrhage', 'Oculomotor Nerve Disorder', 'Rectal Anastomotic Leak', 'Ejection Fraction Decreased', 'Dizziness', 'Tracheal Hemorrhage', 'Esophageal Infection', 'Fall', 'Breast Infection', 'Jejunal Obstruction', 'Wound Complication', 'Chills', 'Ileal Fistula', 'Tracheal Obstruction', 'Phantom Pain', 'Vestibular Disorder', 'Intraoperative Renal Injury', 'Creatinine Increased', 'Immune System Disorders Other', 'Pharyngeal Hemorrhage', 'Sinus Tachycardia', 'Stomal Ulcer', 'Unintended Pregnancy', 'Vascular Access Complication', 'dysphagia', 'Meningismus', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Typhlitis', 'Kidney Infection', 'Peripheral Ischemia', 'Pneumonitis', 'Duodenal Perforation', 'Urinary Tract Obstruction', 'Upper Respiratory Infection', 'Fat Atrophy', 'Floaters', 'Hematoma', 'Joint Range of Motion Decreased', 'Hematuria', 'Small Intestinal Stenosis', 'Avascular Necrosis', 'Autoimmune Disorder', 'Fallopian Tube Obstruction', 'Disseminated Intravascular Coagulation', 'Atelectasis', 'Edema Trunk', 'Muscle Weakness Left-Sided', 'Oral Cavity Fistula', 'Pancreatic Enzymes Decreased', 'Cranial Nerve Infection', 'Apnea', 'Blood Gonadotrophin Abnormal', 'Neuralgia', 'Iron Overload', 'Pharyngitis', 'Cholecystitis', 'Alkaline Phosphatase Increased', 'Upper Gastrointestinal Hemorrhage', 'Nail Ridging', 'Kidney Anastomotic Leak', 'Rectal Stenosis', 'Arteritis Infective', 'Surgical and Medical Procedures Other', 'Postnasal Drip', 'Ileal Hemorrhage', 'Hypohidrosis', 'Skin Induration', 'Cardiac Arrest', 'Chest Wall Pain', 'Prostatic Hemorrhage', 'Scoliosis', 'Hallucinations', 'Joint Range of Motion Decreased Cervical Spine', 'Wound Infection', 'Gynecomastia', 'Colitis', 'Restlessness', 'Infusion Related Reaction', 'Tracheal Mucositis', 'Adrenal Insufficiency', 'Toothache', 'Ataxia', 'Somnolence', 'Hyperkalemia', 'Esophagitis', 'Thromboembolic Event', 'Esophageal Hemorrhage', 'Radiculitis', 'Oligospermia', 'Renal and Urinary Disorders Other', 'Vertigo', 'Burn', 'Urostomy Obstruction', 'Vascular Disorders Other', 'Scleral Disorder', 'Dysgeusia', 'Cerebrospinal Fluid Leakage', 'General Disorders and Administration Site Conditions Other', 'Rectal Hemorrhage', 'Blood Bilirubin Increased', 'Urticaria', 'Carbon Monoxide Diffusing Capacity Decreased', 'Joint Range of Motion Decreased Lumbar Spine', 'Transient Ischemic Attacks', 'Aspartate Aminotransferase Increased', 'Stenosis of Gastrointestinal Stoma', 'Fetal Death', 'Hypernatremia', 'Esophageal Anastomotic Leak', 'Multi-Organ Failure', 'Sleep Apnea', 'Activated Partial Thromboplastin Time Prolonged', 'Lymph Leakage', 'wheezing', 'Abdominal Pain', 'Anemia', 'Atrioventricular Block Complete', 'Urostomy Site Bleeding', 'Colonic Ulcer', 'Lymphocyte Count Increased', 'Nail Infection', 'Neck Edema', 'Delayed Puberty', 'INR Increased', 'Libido Decreased', 'Bile Duct Stenosis', 'Myocarditis', 'Pharyngeal Fistula', 'Tracheal Stenosis', 'Vaginal Obstruction', 'Urinary Incontinence', 'Hypoglossal Nerve Disorder', 'Extraocular Muscle Paresis', 'Metabolism and Nutrition Disorders Other', 'Esophageal Perforation', 'Pulmonary Fistula', 'Rectal Obstruction', 'Duodenal Obstruction', 'Bronchial Fistula', 'Intraoperative Hemorrhage', 'Bladder Perforation', 'Intraoperative Reproductive Tract Injury', 'Seroma', 'Intraoperative Breast Injury', 'Small Intestine Ulcer', 'Gastroesophageal Reflux Disease', 'Gastrointestinal Pain', 'Esophageal Necrosis', 'Suicidal Ideation', 'Congenital', 'Skin and Subcutaneous Tissue Disorders Other', 'Alcohol Intolerance', 'Proteinuria', 'Restrictive Cardiomyopathy', 'Fecal Incontinence', 'Cognitive Disturbance', 'Hypoglycemia', 'Bronchial Obstruction', 'Uveitis', 'Dermatitis Radiation', 'Non-Cardiac Chest Pain', 'Extrapyramidal Disorder', 'Hypoxia', 'Cystitis Noninfective', 'Endocarditis Infective', 'Cheilitis', 'Diarrhea', 'Injury', 'Spinal Fracture', 'Obstruction Gastric', 'Death NOS', 'Blood Prolactin Abnormal', '']",,FollowUp -Hepatitis Sustained Virological Response,Hepatitis Sustained Virological Response,HepatitisSustainedVirologicalResponse,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,FollowUp -Recist Targeted Regions Number,Recist Targeted Regions Number,RecistTargetedRegionsNumber,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",False,,,,FollowUp -Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['Not Reported', 'Indeterminate', 'unknown', 'positive', 'negative', 'Not Performed', '']",,FollowUp -Viral Hepatitis Serologies,Viral Hepatitis Serologies,ViralHepatitisSerologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,False,,"['Not Reported', 'HBV Core Antibody', 'HBV Surface Antibody', 'Hepatitis C Antibody', 'unknown', 'HCV Genotype', 'HBV DNA', 'Hepatitis C Virus RNA', 'HBV Genotype', 'Hepatitis B Surface Antigen', '']",,FollowUp +Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Blood Clots', 'Hypospadias', ""Crohn's Disease"", 'Renal Failure (Requiring Dialysis)', 'Epstein-Barr Virus', 'Cataracts', 'Transient Ischemic Attack', 'Gorlin Syndrome', 'Peripheral Vascular Disease', 'Lupus', 'Denys-Drash Syndrome', 'Intraductal Papillary Mucinous Neoplasm', 'Depression', 'Heart Disease', 'COPD', 'Hepatitis', 'Primary Sclerosing Cholangitis', 'Chronic Renal Failure', 'Glycogen Storage Disease', 'Type II', 'Cancer', 'Li-Fraumeni Syndrome', 'Other Pulmonary Complications', 'Gastroesophageal Reflux Disease', 'Hepatitis B Infection', 'Rubinstein-Taybi Syndrome', 'Glaucoma', 'Insulin Controlled Diabetes', 'Anxiety', 'Allergies', 'Myasthenia Gravis', 'Celiac Disease', 'Gonadal Dysfunction', 'Not Reported', 'Lynch Syndrome', 'MAI', 'Inflammatory Bowel Disease', 'GERD', 'Pancreatitis', 'Hemorrhagic Cystitis', 'Joint Replacement', 'Interstitial Pneumontis or ARDS', 'Diet Controlled Diabetes', 'unknown', 'Hyperlipidemia', 'Sarcoidosis', 'Ulcerative Colitis', 'Alpha-1 Antitrypsin', 'Bronchitis', 'Herpes', 'Chronic Hepatitis', 'Other Cancer Within 5 Years', 'Fanconi Anemia', 'Arrhythmia', 'Cirrhosis', 'Pulmonary Fibrosis', 'Hepatitis C Infection', 'Atrial Fibrillation', 'Diabetic Neuropathy', 'Congestive Heart Failure (CHF)', 'Osteoarthritis', 'Stroke', 'Basal Cell Carcinoma', 'Connective Tissue Disorder', 'Low Grade Liver Dysplastic Nodule', 'Peripheral Neuropathy', 'Adrenocortical Insufficiency', 'Adenocarcinoma', 'DVT/PE', 'Asthma', 'Liver Cirrhosis (Liver Disease)', 'Cryptogenic Organizing Pneumonia', 'Myocardial Infarction', 'ITP', 'Psoriasis', 'Arthritis', 'Turcot Syndrome', 'Hypercholesterolemia', 'Cerebrovascular Disease', 'unknown Etiology', 'Hemihypertrophy', 'Hyperglycemia', 'Avascular Necrosis', 'Acute Renal Failure', 'Hypothyroidism', 'Rheumatoid Arthritis', 'Ischemic Heart Disease', 'Common Variable Immunodeficiency', 'Gout', 'Diabetes', 'Smoking', 'Human Papillomavirus Infection', 'Anemia', 'Pain (Various)', ""Behcet's Disease"", 'Deep Vein Thrombosis / Thromboembolism', 'Dyslipidemia', 'High Grade Liver Dysplastic Nodule', 'Rheumatologic Disease', 'Diverticulitis', 'Pulmonary Hemorrhage', 'Cholelithiasis', 'Headache', 'Sleep apnea', ""Hashimoto's Thyroiditis"", 'Hypercalcemia', 'Hypertension', 'Beckwith-Wiedemann', 'Coronary Artery Disease', 'HUS/TTP', 'Bone Fracture(s)', 'Steatosis', 'Liver Toxicity (Non-Infectious)', 'Hereditary Non-polyposis Colon Cancer', 'Peptic Ulcer (Ulcer)', 'Organ transplant (site)', 'Calcium Channel Blockers', 'Other Nonmalignant Systemic Disease', 'Neuroendocrine Tumor', 'Adenomatous Polyposis Coli', 'Epilepsy', 'Other', 'Nonalcoholic Steatohepatitis', 'Hepatitis A Infection', 'Fibrosis', 'Renal Insufficiency', ""Barrett's Esophagus"", 'Tyrosinemia', 'Familial Adenomatous Polyposis', 'Colon Polyps', 'Peutz-Jeghers Disease', 'Osteoporosis or Osteopenia', 'Biliary Disorder', 'Tuberculosis', 'Pregnancy in Patient or Partner', 'H. pylori Infection', 'Eczema', 'Wagr Syndrome', 'Renal Dialysis', 'Iron Overload', 'HIV / AIDS', 'Kidney Disease', 'Obesity', 'Seizure', '']",,FollowUp +Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['""10""', '""40""', '""70""', '""80""', 'Not Reported', '""20""', '""60""', '""30""', '""100""', '""0""', 'unknown', '""50""', '""90""', '']",,FollowUp +Viral Hepatitis Serologies,Viral Hepatitis Serologies,ViralHepatitisSerologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,False,,"['HCV Genotype', 'HBV DNA', 'Not Reported', 'HBV Core Antibody', 'Hepatitis B Surface Antigen', 'Hepatitis C Virus RNA', 'HBV Surface Antibody', 'Hepatitis C Antibody', 'HBV Genotype', 'unknown', '']",,FollowUp Weight,Weight,Weight,The weight of the patient measured in kilograms.,False,,,,FollowUp -CDC HIV Risk Factors,CDC HIV Risk Factors,CDCHIVRiskFactors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.",False,,"['Not Reported', 'Transfusion Recipient', 'Intravenous Drug User', 'None', 'Heterosexual Contact', 'unknown', 'Hemophiliac', 'Homosexual Contact', '']",,FollowUp -Body Surface Area,Body Surface Area,BodySurfaceArea,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,False,,,,FollowUp -Comorbidity Method of Diagnosis,Comorbidity Method of Diagnosis,ComorbidityMethodofDiagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,False,,"['Not Reported', 'Pathology', 'Histology', 'unknown', 'Radiology', '']",,FollowUp -Days to Adverse Event,Days to Adverse Event,DaystoAdverseEvent,Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable',False,,,,FollowUp -Adverse Event Grade,Adverse Event Grade,AdverseEventGrade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Grade 2', 'Grade 4', 'Grade 1', 'Grade 5', 'Grade 3', '']",,FollowUp -DLCO Ref Predictive Percent,DLCO Ref Predictive Percent,DLCORefPredictivePercent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",False,,,,FollowUp -FEV 1 FVC Pre Bronch Percent,FEV 1 FVC Pre Bronch Percent,FEV1FVCPreBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,False,,,,FollowUp -CD4 Count,CD4 Count,CD4Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,False,,,,FollowUp -Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Peripheral Neuropathy', 'Peutz-Jeghers Disease', 'Hepatitis B Infection', 'Bone Fracture(s)', 'Hyperglycemia', 'Hypothyroidism', 'Other Nonmalignant Systemic Disease', 'Psoriasis', 'Tyrosinemia', 'Cholelithiasis', 'Adrenocortical Insufficiency', 'Congestive Heart Failure (CHF)', 'Obesity', 'Pulmonary Fibrosis', 'Stroke', 'Neuroendocrine Tumor', 'Transient Ischemic Attack', ""Hashimoto's Thyroiditis"", 'ITP', 'Hepatitis A Infection', 'Hemorrhagic Cystitis', 'MAI', 'Rheumatoid Arthritis', 'Li-Fraumeni Syndrome', 'HUS/TTP', 'Hepatitis', 'Osteoarthritis', 'Celiac Disease', 'Pregnancy in Patient or Partner', 'Renal Insufficiency', 'Renal Failure (Requiring Dialysis)', 'Other Cancer Within 5 Years', 'Arthritis', 'Hepatitis C Infection', 'Ulcerative Colitis', 'Acute Renal Failure', 'Asthma', 'Alpha-1 Antitrypsin', 'DVT/PE', 'Heart Disease', 'Renal Dialysis', ""Crohn's Disease"", 'Cataracts', 'Fibrosis', 'Ischemic Heart Disease', ""Behcet's Disease"", 'Liver Cirrhosis (Liver Disease)', 'Turcot Syndrome', 'Dyslipidemia', 'Avascular Necrosis', 'Epilepsy', 'Peptic Ulcer (Ulcer)', 'Diet Controlled Diabetes', 'Cerebrovascular Disease', 'Tuberculosis', 'Herpes', 'Anxiety', 'Hereditary Non-polyposis Colon Cancer', 'Smoking', 'Iron Overload', 'Cancer', 'Rubinstein-Taybi Syndrome', 'Seizure', 'Colon Polyps', 'Type II', 'Intraductal Papillary Mucinous Neoplasm', 'Arrhythmia', 'Wagr Syndrome', 'Pancreatitis', 'Interstitial Pneumontis or ARDS', 'Eczema', 'Calcium Channel Blockers', 'Myasthenia Gravis', 'Epstein-Barr Virus', 'Chronic Renal Failure', 'Kidney Disease', 'H. pylori Infection', 'Denys-Drash Syndrome', 'Gout', 'High Grade Liver Dysplastic Nodule', 'Glycogen Storage Disease', 'Sarcoidosis', 'Organ transplant (site)', 'Inflammatory Bowel Disease', 'Bronchitis', 'Blood Clots', 'Other', 'Deep Vein Thrombosis / Thromboembolism', 'Hypertension', 'Lupus', 'Allergies', 'Fanconi Anemia', 'Peripheral Vascular Disease', 'GERD', 'Hyperlipidemia', 'Other Pulmonary Complications', 'Nonalcoholic Steatohepatitis', 'Common Variable Immunodeficiency', 'Pulmonary Hemorrhage', 'Anemia', ""Barrett's Esophagus"", 'Not Reported', 'Hypospadias', 'Basal Cell Carcinoma', 'Familial Adenomatous Polyposis', 'Hemihypertrophy', 'Biliary Disorder', 'Sleep apnea', 'Cirrhosis', 'Lynch Syndrome', 'Atrial Fibrillation', 'Hypercalcemia', 'Liver Toxicity (Non-Infectious)', 'unknown', 'Gorlin Syndrome', 'Pain (Various)', 'HIV / AIDS', 'Coronary Artery Disease', 'Human Papillomavirus Infection', 'Connective Tissue Disorder', 'Beckwith-Wiedemann', 'Chronic Hepatitis', 'Osteoporosis or Osteopenia', 'Gastroesophageal Reflux Disease', 'Insulin Controlled Diabetes', 'Rheumatologic Disease', 'Gonadal Dysfunction', 'Adenomatous Polyposis Coli', 'Diverticulitis', 'Hypercholesterolemia', 'Glaucoma', 'Headache', 'Cryptogenic Organizing Pneumonia', 'Diabetes', 'Joint Replacement', 'Adenocarcinoma', 'Low Grade Liver Dysplastic Nodule', 'Diabetic Neuropathy', 'Myocardial Infarction', 'Primary Sclerosing Cholangitis', 'Depression', 'Steatosis', 'unknown Etiology', 'COPD', '']",,FollowUp -Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Not Reported', 'Ectopic Pregnancy', 'Miscarriage', 'Stillbirth', 'unknown', 'Live Birth', 'Induced Abortion', '']",,FollowUp -Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['Not Reported', '""70""', '""20""', '""60""', '""30""', '""90""', '""10""', '""50""', 'unknown', '""100""', '""40""', '""80""', '""0""', '']",,FollowUp -Hysterectomy Margins Involved,Hysterectomy Margins Involved,HysterectomyMarginsInvolved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,False,,"['Not Reported', 'Bladder', 'Vagina', 'None', 'unknown', 'Microscopic Parametrium', 'Macroscopic Parametrium', '']",,FollowUp -Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp -Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,Presence or absennce of Barretts esophagus goblet cells.,False,,"['no', 'yes', '']",,FollowUp -Days to Comorbidity,Days to Comorbidity,DaystoComorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable',False,,,,FollowUp -Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Not Reported', 'Injected Insulin', 'Other', 'Alpha-Glucosidase Inhibitor', 'Oral Hypoglycemic', 'Thiazolidinedione', 'Biguanide', 'Insulin', 'Sulfonylurea', 'unknown', 'Diet', '']",,FollowUp Nadir CD4 Count,Nadir CD4 Count,NadirCD4Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,False,,,,FollowUp +Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['negative', 'positive', 'Not Reported', 'Not Performed', 'unknown', 'Indeterminate', '']",,FollowUp +Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Hysterectomy NOS', 'Not performed', 'Not Reported', 'Simple Hysterectomy', 'Radical Hysterectomy', 'unknown', '']",,FollowUp +Risk Factor Treatment,Risk Factor Treatment,RiskFactorTreatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,FollowUp +CD4 Count,CD4 Count,CD4Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,False,,,,FollowUp +Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['Not Reported', 'Methotrexate', 'Anti-TNFTherapy', 'Cyclophosphamide', 'Azathioprine', 'unknown', 'Other', 'None', '']",,FollowUp +Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Thiazolidinedione', 'Insulin', 'Not Reported', 'Oral Hypoglycemic', 'Sulfonylurea', 'Diet', 'Alpha-Glucosidase Inhibitor', 'Biguanide', 'Injected Insulin', 'unknown', 'Other', '']",,FollowUp +Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Ectopic Pregnancy', 'Not Reported', 'Stillbirth', 'Live Birth', 'Miscarriage', 'Induced Abortion', 'unknown', '']",,FollowUp +Comorbidity Method of Diagnosis,Comorbidity Method of Diagnosis,ComorbidityMethodofDiagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,False,,"['Radiology', 'Not Reported', 'Histology', 'Pathology', 'unknown', '']",,FollowUp +ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['""5.0""', 'Not Reported', '""2""', '""1.0""', '""4.0""', '""2.0""', '""5""', '""1""', '""0.0""', '""3.0""', '""0""', '""4""', 'unknown', '""3""', '']",,FollowUp +Body Surface Area,Body Surface Area,BodySurfaceArea,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,False,,,,FollowUp Days to Imaging,Days to Imaging,DaystoImaging,Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable',False,,,,FollowUp -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FollowUp -FEV1 Ref Pre Bronch Percent,FEV1 Ref Pre Bronch Percent,FEV1RefPreBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,False,,,,FollowUp -Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['Not Reported', 'Anti-TNFTherapy', 'Other', 'Cyclophosphamide', 'None', 'unknown', 'Azathioprine', 'Methotrexate', '']",,FollowUp -Risk Factor,Risk Factor,RiskFactor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Hepatitis B Infection', 'Undescended Testis', 'Allergy Animal NOS', 'Cholelithiasis', 'Allergy Food NOS', 'HIV', 'Obesity', 'Allergy Eggs', 'Hepatic Encephalopathy', 'Hay Fever', ""Hashimoto's Thyroiditis"", 'Diabetes NOS', 'Li-Fraumeni Syndrome', 'Thyroid Nodular Hyperplasia', 'Serous tubal intraepithelial carcinoma (STIC)', 'Alpha-1 Antitrypsin Deficiency', 'Parasitic Disease of Biliary Tract', 'Hepatitis C Infection', 'Recurrent Pyogenic Cholangitis', ""Gilbert's Syndrome"", 'Tattoo', 'Nonalcoholic Fatty Liver Disease', 'Allergy Ant', 'Autoimmune Atrophic Chronic Gastritis', 'Fibrosis', ""Behcet's Disease"", 'Tobacco Smoking', 'Turcot Syndrome', 'Gastric Polyp(s)', 'Tobacco Smokeless', 'Iron Overload', 'Cancer', 'Rubinstein-Taybi Syndrome', 'Intestinal Metaplasia', 'Seizure', 'Colon Polyps', 'Hematologic Disorder NOS', 'Wagr Syndrome', 'Pancreatitis', 'Eczema', 'Myasthenia Gravis', 'Epstein-Barr Virus', 'Common variable immune deficiency (CVID)', 'Low Grade Dysplasia', 'Denys-Drash Syndrome', 'Helicobacter Pylori-Associated Gastritis', 'Sarcoidosis', 'Tobacco NOS', 'Hepatitis NOS', 'Sensory Changes', 'Fanconi Anemia', 'Endometriosis', 'Nonalcoholic Steatohepatitis', 'Alcohol Consumption', 'Allergy Nuts', 'Diet', ""Barrett's Esophagus"", 'Not Reported', 'Hypospadias', 'Allergy Fruit', 'Allergy Seafood', 'Diabetes Type I', 'Familial Adenomatous Polyposis', 'Hemihypertrophy', 'Cirrhosis', 'Allergy Dog', 'High Grade Dysplasia', 'Lynch Syndrome', 'Allergy Bee', 'unknown', 'Gorlin Syndrome', 'Diabetes Type II', 'Human Papillomavirus Infection', 'Allergy Wasp', 'Endosalpingiosis', 'Beckwith-Wiedemann', 'Oral Contraceptives', 'Vision Changes', 'Chronic Hepatitis', 'Alcoholic Liver Disease', 'Lymphocytic Thyroiditis', 'Diverticulitis', 'Allergy Dairy or Lactose', 'Headache', 'Hemochromatosis', 'Allergy Mold or Dust', 'Allergy Meat', 'Allergy Processed Foods', 'Reflux Disease', 'Primary Sclerosing Cholangitis', 'Steatosis', 'Allergy Cat', 'Rheumatoid Arthritis', '']",,FollowUp -Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,Date of onset of pancreatitis.,False,,,,FollowUp -Recist Targeted Regions Sum,Recist Targeted Regions Sum,RecistTargetedRegionsSum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",False,,,,FollowUp -FEV1 FVC Post Bronch Percent,FEV1 FVC Post Bronch Percent,FEV1FVCPostBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,False,,,,FollowUp -AIDS Risk Factors,AIDS Risk Factors,AIDSRiskFactors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,False,,"['Encephalopathy', 'Coccidioidomycosis', 'Isosporiasis', 'Salmonella Septicemia', 'Mycobacterium avium Complex', 'Herpes Simplex Virus', 'Mycobacterium', 'Nocardiosis', 'NOS', 'Toxoplasmosis', 'Cytomegalovirus', 'Cryptococcosis', 'pneumonia', 'Progressive Multifocal Leukoencephalopathy', 'Candidiasis', 'Wasting Syndrome', 'Histoplasmosis', 'Mycobacterium tuberculosis', 'Pneumocystis Pneumonia', '']",,FollowUp -Reflux Treatment Type,Reflux Treatment Type,RefluxTreatmentType,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,False,,"['Not Reported', 'Not Applicable', 'Proton Pump Inhibitors', 'H2 Blockers', 'unknown', 'No Treatment', 'Surgically Treated', 'Antacids', 'Medically Treated', '']",,FollowUp -FEV1 Ref Post Bronch Percent,FEV1 Ref Post Bronch Percent,FEV1RefPostBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,False,,,,FollowUp -Hormonal Contraceptive Use,Hormonal Contraceptive Use,HormonalContraceptiveUse,The text term used to indicate whether the patient used hormonal contraceptives.,False,,"['Not Reported', 'Current User', 'Never Used', 'Former User', 'unknown', '']",,FollowUp -ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['Not Reported', '""5""', '""3""', '""0.0""', '""2""', '""1""', '""2.0""', '""1.0""', '""4.0""', '""4""', '""3.0""', 'unknown', '""5.0""', '""0""', '']",,FollowUp -Risk Factor Treatment,Risk Factor Treatment,RiskFactorTreatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,FollowUp -Scan Tracer Used,Scan Tracer Used,ScanTracerUsed,The text term used to describe the type of tracer used during the imaging or scan of the patient.,False,,"['Acetate', 'Axumin', 'PSMA', 'Choline', 'Sodium Fluoride', '']",,FollowUp -Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Not Reported', 'Postmenopausal', 'Perimenopausal', 'unknown', 'Premenopausal', '']",,FollowUp -HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['Not Reported', '""70""', '""33""', '""63""', 'unknown', '""16""', '""56""', '""26""', '""18""', '""31""', '""45""', 'Other', '""68""', '""58""', '""51""', '""59""', '""39""', '""35""', '""82""', '""73""', '""52""', '""66""', '""53""', '']",,FollowUp -HAART Treatment Indicator,HAART Treatment Indicator,HAARTTreatmentIndicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,FollowUp -Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable',True,,,,FollowUp HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FollowUp -Evidence of Recurrence Type,Evidence of Recurrence Type,EvidenceofRecurrenceType,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,False,,"['Positive Biomarkers', 'Convincing Image Source', 'Biopsy with Histologic Confirmation', '']",,FollowUp -Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp -Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Retina', 'Axillary tail of breast', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Parametrium', 'Nasopharynx NOS', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp +Recist Targeted Regions Sum,Recist Targeted Regions Sum,RecistTargetedRegionsSum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",False,,,,FollowUp +Scan Tracer Used,Scan Tracer Used,ScanTracerUsed,The text term used to describe the type of tracer used during the imaging or scan of the patient.,False,,"['Acetate', 'Choline', 'Sodium Fluoride', 'PSMA', 'Axumin', '']",,FollowUp +Days to Comorbidity,Days to Comorbidity,DaystoComorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable',False,,,,FollowUp +HAART Treatment Indicator,HAART Treatment Indicator,HAARTTreatmentIndicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,FollowUp +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FollowUp +Adverse Event Grade,Adverse Event Grade,AdverseEventGrade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Grade 3', 'Grade 5', 'Grade 4', 'Grade 2', 'Grade 1', '']",,FollowUp +Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Ventricle NOS', 'Adrenal gland NOS', 'Upper lobe lung', 'Choroid', 'Pleura NOS', 'External lip NOS', 'Overlapping lesion of biliary tract', 'Waldeyer ring', 'Commissure of lip', 'Overlapping lesion of pancreas', 'Vertebral column', 'Overlapping lesion of lung', 'Nervous system NOS', 'Other ill-defined sites', 'Overlapping lesion of eye and adnexa', 'Duodenum', 'Temporal lobe', 'Lymph nodes of multiple regions', 'Head face or neck NOS', 'unknown primary site', 'Extrahepatic bile duct', 'Bone marrow', 'Meninges NOS', 'Bladder neck', 'Head of pancreas', 'Overlapping lesion of vulva', 'Eyelid', 'Brain stem', 'Tonsillar pillar', 'Anterior surface of epiglottis', 'Female genital tract NOS', 'Ascending colon', 'Supraglottis', 'Overlapping lesion of floor of mouth', 'Upper limb NOS', 'Lacrimal gland', 'Tongue NOS', 'Corpus uteri', 'Ileum', 'Mucosa of lower lip', 'Submandibular gland', 'Thymus', 'Descended testis', 'Overlapping lesion of esophagus', 'Spleen', 'Scrotum NOS', 'Posterior wall of nasopharynx', 'Overlapping lesion of palate', 'Orbit NOS', 'Vagina NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Lower lobe lung', 'Pituitary gland', 'Round ligament', 'Nasal cavity', 'Overlapping lesion of skin', 'Male genital organs NOS', 'Bone of limb NOS', 'Overlapping lesion of hypopharynx', 'Sublingual gland', 'Cerebrum', 'Ventral surface of tongue NOS', 'Intestinal tract NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Mandible', 'Pylorus', 'Pancreatic duct', 'External upper lip', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Abdomen NOS', 'Short bones of lower limb and associated joints', 'Overlapping lesion of nasopharynx', 'Mouth NOS', 'Ureteric orifice', 'Colon NOS', 'Cheek mucosa', 'Pancreas NOS', 'Lower-inner quadrant of breast', 'Retina', 'Renal pelvis', 'Posterior wall of bladder', 'Lymph nodes of inguinal region or leg', 'Penis NOS', 'Clitoris', 'Superior wall of nasopharynx', 'Ovary', 'Tail of pancreas', 'Cloacogenic zone', 'Isthmus uteri', 'Retromolar area', 'Undescended testis', 'Eye NOS', 'skin NOS', 'Lesser curvature of stomach NOS', 'Lower-outer quadrant of breast', 'Mucosa of upper lip', 'Skin of lip NOS', 'Gastrointestinal tract NOS', 'Spinal meninges', 'Anterior mediastinum', 'Overlapping lesion of retroperitoneum and peritoneum', 'Floor of mouth NOS', 'unknown', 'Urachus', 'External ear', 'Lymph nodes of head face and neck', 'Specified parts of peritoneum', 'Optic nerve', 'Other specified parts of pancreas', 'Posterior mediastinum', 'Tonsillar fossa', 'Overlapping lesion of tongue', 'Mucosa of lip NOS', 'Kidney NOS', 'Upper-inner quadrant of breast', 'Mediastinum NOS', 'Overlapping lesion of heart mediastinum and pleura', 'Axillary tail of breast', 'Overlapping lesion of corpus uteri', 'Gastric antrum', 'Body of stomach', 'Overlapping lesion of tonsil', 'Uterine adnexa', 'Lateral floor of mouth', 'Labium minus', 'Middle lobe lung', 'Medulla of adrenal gland', 'Lower limb NOS', 'Hard palate', 'Body of penis', 'Overlapping lesion of digestive system', 'Overlapping lesion of other and unspecified parts of mouth', 'Lower gum', 'Overlapping lesion of rectum anus and anal canal', 'Hypopharynx NOS', 'Overlapping lesion of female genital organs', 'Skin of other and unspecified parts of face', 'Glans penis', 'Accessory sinus NOS', 'Overlapping lesion of endocrine glands and related structures', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Bones of skull and face and associated joints', 'Vestibule of mouth', 'Border of tongue', 'Parametrium', 'Ciliary body', 'Soft palate NOS', 'Overlapping lesion of cervix uteri', 'Gum NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Skin of trunk', 'Cranial nerve NOS', 'Ampulla of Vater', 'Palate NOS', 'Pineal gland', 'Lymph nodes of axilla or arm', 'Base of tongue NOS', 'Middle ear', 'Breast NOS', 'Parietal lobe', 'Frontal sinus', 'Overlapping lesion of larynx', 'Retroperitoneum', 'Paraurethral gland', 'Overlapping lesion of urinary organs', 'Connective subcutaneous and other soft tissues NOS', 'Lateral wall of oropharynx', 'Main bronchus', 'Liver', 'Lip NOS', 'Biliary tract NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Anterior 2/3 of tongue NOS', 'Skin of scalp and neck', 'Short bones of upper limb and associated joints', 'Jejunum', 'Overlapping lesion of ill-defined sites', 'Sphenoid sinus', 'Urethra', 'Trachea', 'Hematopoietic system NOS', 'Fallopian tube', 'Cerebellum NOS', 'Carotid body', 'Other specified parts of male genital organs', 'Connective subcutaneous and other soft tissues of abdomen', 'skin of upper limb and shoulder', 'Not Reported', 'Lateral wall of nasopharynx', 'Endocrine gland NOS', 'Heart', 'Dorsal surface of tongue NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Central portion of breast', 'Endometrium', 'Appendix', 'Cerebral meninges', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peritoneum NOS', 'Craniopharyngeal duct', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Ethmoid sinus', 'Exocervix', 'Pharynx NOS', 'Anal canal', 'Aortic body and other paraganglia', 'Labium majus', 'Lingual tonsil', 'Ill-defined sites within respiratory system', 'Lower third of esophagus', 'Overlapping lesion of bones joints and articular cartilage', 'Rectosigmoid junction', 'Placenta', 'Bone NOS', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lateral wall of bladder', 'Cecum', 'Parathyroid gland', 'Cortex of adrenal gland', 'Upper-outer quadrant of breast', 'Vulva NOS', 'Prepuce', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Greater curvature of stomach NOS', 'Autonomic nervous system NOS', 'Nasopharynx NOS', 'Anus NOS', 'Overlapping lesion of male genital organs', 'Descending colon', 'Long bones of lower limb and associated joints', 'Urinary system NOS', 'Cardia NOS', 'Lung NOS', 'Frontal lobe', 'Thoracic esophagus', 'Overlapping lesion of lip', 'Cervical esophagus', 'Uterus NOS', 'Major salivary gland NOS', 'Maxillary sinus', 'Intrathoracic lymph nodes', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Posterior wall of oropharynx', 'Epididymis', 'Spermatic cord', 'Pelvic lymph nodes', 'Dome of bladder', 'Middle third of esophagus', 'Pelvis NOS', 'Tonsil NOS', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cervix uteri', 'Nipple', 'Conjunctiva', 'Olfactory nerve', 'Fundus uteri', 'Anterior floor of mouth', 'Oropharynx NOS', 'Meckel diverticulum', 'Esophagus NOS', 'Intra-abdominal lymph nodes', 'Lymph node NOS', 'Small intestine NOS', 'Brain NOS', 'Overlapping lesion of major salivary glands', 'Vallecula', 'Upper gum', 'Overlapping lesion of small intestine', 'Overlapping lesion of breast', 'Anterior wall of nasopharynx', 'Cauda equina', 'Myometrium', 'skin of lower limb and hip', 'Overlapping lesion of accessory sinuses', 'Hypopharyngeal aspect of aryepiglottic fold', 'Hepatic flexure of colon', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Overlapping lesion of stomach', 'Postcricoid region', 'Uvula', 'Splenic flexure of colon', 'Overlapping lesion of bladder', 'Glottis', 'Pyriform sinus', 'Thorax NOS', 'Trigone of bladder', 'Fundus of stomach', 'Abdominal esophagus', 'Posterior wall of hypopharynx', 'Overlapping lesion of penis', 'Connective subcutaneous and other soft tissues of thorax', 'Blood', 'Body of pancreas', 'Bladder NOS', 'Occipital lobe', 'Intrahepatic bile duct', 'Spinal cord', 'Laryngeal cartilage', 'Transverse colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sigmoid colon', 'Cornea NOS', 'Prostate gland', 'Endocervix', 'Overlapping lesions of oropharynx', 'Overlapping lesion of colon', 'Upper respiratory tract NOS', 'Islets of Langerhans', 'Broad ligament', 'Parotid gland', 'Anterior wall of bladder', 'Rib sternum clavicle and associated joints', 'Long bones of upper limb scapula and associated joints', 'Gallbladder', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Upper third of esophagus', 'Other specified parts of female genital organs', 'Thyroid gland', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of pelvis', 'Reticuloendothelial system NOS', 'Acoustic nerve', 'Larynx NOS', 'Stomach NOS', 'Testis NOS', 'External lower lip', 'Subglottis', 'Ureter', 'Overlapping lesion of brain', 'Rectum NOS', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp -Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Not Reported', 'Distant', 'Biochemical', 'Regional', 'Local', 'unknown', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp +Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp -AJCC Pathologic M,AJCC Pathologic M,AJCCPathologicM,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).",False,,"['Not Reported', 'MX', 'M1a', 'M0', 'M1b', 'cM0 (i+)', 'unknown', 'M1c', 'M1', '']",,Diagnosis -Non Nodal Tumor Deposits,Non Nodal Tumor Deposits,NonNodalTumorDeposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Diagnosis -Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Intraductal papillary adenocarcinoma with invasion', 'Multiple myeloma', 'Teratoma malignant NOS', 'Intraductal carcinoma noninfiltrating NOS', 'Renal medullary carcinoma', 'Diffuse melanocytosis', 'Tubulovillous adenoma NOS', 'Mucosal-associated lymphoid tissue lymphoma', 'Hepatoid adenocarcinoma', 'Osteoblastoma malignant', 'Cervical intraepithelial neoplasia low grade', 'Non-Hodgkin lymphoma NOS', 'Therapy related myeloid neoplasm', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Glioblastoma', 'Rhabdomyoma NOS', 'Precursor T-cell lymphoblastic lymphoma', 'Mixed medullary-follicular carcinoma', 'Chronic monocytic leukemia', 'Squamous cell carcinoma clear cell type', 'Hepatocellular adenoma', 'Non-small cell carcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Malignant melanoma in congenital melanocytic nevus', 'Neuroepithelioma NOS', 'Bronchiolar carcinoma', 'Adenocarcinoma in situ in adenomatous polyp', 'Melanoma in situ', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Chondrosarcoma grade 2/3', 'Eosinophil adenoma', 'Transitional cell carcinoma in situ', 'Tubulocystic renal cell carcinoma', 'Intraepidermal squamous cell carcinoma Bowen type', 'c-ALL', 'Burkitt lymphoma NOS (Includes all variants)', 'Pleomorphic carcinoma', 'Adenocarcinoma in situ non-mucinous', 'Adenocarcinoma metastatic NOS', 'Papillary urothelial carcinoma', 'Carcinoma in situ in adenomatous polyp', 'Basophil carcinoma', 'Large cell carcinoma NOS', 'Papillary cystadenoma NOS', 'Chronic myelogenous leukemia BCR-ABL positive', 'Papillary carcinoma NOS', 'Eosinophil carcinoma', 'Malignant lymphoma lymphoblastic NOS', 'Meningioma malignant', 'Malignant lymphoma small B lymphocytic NOS', 'Undifferentiated pleomorphic sarcoma', 'Adenocarcinoma diffuse type', 'Glioma malignant', 'Paget disease extramammary', 'Papillotubular adenocarcinoma', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Kaposi sarcoma', 'Melanotic medulloblastoma', 'Hodgkin granuloma', 'Hodgkin lymphoma nodular sclerosis NOS', 'Bronchio-alveolar carcinoma mucinous', 'Precancerous melanosis NOS', 'High-grade serous carcinoma', 'Hepatoid carcinoma', 'Splenic diffuse red pulp small B-cell lymphoma', 'Neoplasm metastatic', 'Secondary carcinoma', 'Lymphoma NOS', 'Precursor B-cell lymphoblastic leukemia', 'T-cell large granular lymphocytic leukemia', 'Astrocytoma anaplastic', 'Renal cell adenocarcinoma', 'Papillary transitional cell carcinoma', 'Pancreatoblastoma', 'Pleomorphic lobular carcinoma in situ', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Paraganglioma malignant', 'Sclerosing hepatic carcinoma', 'Infiltrating duct carcinoma NOS', 'Acute leukemia Burkitt type', 'Gastrinoma NOS', 'Teratoma NOS', 'Renal carcinoma collecting duct type', 'Capillary hemangioma', 'Unclassified tumor borderline malignancy', 'Undifferentiated round cell sarcoma', 'Burkitt tumor', 'Tubular adenocarcinoma', 'Medullary osteosarcoma', 'Intraductal tubulopapillary neoplasm', 'Liposarcoma NOS', 'Mixed tumor NOS', 'Papillary microcarcinoma', 'Adenocarcinoma in polypoid adenoma', 'Carcinoma intestinal type', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Meningioma NOS', 'Papillary meningioma', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Adenocarcinoma NOS', 'Combined small cell-adenocarcinoma', 'Gastrin cell tumor', 'Haemangioblastoma', 'Gastrin cell tumor malignant', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Liver cell adenoma', 'Myeloid leukemia NOS', 'Undifferentiated spindle cell sarcoma', 'Tumor secondary', 'Basal cell adenocarcinoma', 'Papillary serous cystadenocarcinoma', 'Mammary carcinoma in situ', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Pigmented nevus NOS', 'Ganglioglioma NOS', 'Malignant lymphoma immunoblastic NOS', 'Tumor embolus', 'Malignant melanoma regressing', 'Dermatofibroma NOS', 'Pleomorphic lobular carcinoma', 'Nephroblastoma NOS', 'Meningioma anaplastic', 'Hodgkin paragranuloma NOS', 'Hodgkin disease NOS', 'Capillary lymphangioma', 'Malignancy', 'Interstitial cell tumor malignant', 'Papillary serous adenocarcinoma', 'Sarcoma NOS', 'Meningeal melanoma', 'Chronic myeloproliferative disease NOS', 'Basophil adenocarcinoma', 'Malignant lymphoma large B-cell NOS', 'Tubular carcinoid', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Chronic myelomonocytic leukemia NOS', 'Acute myeloid leukemia MLL', 'Intraductal carcinoma clinging', 'Malignant lymphoma Hodgkin', 'Osteosarcoma NOS', 'Adenocarcinoid tumor', 'Nevus NOS', 'Hodgkin lymphoma NOS', 'Tubular adenoma NOS', 'Eosinophilic granuloma', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Intradermal nevus', 'Malignant lymphoma lymphocytic diffuse NOS', 'Intraductal and lobular carcinoma', 'Pituitary carcinoma NOS', 'Medullary carcinoma NOS', 'Melanotic progonoma', 'Epidermoid carcinoma NOS', 'Basal cell tumor', 'Mixed small cell carcinoma', 'Acute lymphoid leukemia', 'Bile duct adenocarcinoma', 'Serous cystadenocarcinoma NOS', 'Small cell sarcoma', 'Juvenile myelomonocytic leukemia', 'Adenocarcinoma in villous adenoma', 'Eosinophil adenocarcinoma', 'Pancreatic endocrine tumor benign', 'Squamous cell carcinoma adenoid', 'Tubulolobular carcinoma', 'Bronchial adenoma carcinoid', 'Melanotic neurofibroma', 'Bile duct carcinoma', 'Intraductal papillary carcinoma', 'Malignant lymphoma mixed cell type nodular', 'Pulmonary artery intimal sarcoma', 'Melanocytic nevus', 'Chronic lymphoid leukemia', 'Precursor B-cell lymphoblastic lymphoma', 'Precursor T-cell lymphoblastic leukemia', 'Preleukemia', 'Acute basophilic leukaemia', 'Adenocarcinoma in situ NOS', 'Malignant lymphoma large B-cell diffuse NOS', 'Burkitt cell leukemia', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Mixed squamous cell and glandular papilloma', 'Papillomatosis NOS', 'Combined large cell neuroendocrine carcinoma', 'Mucous adenocarcinoma', 'Bronchiolar adenocarcinoma', 'Epidermoid carcinoma in situ NOS', 'Malignant melanoma in giant pigmented nevus', 'Chronic myelomonocytic leukemia Type II', 'Typical carcinoid', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Monocytic leukemia NOS', 'Rhabdoid meningioma', 'Adenocarcinoma of anal glands', 'Papillary squamous cell carcinoma in situ', 'Myeloma NOS', 'Adenocarcinoma of anal ducts', 'Pulmonary blastoma', 'Tumor cells benign', 'Carcinoma in a polyp NOS', 'Interstitial cell tumor NOS', 'Epithelial tumor benign', 'Tubular androblastoma with lipid storage', 'Burkitt-like lymphoma', 'Malignant lymphoma lymphocytic nodular NOS', 'Adenocarcinoma in situ mucinous', 'Preleukemic syndrome', 'Ductal carcinoma in situ NOS', 'Intraepidermal carcinoma NOS', 'Malignant lymphoma mixed cell type follicular', 'Papillary adenocarcinoma NOS', 'B-ALL', 'Carcinoma undifferentiated NOS', 'Cementoma NOS', 'Pancreatobiliary-type carcinoma', 'Papillary tumor of the pineal region', 'Chronic myelomonocytic leukemia in transformation', 'Endometrioid adenocarcinoma NOS', 'Papillary serous cystadenoma NOS', 'Interstitial cell tumor benign', 'Neoplasm benign', 'Lobular and ductal carcinoma', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Melanocytoma NOS', 'Acute lymphatic leukemia', 'Acute lymphoblastic leukemia mature B-cell type', 'Chronic granulocytic leukemia NOS', 'Malignant lymphoma nodular NOS', 'Squamous cell carcinoma in situ NOS', 'Acute lymphoblastic leukemia precursor cell type', 'Infiltrating duct and cribriform carcinoma', 'Meningeal melanocytoma', 'Familial adenomatous polyposis', 'Malignant lymphoma non-Hodgkin NOS', 'Papillotubular adenoma', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Small congenital nevus', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Mixed medullary-papillary carcinoma', 'Esophageal intraepithelial neoplasia high grade', 'Melanoma NOS', 'Bile duct adenoma', 'Neoplasm NOS', 'Gastrointestinal stromal tumor malignant', 'Tumor NOS', 'Chondroma NOS', 'Precursor cell lymphoblastic leukemia NOS', 'Basal cell carcinoma NOS', 'Squamous cell carcinoma NOS', 'Transitional carcinoma', 'Undifferentiated sarcoma', 'Undifferentiated epithelioid sarcoma', 'Neoplasm malignant uncertain whether primary or metastatic', 'Papillary and follicular carcinoma', 'Pro-T ALL', 'Rhabdoid sarcoma', 'Renal cell carcinoma unclassified', 'Adult T-cell lymphoma', 'Papillary epidermoid carcinoma', 'Hodgkin lymphoma mixed cellularity NOS', 'Unclassified tumor benign', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Undifferentiated leukaemia', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Liposarcoma well differentiated', 'Paget disease of breast', 'Chronic lymphocytic leukemia', 'Renal cell carcinoma NOS', 'Adenocarcinoma intestinal type', 'Duct carcinoma NOS', 'Malignant lymphoma diffuse NOS', 'Diffuse large B-cell lymphoma NOS', 'Inflammatory carcinoma', 'Chronic myeloid leukemia NOS', 'Carcinoma metastatic NOS', 'Transitional cell carcinoma', 'Tumor metastatic', 'Melanotic MPNST', 'Papillary adenoma NOS', 'Pancreatic endocrine tumor NOS', 'Tubular carcinoma', 'T-cell lymphoma NOS', 'Astrocytoma NOS', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Malignant melanoma in precancerous melanosis', 'Glioma NOS', 'Chronic lymphatic leukemia', 'Lymphocytic leukemia NOS', 'Duct adenocarcinoma NOS', 'Bronchial-associated lymphoid tissue lymphoma', 'Central neurocytoma', 'Hodgkin sarcoma', 'Papillary squamous cell carcinoma', 'Pulmonary adenomatosis', 'Malignant melanoma in Hutchinson melanotic freckle', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Dysplastic nevus', 'Cancer', 'Lobular carcinoma NOS', 'Mixed tumor malignant NOS', 'Sclerosing hemangioma', 'Chronic myeloproliferative disorder', 'Non-lymphocytic leukemia NOS', 'Adenocarcinoma pancreatobiliary type', 'Intraductal tubular-papillary neoplasm high grade', 'Neoplasm secondary', 'Hepatocarcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Renal cell carcinoma sarcomatoid', 'Renal cell carcinoma chromophobe type', 'Lobular carcinoma noninfiltrating', 'Melanoameloblastoma', 'Cerebellar sarcoma NOS', 'Diffuse astrocytoma IDH-wildtype', 'Tubulo-papillary adenoma', 'Rhabdomyosarcoma with ganglionic differentiation', 'Non-invasive low grade serous carcinoma', 'Serous surface papillary carcinoma', 'Adenocarcinoma endocervical type', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Peripheral T-cell lymphoma large cell', 'Pancreatic microadenoma', 'Acute myelomonocytic leukemia', 'Ependymoma NOS', 'T-cell large granular lymphocytosis', 'Pancreatic endocrine tumor malignant', 'Liposarcoma differentiated', 'Undifferentiated high-grade pleomorphic sarcoma', 'Chronic neutrophilic leukemia', 'Malignant lymphoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Malignant melanoma in junctional nevus', 'Hepatocellular carcinoma NOS', 'Malignant lymphoma lymphocytic NOS', 'Pleomorphic lipoma', 'Papilloma of bladder', 'Bronchiolo-alveolar carcinoma NOS', 'Acute lymphoblastic leukemia NOS', 'Pituitary adenoma NOS', 'Adult T-cell lymphoma/leukemia', 'Not Reported', 'Tumor cells uncertain whether benign or malignant', 'Splenic lymphoma with villous lymphocytes', 'unknown', 'Renal cell carcinoma spindle cell', 'Pleomorphic adenoma', 'Paget disease and infiltrating duct carcinoma of breast', 'Duct carcinoma desmoplastic type', 'Oat cell carcinoma', 'Nonpigmented nevus', 'Endometrioid adenofibroma NOS', 'Paget disease and intraductal carcinoma of breast', 'Unclassified tumor uncertain whether benign or malignant', 'Tumorlet benign', 'Bronchial adenoma NOS', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Carcinoma in situ in a polyp NOS', 'Chronic myelocytic leukemia NOS', 'Adenocarcinoma in a polyp NOS', 'Adult rhabdomyoma', 'Paget disease mammary', 'Melanotic neuroectodermal tumor', 'Neuroblastoma NOS', 'Intravascular B-cell lymphoma', 'Malignant lymphoma large cell NOS', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Inflammatory adenocarcinoma', 'Prostatic intraepithelial neoplasia grade III', 'Gastrinoma malignant', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Pleomorphic liposarcoma', 'Rhabdosarcoma', 'Intraductal carcinoma NOS', 'Primary amyloidosis', 'Small cell neuroendocrine carcinoma', 'Intraductal micropapillary carcinoma', 'Intraductal papillary adenocarcinoma NOS', 'Combined/mixed carcinoid and adenocarcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Neoplasm malignant', 'Papillary glioneuronal tumor', 'Adenocarcinoma combined with other types of carcinoma', 'Adenocarcinoma in adenomatous polyp', 'Liver cell carcinoma', 'Endometrioid carcinoma NOS', 'Neoplasm uncertain whether benign or malignant', 'Papillary carcinoma in situ', 'Carcinoma in situ NOS', 'Papillary adenocarcinoma follicular variant', 'Spindle cell melanoma NOS', 'Undifferentiated uterine sarcoma', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Intraductal carcinoma solid type', 'Pro-B ALL', 'Rhabdomyosarcoma NOS', 'Dermal nevus', 'Combined small cell carcinoma', 'Ductal carcinoma NOS', 'Pagetoid reticulosis', 'Chronic granulocytic leukemia BCR/ABL', 'Medulloblastoma NOS', 'Secretory carcinoma of breast', 'Bronchial adenoma cylindroid', 'Infiltrating duct and colloid carcinoma', 'Diffuse astrocytoma IDH-mutant', 'Bile duct cystadenoma', 'Cervical intraepithelial neoplasia grade III', 'Splenic marginal zone B-cell lymphoma', 'Medullary adenocarcinoma', 'Small cell osteosarcoma', 'Papilloma NOS', 'B lymphoblastic leukemia/lymphoma NOS', 'Pigmented basal cell carcinoma', 'Lobular adenocarcinoma', 'Melanoma malignant of soft parts', 'Infiltrating basal cell carcinoma NOS', 'Combined small cell-large carcinoma', 'Paraganglioma NOS', 'Adenocarcinoma in situ in a polyp NOS', 'Carcinoma in adenomatous polyp', 'Acute leukemia NOS', 'Chronic leukemia NOS', 'Adenocarcinoma in situ in tubular adenoma', 'Cerebellar liponeurocytoma', 'Melanotic psammomatous MPNST', 'Bile duct cystadenocarcinoma', 'Tumor malignant NOS', 'Myelocytic leukemia NOS', 'Unclassified tumor malignant', 'Lymphatic leukemic NOS', 'Malignant lymphoma mixed cell type diffuse', 'Pancreatic endocrine tumor nonfunctioning', 'Eosinophilic leukemia', 'Acute myeloid leukemia minimal differentiation', 'Neurofibroma NOS', 'Endometrial sarcoma NOS', 'Basophil adenoma', 'Malignant melanoma NOS', 'Melanocytoma eyeball', 'Small cell carcinoma NOS', 'Mixed pineal tumor', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Combined small cell-squamous cell carcinoma', 'Duct adenoma NOS', 'Intraductal carcinoma and lobular carcinoma in situ', 'Intracystic papilloma', 'Adenocarcinoma in tubular adenoma', 'Micropapillary carcinoma NOS', 'Paraganglioma benign', 'Splenic marginal zone lymphoma NOS', 'Carcinoma NOS', 'Tubulopapillary adenocarcinoma', 'Ewing sarcoma', 'Neurofibrosarcoma', 'Carcinoma diffuse type', 'Diffuse astrocytoma low grade', 'Pancreatobiliary neoplasm non-invasive', 'Rodent ulcer', 'Rhabdoid tumor NOS', 'Basal cell adenoma', 'Tumor benign', 'Neuroendocrine carcinoma NOS', 'Carcinoma in pleomorphic adenoma', 'Peripheral T-cell lymphoma NOS', 'Tubular androblastoma NOS', 'Carcinosarcoma NOS', 'Astrocytoma low grade', 'Osteoblastoma NOS', 'Hepatocholangiocarcinoma', 'Acinar cell carcinoma', 'Epithelial tumor malignant', 'Endometrioid adenoma NOS', 'Acute lymphocytic leukemia', 'Myoepithelioma', 'Pigmented adenoma', 'Lymphoblastoma', 'Papillomatosis glandular', 'Lymphoblastic leukemia NOS', 'Duct cell carcinoma', 'Acute myeloid leukemia NOS', 'Bronchiolo-alveolar carcinoma Clara cell', 'Chronic myelomonocytic leukemia Type 1', 'Intraductal tubular-papillary neoplasm low grade', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Acute promyelocytic leukemia NOS', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Carcinoma anaplastic NOS', 'Lobular carcinoma in situ NOS', 'T lymphoblastic leukemia/lymphoma', 'Tumor cells malignant', 'Papillary adenofibroma', 'Neurofibromatosis NOS', 'Neurosarcoma', 'Papillary renal cell carcinoma', 'Central neuroblastoma', 'Basal cell epithelioma', 'Haemangiosarcoma', 'Tumor cells NOS', 'Melanotic schwannoma', 'B cell lymphoma NOS', 'Skin appendage carcinoma', 'Spindle cell carcinoma NOS']",,Diagnosis -Tumor Focality,Tumor Focality,TumorFocality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,False,,"['Not Reported', 'Unifocal', 'Multifocal', 'unknown', '']",,Diagnosis -INPC Histologic Group,INPC Histologic Group,INPCHistologicGroup,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.",False,,"['Not Reported', 'Favorable', 'Unfavorable', 'unknown', '']",,Diagnosis -Lymphatic Invasion Present,Lymphatic Invasion Present,LymphaticInvasionPresent,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement",False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Diagnosis -Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,Diagnosis -AJCC Pathologic N,AJCC Pathologic N,AJCCPathologicN,The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.,False,,"['Not Reported', 'N1bII', 'N0', 'N3c', 'N0 (mol+)', 'N2', 'unknown', 'N1bIV', 'N0 (i+)', 'N2a', 'N0 (i-)', 'N3', 'N2b', 'N1b', 'NX', 'N4', 'N1c', 'N2c', 'N3b', 'N1bI', 'N1', 'N3a', 'N1mi', 'N1bIII', 'N1a', 'N0 (mol-)', '']",,Diagnosis -Mitotic Count,Mitotic Count,MitoticCount,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",False,,,,Diagnosis -Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Not Reported', 'Indeterminate', 'unknown', 'Present', 'Absent', '']",,Diagnosis -AJCC Clinical Stage,AJCC Clinical Stage,AJCCClinicalStage,"Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.",False,,"['Not Reported', 'Stage IB', 'Stage 0', 'Stage IB2', 'Stage 0is', 'Stage III', 'Stage IIA', 'Stage II', 'Stage IS', 'unknown', 'Stage IIA1', 'Stage Tis', 'Stage IIIA', 'Stage IA1', 'Stage IVA', 'Stage IIC', 'Stage IVB', 'Stage IIIC', 'Stage IV', 'Stage IB1', 'Stage IIIB', 'Stage I', 'Stage IA2', 'Stage X', 'Stage IC', 'Stage IIIC2', 'Stage IIC1', 'Stage IIB', 'Stage 0a', 'Stage IVC', 'Stage IA', 'Stage IIIC1', 'Stage IIA2', '']",,Diagnosis -Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis -Classification of Tumor,Classification of Tumor,ClassificationofTumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,False,,"['Not Reported', 'Recurrence', 'Other', 'Primary', 'Not Allowed To Collect', 'unknown', 'Metastasis', '']",,Diagnosis -International Prognostic Index,International Prognostic Index,InternationalPrognosticIndex,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.",False,,"['Low-Intermediate Risk', 'High Risk', 'Low Risk', 'High-Intermediate Risk', '']",,Diagnosis -Gleason Grade Group,Gleason Grade Group,GleasonGradeGroup,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Group 5', 'Group 3', 'Group 4', 'Group 2', 'Group 1', '']",,Diagnosis -Perineural Invasion Present,Perineural Invasion Present,PerineuralInvasionPresent,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Diagnosis -Primary Gleason Grade,Primary Gleason Grade,PrimaryGleasonGrade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 5', 'Pattern 2', 'Pattern 1', 'Pattern 3', 'Pattern 4', '']",,Diagnosis -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Diagnosis -Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,,"['Not Reported', 'Low Grade', 'Not Applicable', 'G2', 'High Grade', 'G3', 'G4', 'G1', 'GX', 'unknown', 'Intermediate Grade', 'GB', '']",,Diagnosis -IRS Stage,IRS Stage,IRSStage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Not Reported', '2', '1', '3', 'unknown', '4', '']",,Diagnosis +Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Biochemical', 'Not Reported', 'Regional', 'Distant', 'Local', 'unknown', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp +Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis +Peritoneal Fluid Cytological Status,Peritoneal Fluid Cytological Status,PeritonealFluidCytologicalStatus,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,False,,"['Malignant', 'Not Reported', 'Non-Malignant', 'Atypical', 'Unsatisfactory', 'unknown', '']",,Diagnosis +Margins Involved Site,Margins Involved Site,MarginsInvolvedSite,The text term used to describe the anatomic sites that were involved in the survival margins.,False,,"['Renal Vein', 'Renal Capsule', 'Ureter', 'Perinephric Fat', 'Renal', 'Parenchyma', 'Renal Sinus', 'Gerota Fascia', '']",,Diagnosis Days to Diagnosis,Days to Diagnosis,DaystoDiagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable',False,,,,Diagnosis -Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['Not Reported', 'Biochemical evidence of disease without structural correlate', 'Not Applicable', 'unknown tumor status', 'Loco-regional recurrence/progression', 'Not Allowed To Collect', 'Tumor free', 'With tumor', 'Distant met recurrence/progression']",,Diagnosis -Metastasis at Diagnosis Site,Metastasis at Diagnosis Site,MetastasisatDiagnosisSite,Text term to identify an anatomic site in which metastatic disease involvement is found.,False,,"['Not Reported', 'Lymph Node NOS', 'Pleura', 'Abdomen', 'Distant Nodes', 'unknown', 'Soft Tissue', 'Scalp', 'Distant Organ', 'Kidney', 'Adrenal Gland', 'Peritoneal Cavity', 'Peritoneum', 'Pelvis', 'Central Nervous System', 'Ovary', 'Skin', 'Liver', 'Spinal Cord', 'Bone Marrow', 'Ascites', 'Bone', 'Brain', 'Groin', 'Cerebrospinal Fluid', 'Lung', 'Inguinal', 'Colon', 'Lymph Node', 'Mediastinum', 'Axillary', 'Omentum', 'Small Intestine', '']",,Diagnosis -AJCC Clinical T,AJCC Clinical T,AJCCClinicalT,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['Not Reported', 'T1b1', 'Tis (LCIS)', 'T4a', 'T4b', 'unknown', 'T2a', 'T4e', 'T3b', 'T1a', 'T2a2', 'T1mi', 'T4d', 'Tis', 'T4c', 'T3c', 'T4', 'Ta', 'T0', 'T1a1', 'T2a1', 'T1b', 'T1a2', 'T1', 'T2d', 'T3d', 'T2c', 'T1b2', 'T1c', 'T3', 'T2b', 'TX', ""Tis (Paget's)"", 'T2', 'T3a', 'Tis (DCIS)', '']",,Diagnosis +Cog Neuroblastoma Risk Group,Cog Neuroblastoma Risk Group,CogNeuroblastomaRiskGroup,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,False,,"['Low Risk', 'High Risk', 'Not Reported', 'Intermediate Risk', 'unknown', '']",,Diagnosis +Gleason Grade Group,Gleason Grade Group,GleasonGradeGroup,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Group 2', 'Group 5', 'Group 4', 'Group 3', 'Group 1', '']",,Diagnosis +Lymph Nodes Tested,Lymph Nodes Tested,LymphNodesTested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,False,,,,Diagnosis +Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,Diagnosis +Vascular Invasion Present,Vascular Invasion Present,VascularInvasionPresent,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,False,,"['Not Reported', 'Not Allowed To Collect', 'no', 'Yes - Vascular Invasion Present', 'unknown', '']",,Diagnosis +Percent Tumor Invasion,Percent Tumor Invasion,PercentTumorInvasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,False,,,,Diagnosis +Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,Diagnosis +First Symptom Prior to Diagnosis,First Symptom Prior to Diagnosis,FirstSymptomPriortoDiagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,False,,"['Visual Changes', 'Not Reported', 'Sensory Changes', 'Motor or Movement Changes', 'Headaches', 'Seizures', 'Altered Mental Status', 'unknown', '']",,Diagnosis +Tumor Depth,Tumor Depth,TumorDepth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",False,,,,Diagnosis +ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['Not Reported', 'III', 'II', 'unknown', 'I', '']",,Diagnosis +Mitotic Count,Mitotic Count,MitoticCount,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",False,,,,Diagnosis +Gleason Grade Tertiary,Gleason Grade Tertiary,GleasonGradeTertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,False,,"['Pattern 4', 'Pattern 5', '']",,Diagnosis +Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,,"['GB', 'G1', 'Intermediate Grade', 'Not Reported', 'GX', 'G4', 'G2', 'High Grade', 'unknown', 'G3', 'Not Applicable', 'Low Grade', '']",,Diagnosis +Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Laparoscopy', 'Biopsy', 'Not Reported', 'Physical Exam', 'Thoracentesis', 'Core Biopsy', 'Debulking', 'Diagnostic Imaging', 'Laparotomy', 'Ultrasound Guided Biopsy', 'Excisional Biopsy', 'Blood Draw', 'Pathologic Review', 'Dilation and Curettage Procedure', 'Autopsy', 'Surgical Resection', 'unknown', 'Incisional Biopsy', 'Other', 'Pap Smear', 'Cystoscopy', 'Fine Needle Aspiration', 'Enucleation', 'Cytology', 'Bone Marrow Aspirate', '']",,Diagnosis Gross Tumor Weight,Gross Tumor Weight,GrossTumorWeight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",False,,,,Diagnosis -Ovarian Surface Involvement,Ovarian Surface Involvement,OvarianSurfaceInvolvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,False,,"['Not Reported', 'Indeterminate', 'unknown', 'Present', 'Absent', '']",,Diagnosis +Prior Treatment,Prior Treatment,PriorTreatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,False,,"['Not Reported', 'Not Allowed To Collect', 'no', 'yes', 'unknown', '']",,Diagnosis +Micropapillary Features,Micropapillary Features,MicropapillaryFeatures,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,False,,"['unknown', 'Present', 'Absent', 'Not Reported', '']",,Diagnosis +Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Absent', 'Not Reported', 'unknown', 'Present', 'Indeterminate', '']",,Diagnosis Breslow Thickness,Breslow Thickness,BreslowThickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.",False,,,,Diagnosis -Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Not Reported', 'Unilateral', 'Bilateral', 'unknown', 'Right', 'Midline', 'Left', '']",,Diagnosis -Gleason Grade Tertiary,Gleason Grade Tertiary,GleasonGradeTertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,False,,"['Pattern 5', 'Pattern 4', '']",,Diagnosis +Lymphatic Invasion Present,Lymphatic Invasion Present,LymphaticInvasionPresent,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement",False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Diagnosis +Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Ovarian Capsule Ruptured', 'Ovarian Capsule Fragmented', 'Not Reported', 'Ovarian Capsule Intact', 'unknown', '']",,Diagnosis +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Diagnosis +Anaplasia Present Type,Anaplasia Present Type,AnaplasiaPresentType,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.",False,,"['Focal', 'Equivocal', 'Absent', 'Not Reported', 'Sclerosis', 'Diffuse', 'unknown', 'Present', '']",,Diagnosis +Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Not Reported', 'Right', 'Bilateral', 'Unilateral', 'unknown', 'Left', 'Midline', '']",,Diagnosis +Synchronous Malignancy,Synchronous Malignancy,SynchronousMalignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.",False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Diagnosis +Classification of Tumor,Classification of Tumor,ClassificationofTumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,False,,"['Primary', 'Not Reported', 'Not Allowed To Collect', 'Metastasis', 'unknown', 'Other', 'Recurrence', '']",,Diagnosis +Mitosis Karyorrhexis Index,Mitosis Karyorrhexis Index,MitosisKaryorrhexisIndex,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,False,,"['Not Reported', 'Low', 'High', 'Intermediate', 'unknown', '']",,Diagnosis +Pregnant at Diagnosis,Pregnant at Diagnosis,PregnantatDiagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Diagnosis +Tumor Focality,Tumor Focality,TumorFocality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,False,,"['unknown', 'Unifocal', 'Multifocal', 'Not Reported', '']",,Diagnosis +Supratentorial Localization,Supratentorial Localization,SupratentorialLocalization,Text term to specify the location of the supratentorial tumor.,False,,"['Deep Gray', 'Spinal Cord', 'Not Reported', 'White Matter', 'Cerebral Cortex', 'unknown', '']",,Diagnosis +International Prognostic Index,International Prognostic Index,InternationalPrognosticIndex,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.",False,,"['High-Intermediate Risk', 'Low Risk', 'High Risk', 'Low-Intermediate Risk', '']",,Diagnosis +Anaplasia Present,Anaplasia Present,AnaplasiaPresent,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,False,,"['unknown', 'no', 'Not Reported', 'Yes - Anaplasia Present', '']",,Diagnosis +IRS Stage,IRS Stage,IRSStage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['3', 'Not Reported', '4', '2', '1', 'unknown', '']",,Diagnosis +Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Parotid', 'Not Reported', 'Supraclavicular', 'Retroperitoneal', 'Cervical', 'Iliac-external', 'Submandibular', 'Epitrochlear', 'Femoral', 'NOS', 'Mediastinal', 'Occipital', 'unknown', 'None', 'Splenic', 'Paraaortic', 'Hilar', 'Iliac', 'Axillary', 'Iliac-common', 'Mesenteric', 'Popliteal', 'Inguinal', '']",,Diagnosis +Primary Gleason Grade,Primary Gleason Grade,PrimaryGleasonGrade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 4', 'Pattern 5', 'Pattern 1', 'Pattern 3', 'Pattern 2', '']",,Diagnosis +Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Extramural', 'No Vascular Invasion', 'Not Reported', 'Macro', 'Micro', 'unknown', 'Intramural', '']",,Diagnosis +AJCC Pathologic Stage,AJCC Pathologic Stage,AJCCPathologicStage,"The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.",False,,"['Stage I', 'Stage IIIC', 'Not Reported', 'Stage IIA2', 'Stage Tis', 'Stage 0a', 'Stage IA1', 'Stage IB1', 'Stage IA', 'Stage 0is', 'Stage IIIC2', 'Stage IC', 'Stage IIA', 'Stage IIB', 'Stage III', 'Stage 0', 'Stage IIIB', 'Stage IVC', 'Stage IIC1', 'unknown', 'Stage IS', 'Stage IB2', 'Stage IIIC1', 'Stage IVB', 'Stage II', 'Stage IIIA', 'Stage IB', 'Stage X', 'Stage IVA', 'Stage IV', 'Stage IIA1', 'Stage IIC', 'Stage IA2', '']",,Diagnosis +AJCC Clinical T,AJCC Clinical T,AJCCClinicalT,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['T2a1', 'T1b1', 'Not Reported', 'Tis (DCIS)', 'T0', ""Tis (Paget's)"", 'T1b', 'Tis (LCIS)', 'T1b2', 'T2c', 'T3d', 'T4e', 'T2d', 'T2b', 'T1c', 'Ta', 'T4d', 'T1', 'T4a', 'unknown', 'T3a', 'T1a2', 'T2a', 'T3c', 'TX', 'T1a', 'T3b', 'T2a2', 'T4', 'T1mi', 'T4c', 'Tis', 'T4b', 'T2', 'T1a1', 'T3', '']",,Diagnosis +INSS Stage,INSS Stage,INSSStage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).",False,,"['Not Reported', 'Stage 2A', 'Stage 2B', 'Stage 4S', 'Stage 1', 'unknown', 'Stage 4', 'Stage 3', '']",,Diagnosis +WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['G1', 'Not Reported', 'GX', 'G2', 'unknown', 'G3', '']",,Diagnosis +Secondary Gleason Grade,Secondary Gleason Grade,SecondaryGleasonGrade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 4', 'Pattern 5', 'Pattern 1', 'Pattern 3', 'Pattern 2', '']",,Diagnosis +Year of Diagnosis,Year of Diagnosis,YearofDiagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,False,,,,Diagnosis +Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['Not Determined', 'Not Reported', 'Non-WNT/non-SHH Activated', 'WNT-Activated', 'unknown', 'SHH-Activated', '']",,Diagnosis +AJCC Clinical Stage,AJCC Clinical Stage,AJCCClinicalStage,"Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.",False,,"['Stage I', 'Stage IIIC', 'Not Reported', 'Stage IIA2', 'Stage Tis', 'Stage 0a', 'Stage IA1', 'Stage IB1', 'Stage IA', 'Stage 0is', 'Stage IIIC2', 'Stage IC', 'Stage IIA', 'Stage IIB', 'Stage III', 'Stage 0', 'Stage IIIB', 'Stage IVC', 'Stage IIC1', 'unknown', 'Stage IS', 'Stage IB2', 'Stage IIIC1', 'Stage IVB', 'Stage II', 'Stage IIIA', 'Stage IB', 'Stage X', 'Stage IVA', 'Stage IV', 'Stage IIA1', 'Stage IIC', 'Stage IA2', '']",,Diagnosis +Metastasis at Diagnosis Site,Metastasis at Diagnosis Site,MetastasisatDiagnosisSite,Text term to identify an anatomic site in which metastatic disease involvement is found.,False,,"['Groin', 'Soft Tissue', 'Not Reported', 'Peritoneum', 'Bone Marrow', 'Lymph Node NOS', 'Kidney', 'Adrenal Gland', 'Omentum', 'Abdomen', 'Pelvis', 'Scalp', 'Lymph Node', 'Skin', 'Distant Nodes', 'Spinal Cord', 'Pleura', 'Liver', 'Central Nervous System', 'unknown', 'Brain', 'Ascites', 'Axillary', 'Bone', 'Ovary', 'Cerebrospinal Fluid', 'Lung', 'Peritoneal Cavity', 'Mediastinum', 'Colon', 'Small Intestine', 'Distant Organ', 'Inguinal', '']",,Diagnosis +AJCC Pathologic M,AJCC Pathologic M,AJCCPathologicM,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).",False,,"['Not Reported', 'M0', 'M1a', 'M1c', 'MX', 'M1', 'cM0 (i+)', 'unknown', 'M1b', '']",,Diagnosis +INRG Stage,INRG Stage,INRGStage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).",False,,"['Not Reported', 'Ms', 'M', 'unknown', 'L2', 'L1', '']",,Diagnosis +AJCC Staging System Edition,AJCC Staging System Edition,AJCCStagingSystemEdition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.",False,,"['3rd', '4th', 'Not Reported', '7th', '5th', '6th', '8th', 'unknown', '2nd', '1st', '']",,Diagnosis +Tumor Confined to Organ of Origin,Tumor Confined to Organ of Origin,TumorConfinedtoOrganofOrigin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Diagnosis Greatest Tumor Dimension,Greatest Tumor Dimension,GreatestTumorDimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,False,,,,Diagnosis -Tumor Depth,Tumor Depth,TumorDepth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",False,,,,Diagnosis -Cog Neuroblastoma Risk Group,Cog Neuroblastoma Risk Group,CogNeuroblastomaRiskGroup,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,False,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'unknown', 'Low Risk', '']",,Diagnosis -Vascular Invasion Present,Vascular Invasion Present,VascularInvasionPresent,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,False,,"['Not Reported', 'no', 'Not Allowed To Collect', 'Yes - Vascular Invasion Present', 'unknown', '']",,Diagnosis -Cog Rhabdomyosarcoma Risk Group,Cog Rhabdomyosarcoma Risk Group,CogRhabdomyosarcomaRiskGroup,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).",False,,"['Not Reported', 'High Risk', 'Intermediate Risk', 'unknown', 'Low Risk', '']",,Diagnosis -IGCCCG Stage,IGCCCG Stage,IGCCCGStage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.",False,,"['Not Reported', 'Poor Prognosis', 'Intermediate Prognosis', 'unknown', 'Good Prognosis', '']",,Diagnosis -Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Not Reported', 'Iliac', 'unknown', 'Paraaortic', 'Iliac-external', 'Supraclavicular', 'Occipital', 'Hilar', 'Parotid', 'NOS', 'Retroperitoneal', 'Femoral', 'Submandibular', 'Inguinal', 'Popliteal', 'Splenic', 'Cervical', 'Epitrochlear', 'Axillary', 'None', 'Mediastinal', 'Iliac-common', 'Mesenteric', '']",,Diagnosis -Micropapillary Features,Micropapillary Features,MicropapillaryFeatures,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,False,,"['Not Reported', 'unknown', 'Present', 'Absent', '']",,Diagnosis +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Diagnosis +Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,Diagnosis +IGCCCG Stage,IGCCCG Stage,IGCCCGStage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.",False,,"['Not Reported', 'Poor Prognosis', 'Good Prognosis', 'Intermediate Prognosis', 'unknown', '']",,Diagnosis +Non Nodal Tumor Deposits,Non Nodal Tumor Deposits,NonNodalTumorDeposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Diagnosis +Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis +AJCC Clinical N,AJCC Clinical N,AJCCClinicalN,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['N3', 'Not Reported', 'N4', 'N0 (i+)', 'N2', 'N3b', 'N0 (i-)', 'N1bIII', 'N0', 'N1c', 'unknown', 'N2b', 'N3c', 'N2a', 'NX', 'N0 (mol-)', 'N1', 'N1b', 'N2c', 'N1bI', 'N1mi', 'N0 (mol+)', 'N1bIV', 'N1a', 'N1bII', 'N3a', '']",,Diagnosis +Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Yes - Progression or Recurrence', 'unknown', 'no', 'Not Reported']",,Diagnosis +IRS Group,IRS Group,IRSGroup,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Group IIIb', 'Not Reported', 'Group II', 'Group III', 'Group Ia', 'Group Ib', 'Group IIc', 'Group IIa', 'unknown', 'Group I', 'Group IV', 'Group IIIa', '']",,Diagnosis Morphology,Morphology,Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",True,,,,Diagnosis -Supratentorial Localization,Supratentorial Localization,SupratentorialLocalization,Text term to specify the location of the supratentorial tumor.,False,,"['Not Reported', 'White Matter', 'Deep Gray', 'unknown', 'Spinal Cord', 'Cerebral Cortex', '']",,Diagnosis -Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Not Reported', 'Surgical Resection', 'Excisional Biopsy', 'unknown', 'Autopsy', 'Incisional Biopsy', 'Thoracentesis', 'Fine Needle Aspiration', 'Cytology', 'Ultrasound Guided Biopsy', 'Laparotomy', 'Bone Marrow Aspirate', 'Other', 'Diagnostic Imaging', 'Pap Smear', 'Laparoscopy', 'Debulking', 'Blood Draw', 'Biopsy', 'Physical Exam', 'Core Biopsy', 'Cystoscopy', 'Pathologic Review', 'Enucleation', 'Dilation and Curettage Procedure', '']",,Diagnosis -Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['RP-Response', 'DU-Disease Unchanged', 'CPD-Clinical Progression', 'sCR-Stringent Complete Response', 'PSR-Pseudoresponse', 'Non-CR/Non-PD-Non-CR/Non-PD', 'IPD-Immunoprogression', 'IMR-Immunoresponse', 'RPD-Radiographic Progressive Disease', 'MR-Minimal/Marginal Response', 'SPD-Surgical Progression', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'CRU-Complete Response Unconfirmed', 'RD-Responsive Disease', 'PR-Partial Response', 'MX-Mixed Response', 'SD-Stable Disease', 'PPD-Pseudoprogression', 'PB-Palliative Benefit', 'NPB-No Palliative Benefit', 'CR-Complete Response', 'AJ-Adjuvant Therapy', 'NR-No Response', 'PD-Progressive Disease', 'TE-Too Early', '']",,Diagnosis -AJCC Clinical N,AJCC Clinical N,AJCCClinicalN,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['Not Reported', 'N1bII', 'N0', 'N3c', 'N0 (mol+)', 'N2', 'unknown', 'N1bIV', 'N0 (i+)', 'N2a', 'N0 (i-)', 'N3', 'N2b', 'N1b', 'NX', 'N4', 'N1c', 'N2c', 'N3b', 'N1bI', 'N1', 'N3a', 'N1mi', 'N1bIII', 'N1a', 'N0 (mol-)', '']",,Diagnosis -Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Not Reported', 'Ovarian Capsule Fragmented', 'Ovarian Capsule Intact', 'Ovarian Capsule Ruptured', 'unknown', '']",,Diagnosis -ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['Not Reported', 'I', 'II', 'unknown', 'III', '']",,Diagnosis -Peritoneal Fluid Cytological Status,Peritoneal Fluid Cytological Status,PeritonealFluidCytologicalStatus,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,False,,"['Not Reported', 'Non-Malignant', 'Malignant', 'Unsatisfactory', 'unknown', 'Atypical', '']",,Diagnosis -Prior Treatment,Prior Treatment,PriorTreatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,False,,"['Not Reported', 'no', 'yes', 'Not Allowed To Collect', 'unknown', '']",,Diagnosis -Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body']",,Diagnosis -Pregnant at Diagnosis,Pregnant at Diagnosis,PregnantatDiagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Diagnosis +INPC Histologic Group,INPC Histologic Group,INPCHistologicGroup,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.",False,,"['unknown', 'Unfavorable', 'Not Reported', 'Favorable', '']",,Diagnosis Gleason Patterns Percent,Gleason Patterns Percent,GleasonPatternsPercent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.",False,,,,Diagnosis -Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'unknown', 'no']",,Diagnosis +Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Reported', 'Not Allowed To Collect', 'no', 'yes', 'unknown', '']",,Diagnosis +WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Not Reported', 'Grade I', 'Grade II', 'Grade III', 'Grade IV', 'Grade Not Assigned', 'unknown', '']",,Diagnosis Lymph Nodes Positive,Lymph Nodes Positive,LymphNodesPositive,The number of lymph nodes involved with disease as determined by pathologic examination.,False,,,,Diagnosis -INRG Stage,INRG Stage,INRGStage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).",False,,"['Not Reported', 'L1', 'M', 'unknown', 'L2', 'Ms', '']",,Diagnosis -AJCC Clinical M,AJCC Clinical M,AJCCClinicalM,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['Not Reported', 'MX', 'M1a', 'M0', 'M1b', 'cM0 (i+)', 'unknown', 'M1c', 'M1', '']",,Diagnosis -AJCC Pathologic T,AJCC Pathologic T,AJCCPathologicT,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).",False,,"['Not Reported', 'T1b1', 'Tis (LCIS)', 'T4a', 'T4b', 'unknown', 'T2a', 'T4e', 'T3b', 'T1a', 'T2a2', 'T1mi', 'T4d', 'Tis', 'T4c', 'T3c', 'T4', 'Ta', 'T0', 'T1a1', 'T2a1', 'T1b', 'T1a2', 'T1', 'T2d', 'T3d', 'T2c', 'T1b2', 'T1c', 'T3', 'T2b', 'TX', ""Tis (Paget's)"", 'T2', 'T3a', 'Tis (DCIS)', '']",,Diagnosis -Lymph Nodes Tested,Lymph Nodes Tested,LymphNodesTested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,False,,,,Diagnosis -Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['Not Reported', 'R0', 'R1', 'unknown', 'RX', 'R2', '']",,Diagnosis -Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,Diagnosis -Mitosis Karyorrhexis Index,Mitosis Karyorrhexis Index,MitosisKaryorrhexisIndex,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,False,,"['Not Reported', 'Low', 'Intermediate', 'unknown', 'High', '']",,Diagnosis -WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Not Reported', 'Grade III', 'Grade IV', 'Grade II', 'Grade I', 'Grade Not Assigned', 'unknown', '']",,Diagnosis -WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['Not Reported', 'G2', 'G3', 'G1', 'GX', 'unknown', '']",,Diagnosis -Margins Involved Site,Margins Involved Site,MarginsInvolvedSite,The text term used to describe the anatomic sites that were involved in the survival margins.,False,,"['Ureter', 'Renal Capsule', 'Perinephric Fat', 'Gerota Fascia', 'Parenchyma', 'Renal', 'Renal Sinus', 'Renal Vein', '']",,Diagnosis -Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,Diagnosis -Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['Not Reported', 'Regional Metastasis', 'No Metastasis', 'Distant Metastasis', 'Metastasis NOS', 'unknown', '']",,Diagnosis -Tumor Confined to Organ of Origin,Tumor Confined to Organ of Origin,TumorConfinedtoOrganofOrigin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Diagnosis -Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Reported', 'no', 'yes', 'Not Allowed To Collect', 'unknown', '']",,Diagnosis -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body']",,Diagnosis -INSS Stage,INSS Stage,INSSStage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).",False,,"['Not Reported', 'Stage 4', 'Stage 3', 'Stage 1', 'Stage 2A', 'unknown', 'Stage 2B', 'Stage 4S', '']",,Diagnosis -Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['Not Reported', 'WNT-Activated', 'Not Determined', 'Non-WNT/non-SHH Activated', 'SHH-Activated', 'unknown', '']",,Diagnosis -Year of Diagnosis,Year of Diagnosis,YearofDiagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,False,,,,Diagnosis -Precancerous Condition Type,Precancerous Condition Type,PrecancerousConditionType,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,False,,"['Invasive melanoma', 'Not Applicable', 'No diagnosis possible', 'Invasive melanoma - superficial spreading', 'Severe dysplasia', 'Invasive melanoma - lentigo maligna', 'Atypical melanocytic proliferation', 'Squamous metaplasia - immature', 'Adenocarcinoma in situ - mucinous', 'Mild dysplasia', 'Atypical adenomatous hyperplasia', 'Scar - no residual melanoma', 'Squamous metaplasia - mature', 'Melanocytic hyperplasia', 'Invasive melanoma - acral lentiginous', 'Invasive melanoma - desmoplastic', 'Other', 'Acral-lentiginous', 'Reserve cell hyperplasia', 'Superficial spreading', 'Benign tumor NOS', 'Invasive melanoma - nevoid', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Atypical Adenomatous Lung Hyperplasia', 'Normal', 'Normal WDA', 'Melanoma in situ not otherwise classified', 'Melanoma in situ', 'Prostatic Intraepithelial Neoplasia', 'Hamartoma', 'Neuroendocrine cell hyperplasia', 'Persistent melanoma in situ', 'Adenocarcinoma in situ - non mucinous', 'Lentigo maligna type', 'Melanoma in situ arising in a giant congenital nevus', 'Squamous carcinoma in situ', 'Carcinoma NOS', 'Pancreatic Intraepithelial Neoplasia', 'Ductal Carcinoma In Situ', 'Invasive melanoma - nodular type', 'Moderate dysplasia', '']",,Diagnosis -First Symptom Prior to Diagnosis,First Symptom Prior to Diagnosis,FirstSymptomPriortoDiagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,False,,"['Not Reported', 'Headaches', 'Motor or Movement Changes', 'Visual Changes', 'Sensory Changes', 'unknown', 'Altered Mental Status', 'Seizures', '']",,Diagnosis -Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Not Reported', 'No Vascular Invasion', 'Micro', 'Macro', 'Intramural', 'unknown', 'Extramural', '']",,Diagnosis -Percent Tumor Invasion,Percent Tumor Invasion,PercentTumorInvasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,False,,,,Diagnosis -Anaplasia Present Type,Anaplasia Present Type,AnaplasiaPresentType,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.",False,,"['Not Reported', 'Diffuse', 'Focal', 'Sclerosis', 'unknown', 'Present', 'Absent', 'Equivocal', '']",,Diagnosis -AJCC Pathologic Stage,AJCC Pathologic Stage,AJCCPathologicStage,"The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.",False,,"['Not Reported', 'Stage IB', 'Stage 0', 'Stage IB2', 'Stage 0is', 'Stage III', 'Stage IIA', 'Stage II', 'Stage IS', 'unknown', 'Stage IIA1', 'Stage Tis', 'Stage IIIA', 'Stage IA1', 'Stage IVA', 'Stage IIC', 'Stage IVB', 'Stage IIIC', 'Stage IV', 'Stage IB1', 'Stage IIIB', 'Stage I', 'Stage IA2', 'Stage X', 'Stage IC', 'Stage IIIC2', 'Stage IIC1', 'Stage IIB', 'Stage 0a', 'Stage IVC', 'Stage IA', 'Stage IIIC1', 'Stage IIA2', '']",,Diagnosis -AJCC Staging System Edition,AJCC Staging System Edition,AJCCStagingSystemEdition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.",False,,"['Not Reported', '7th', '4th', '6th', '8th', '1st', '3rd', '2nd', 'unknown', '5th', '']",,Diagnosis -Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis -INPC Grade,INPC Grade,INPCGrade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).",False,,"['Not Reported', 'Undifferentiated', 'Differentiating', 'unknown', 'Poorly Differentiated', '']",,Diagnosis -Synchronous Malignancy,Synchronous Malignancy,SynchronousMalignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.",False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Diagnosis -IRS Group,IRS Group,IRSGroup,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Not Reported', 'Group III', 'Group IIIa', 'Group IIIb', 'Group II', 'Group Ia', 'Group IIa', 'Group IIc', 'Group Ib', 'unknown', 'Group I', 'Group IV', '']",,Diagnosis -Secondary Gleason Grade,Secondary Gleason Grade,SecondaryGleasonGrade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 5', 'Pattern 2', 'Pattern 1', 'Pattern 3', 'Pattern 4', '']",,Diagnosis -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Diagnosis -Anaplasia Present,Anaplasia Present,AnaplasiaPresent,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,False,,"['Not Reported', 'Yes - Anaplasia Present', 'unknown', 'no', '']",,Diagnosis -Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis -Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Retina', 'Axillary tail of breast', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Parametrium', 'Nasopharynx NOS', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis +Ovarian Surface Involvement,Ovarian Surface Involvement,OvarianSurfaceInvolvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,False,,"['Absent', 'Not Reported', 'unknown', 'Present', 'Indeterminate', '']",,Diagnosis +Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['unknown tumor status', 'Loco-regional recurrence/progression', 'Not Reported', 'Distant met recurrence/progression', 'Tumor free', 'Not Allowed To Collect', 'Biochemical evidence of disease without structural correlate', 'Not Applicable', 'With tumor']",,Diagnosis +Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['Metastasis NOS', 'Not Reported', 'Regional Metastasis', 'unknown', 'Distant Metastasis', 'No Metastasis', '']",,Diagnosis +Perineural Invasion Present,Perineural Invasion Present,PerineuralInvasionPresent,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Diagnosis +Cog Rhabdomyosarcoma Risk Group,Cog Rhabdomyosarcoma Risk Group,CogRhabdomyosarcomaRiskGroup,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).",False,,"['Low Risk', 'High Risk', 'Not Reported', 'Intermediate Risk', 'unknown', '']",,Diagnosis +Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Ventricle NOS', 'Adrenal gland NOS', 'Upper lobe lung', 'Choroid', 'Pleura NOS', 'External lip NOS', 'Overlapping lesion of biliary tract', 'Waldeyer ring', 'Commissure of lip', 'Overlapping lesion of pancreas', 'Vertebral column', 'Overlapping lesion of lung', 'Nervous system NOS', 'Other ill-defined sites', 'Overlapping lesion of eye and adnexa', 'Duodenum', 'Temporal lobe', 'Lymph nodes of multiple regions', 'Head face or neck NOS', 'unknown primary site', 'Extrahepatic bile duct', 'Bone marrow', 'Meninges NOS', 'Bladder neck', 'Head of pancreas', 'Overlapping lesion of vulva', 'Eyelid', 'Brain stem', 'Tonsillar pillar', 'Anterior surface of epiglottis', 'Female genital tract NOS', 'Ascending colon', 'Supraglottis', 'Overlapping lesion of floor of mouth', 'Upper limb NOS', 'Lacrimal gland', 'Tongue NOS', 'Corpus uteri', 'Ileum', 'Mucosa of lower lip', 'Submandibular gland', 'Thymus', 'Descended testis', 'Overlapping lesion of esophagus', 'Spleen', 'Scrotum NOS', 'Posterior wall of nasopharynx', 'Overlapping lesion of palate', 'Orbit NOS', 'Vagina NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Lower lobe lung', 'Pituitary gland', 'Round ligament', 'Nasal cavity', 'Overlapping lesion of skin', 'Male genital organs NOS', 'Bone of limb NOS', 'Overlapping lesion of hypopharynx', 'Sublingual gland', 'Cerebrum', 'Ventral surface of tongue NOS', 'Intestinal tract NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Mandible', 'Pylorus', 'Pancreatic duct', 'External upper lip', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Abdomen NOS', 'Short bones of lower limb and associated joints', 'Overlapping lesion of nasopharynx', 'Mouth NOS', 'Ureteric orifice', 'Colon NOS', 'Cheek mucosa', 'Pancreas NOS', 'Lower-inner quadrant of breast', 'Retina', 'Renal pelvis', 'Posterior wall of bladder', 'Lymph nodes of inguinal region or leg', 'Penis NOS', 'Clitoris', 'Superior wall of nasopharynx', 'Ovary', 'Tail of pancreas', 'Cloacogenic zone', 'Isthmus uteri', 'Retromolar area', 'Undescended testis', 'Eye NOS', 'skin NOS', 'Lesser curvature of stomach NOS', 'Lower-outer quadrant of breast', 'Mucosa of upper lip', 'Skin of lip NOS', 'Gastrointestinal tract NOS', 'Spinal meninges', 'Anterior mediastinum', 'Paraspinal', 'Overlapping lesion of retroperitoneum and peritoneum', 'Floor of mouth NOS', 'unknown', 'Urachus', 'External ear', 'Lymph nodes of head face and neck', 'Specified parts of peritoneum', 'Optic nerve', 'Other specified parts of pancreas', 'Posterior mediastinum', 'Tonsillar fossa', 'Overlapping lesion of tongue', 'Mucosa of lip NOS', 'Kidney NOS', 'Upper-inner quadrant of breast', 'Mediastinum NOS', 'Overlapping lesion of heart mediastinum and pleura', 'Axillary tail of breast', 'Overlapping lesion of corpus uteri', 'Gastric antrum', 'Body of stomach', 'Overlapping lesion of tonsil', 'Uterine adnexa', 'Lateral floor of mouth', 'Labium minus', 'Middle lobe lung', 'Medulla of adrenal gland', 'Lower limb NOS', 'Hard palate', 'Body of penis', 'Overlapping lesion of digestive system', 'Overlapping lesion of other and unspecified parts of mouth', 'Lower gum', 'Overlapping lesion of rectum anus and anal canal', 'Hypopharynx NOS', 'Overlapping lesion of female genital organs', 'Skin of other and unspecified parts of face', 'Glans penis', 'Accessory sinus NOS', 'Overlapping lesion of endocrine glands and related structures', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Bones of skull and face and associated joints', 'Vestibule of mouth', 'Border of tongue', 'Parametrium', 'Ciliary body', 'Soft palate NOS', 'Overlapping lesion of cervix uteri', 'Gum NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Skin of trunk', 'Cranial nerve NOS', 'Ampulla of Vater', 'Palate NOS', 'Pineal gland', 'Lymph nodes of axilla or arm', 'Base of tongue NOS', 'Middle ear', 'Breast NOS', 'Parietal lobe', 'Frontal sinus', 'Overlapping lesion of larynx', 'Retroperitoneum', 'Paraurethral gland', 'Overlapping lesion of urinary organs', 'Connective subcutaneous and other soft tissues NOS', 'Lateral wall of oropharynx', 'Main bronchus', 'Liver', 'Lip NOS', 'Biliary tract NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Anterior 2/3 of tongue NOS', 'Skin of scalp and neck', 'Short bones of upper limb and associated joints', 'Jejunum', 'Overlapping lesion of ill-defined sites', 'Sphenoid sinus', 'Urethra', 'Trachea', 'Hematopoietic system NOS', 'Fallopian tube', 'Cerebellum NOS', 'Carotid body', 'Other specified parts of male genital organs', 'Connective subcutaneous and other soft tissues of abdomen', 'skin of upper limb and shoulder', 'Not Reported', 'Lateral wall of nasopharynx', 'Endocrine gland NOS', 'Heart', 'Dorsal surface of tongue NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Central portion of breast', 'Endometrium', 'Appendix', 'Cerebral meninges', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peritoneum NOS', 'Craniopharyngeal duct', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Ethmoid sinus', 'Exocervix', 'Pharynx NOS', 'Anal canal', 'Aortic body and other paraganglia', 'Labium majus', 'Lingual tonsil', 'Ill-defined sites within respiratory system', 'Lower third of esophagus', 'Overlapping lesion of bones joints and articular cartilage', 'Rectosigmoid junction', 'Placenta', 'Bone NOS', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lateral wall of bladder', 'Cecum', 'Parathyroid gland', 'Cortex of adrenal gland', 'Upper-outer quadrant of breast', 'Vulva NOS', 'Prepuce', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Greater curvature of stomach NOS', 'Autonomic nervous system NOS', 'Nasopharynx NOS', 'Anus NOS', 'Overlapping lesion of male genital organs', 'Descending colon', 'Long bones of lower limb and associated joints', 'Urinary system NOS', 'Cardia NOS', 'Lung NOS', 'Frontal lobe', 'Thoracic esophagus', 'Overlapping lesion of lip', 'Cervical esophagus', 'Uterus NOS', 'Major salivary gland NOS', 'Maxillary sinus', 'Intrathoracic lymph nodes', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Posterior wall of oropharynx', 'Epididymis', 'Spermatic cord', 'Pelvic lymph nodes', 'Dome of bladder', 'Middle third of esophagus', 'Pelvis NOS', 'Tonsil NOS', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cervix uteri', 'Nipple', 'Conjunctiva', 'Olfactory nerve', 'Fundus uteri', 'Anterior floor of mouth', 'Oropharynx NOS', 'Meckel diverticulum', 'Esophagus NOS', 'Intra-abdominal lymph nodes', 'Lymph node NOS', 'Small intestine NOS', 'Brain NOS', 'Overlapping lesion of major salivary glands', 'Vallecula', 'Upper gum', 'Overlapping lesion of small intestine', 'Overlapping lesion of breast', 'Anterior wall of nasopharynx', 'Cauda equina', 'Myometrium', 'skin of lower limb and hip', 'Overlapping lesion of accessory sinuses', 'Hypopharyngeal aspect of aryepiglottic fold', 'Hepatic flexure of colon', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Overlapping lesion of stomach', 'Postcricoid region', 'Uvula', 'Splenic flexure of colon', 'Overlapping lesion of bladder', 'Glottis', 'Pyriform sinus', 'Thorax NOS', 'Trigone of bladder', 'Fundus of stomach', 'Abdominal esophagus', 'Posterior wall of hypopharynx', 'Overlapping lesion of penis', 'Connective subcutaneous and other soft tissues of thorax', 'Blood', 'Body of pancreas', 'Bladder NOS', 'Occipital lobe', 'Intrahepatic bile duct', 'Spinal cord', 'Laryngeal cartilage', 'Transverse colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sigmoid colon', 'Cornea NOS', 'Prostate gland', 'Endocervix', 'Overlapping lesions of oropharynx', 'Overlapping lesion of colon', 'Upper respiratory tract NOS', 'Islets of Langerhans', 'Broad ligament', 'Parotid gland', 'Anterior wall of bladder', 'Rib sternum clavicle and associated joints', 'Long bones of upper limb scapula and associated joints', 'Gallbladder', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Upper third of esophagus', 'Other specified parts of female genital organs', 'Thyroid gland', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of pelvis', 'Reticuloendothelial system NOS', 'Acoustic nerve', 'Larynx NOS', 'Stomach NOS', 'Testis NOS', 'External lower lip', 'Subglottis', 'Ureter', 'Overlapping lesion of brain', 'Rectum NOS']",,Diagnosis +INPC Grade,INPC Grade,INPCGrade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).",False,,"['Not Reported', 'Differentiating', 'Undifferentiated', 'unknown', 'Poorly Differentiated', '']",,Diagnosis +Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Intravascular B-cell lymphoma', 'Tubular androblastoma with lipid storage', 'Myeloma NOS', 'Papilloma of bladder', 'Rhabdomyosarcoma NOS', 'Lymphoma NOS', 'Mixed small cell carcinoma', 'Capillary lymphangioma', 'Splenic marginal zone lymphoma NOS', 'Tumor cells benign', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Precancerous melanosis NOS', 'Neuroblastoma NOS', 'Intraductal carcinoma and lobular carcinoma in situ', 'Hepatoid carcinoma', 'Tumor benign', 'Mixed pineal tumor', 'Basophil adenoma', 'Malignant melanoma in junctional nevus', 'Combined large cell neuroendocrine carcinoma', 'Nephroblastoma NOS', 'Non-Hodgkin lymphoma NOS', 'Secretory carcinoma of breast', 'Malignant lymphoma nodular NOS', 'Cancer', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Diffuse astrocytoma IDH-mutant', 'Papillomatosis glandular', 'Malignant lymphoma NOS', 'Paget disease and intraductal carcinoma of breast', 'Intraductal carcinoma noninfiltrating NOS', 'Small cell sarcoma', 'Basal cell epithelioma', 'Tumor cells malignant', 'Adenocarcinoid tumor', 'Carcinoma undifferentiated NOS', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Tubulocystic renal cell carcinoma', 'Burkitt lymphoma NOS (Includes all variants)', 'Epidermoid carcinoma in situ NOS', 'Carcinoma in adenomatous polyp', 'Malignant lymphoma large cell NOS', 'Central neurocytoma', 'Bronchio-alveolar carcinoma mucinous', 'Paget disease and infiltrating duct carcinoma of breast', 'Eosinophilic leukemia', 'Adenocarcinoma endocervical type', 'Spindle cell melanoma NOS', 'Osteoblastoma NOS', 'Lobular carcinoma in situ NOS', 'Intraductal tubular-papillary neoplasm high grade', 'Tubular carcinoid', 'Acute myeloid leukemia MLL', 'Pancreatoblastoma', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Pleomorphic lipoma', 'Malignant lymphoma lymphocytic NOS', 'Chronic myelogenous leukemia BCR-ABL positive', 'Melanotic neurofibroma', 'Bile duct cystadenocarcinoma', 'Malignant melanoma in precancerous melanosis', 'Meningeal melanocytoma', 'Dysplastic nevus', 'Pituitary adenoma NOS', 'Duct cell carcinoma', 'Papillary epidermoid carcinoma', 'Eosinophilic granuloma', 'Preleukemia', 'B cell lymphoma NOS', 'Malignant lymphoma mixed cell type nodular', 'Intradermal nevus', 'Adenocarcinoma intestinal type', 'Squamous cell carcinoma adenoid', 'Acute lymphoblastic leukemia precursor cell type', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Esophageal intraepithelial neoplasia high grade', 'Melanoma NOS', 'Adult rhabdomyoma', 'Hodgkin disease NOS', 'Small cell neuroendocrine carcinoma', 'Intraductal and lobular carcinoma', 'Osteosarcoma NOS', 'Basal cell carcinoma NOS', 'Neurofibroma NOS', 'Melanocytoma NOS', 'Hodgkin granuloma', 'Mixed tumor malignant NOS', 'Hepatocholangiocarcinoma', 'Multiple myeloma', 'Papillary squamous cell carcinoma', 'Papillary adenocarcinoma NOS', 'Chronic monocytic leukemia', 'Undifferentiated spindle cell sarcoma', 'Hodgkin lymphoma mixed cellularity NOS', 'Intraductal carcinoma solid type', 'Undifferentiated high-grade pleomorphic sarcoma', 'Splenic lymphoma with villous lymphocytes', 'Intracystic papilloma', 'Serous cystadenocarcinoma NOS', 'Lymphocytic leukemia NOS', 'Mixed tumor NOS', 'Tubulopapillary adenocarcinoma', 'Papillary serous cystadenocarcinoma', 'Basal cell adenoma', 'Carcinoma intestinal type', 'Skin appendage carcinoma', 'Transitional cell carcinoma in situ', 'Chronic myeloid leukemia NOS', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Melanotic schwannoma', 'Pancreatic endocrine tumor NOS', 'Teratoma NOS', 'Capillary hemangioma', 'Sarcoma NOS', 'Adenocarcinoma diffuse type', 'Acute myelomonocytic leukemia', 'Chondrosarcoma grade 2/3', 'Renal cell carcinoma unclassified', 'Splenic marginal zone B-cell lymphoma', 'Gastrinoma NOS', 'Neoplasm secondary', 'Spindle cell carcinoma NOS', 'Basophil adenocarcinoma', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Acute basophilic leukaemia', 'Bile duct adenocarcinoma', 'Rhabdoid sarcoma', 'Carcinoma diffuse type', 'Pro-T ALL', 'Medullary adenocarcinoma', 'Intraductal micropapillary carcinoma', 'Pigmented basal cell carcinoma', 'Malignant lymphoma diffuse NOS', 'Neoplasm malignant', 'Kaposi sarcoma', 'Gastrinoma malignant', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'Bronchiolar adenocarcinoma', 'Acute leukemia Burkitt type', 'Non-small cell carcinoma', 'Rhabdosarcoma', 'Myelocytic leukemia NOS', 'Melanoma in situ', 'Malignant lymphoma small B lymphocytic NOS', 'Endometrioid adenofibroma NOS', 'Infiltrating basal cell carcinoma NOS', 'Adenocarcinoma in situ mucinous', 'Tumor NOS', 'Hodgkin sarcoma', 'Adult T-cell lymphoma', 'Pulmonary blastoma', 'Melanotic medulloblastoma', 'Undifferentiated sarcoma', 'Unclassified tumor benign', 'Acute lymphoblastic leukemia NOS', 'Interstitial cell tumor malignant', 'Mammary carcinoma in situ', 'Melanotic neuroectodermal tumor', 'Chronic granulocytic leukemia NOS', 'Interstitial cell tumor NOS', 'Therapy related myeloid neoplasm', 'Pro-B ALL', 'Intraductal carcinoma clinging', 'Malignant lymphoma mixed cell type follicular', 'Lymphoblastoma', 'Adenocarcinoma in villous adenoma', 'Bile duct carcinoma', 'unknown', 'Duct carcinoma desmoplastic type', 'Haemangioblastoma', 'Medullary carcinoma NOS', 'Neoplasm malignant uncertain whether primary or metastatic', 'Bronchial adenoma NOS', 'Unclassified tumor malignant', 'Cementoma NOS', 'Meningioma anaplastic', 'Pancreatobiliary neoplasm non-invasive', 'Intraductal papillary adenocarcinoma NOS', 'Rhabdomyoma NOS', 'Neoplasm uncertain whether benign or malignant', 'High-grade serous carcinoma', 'Teratoma malignant NOS', 'Adenocarcinoma in situ in a polyp NOS', 'Bile duct cystadenoma', 'Papillary squamous cell carcinoma in situ', 'Nonpigmented nevus', 'Undifferentiated uterine sarcoma', 'Lobular adenocarcinoma', 'Pituitary carcinoma NOS', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Cervical intraepithelial neoplasia grade III', 'Melanotic MPNST', 'Monocytic leukemia NOS', 'Neoplasm NOS', 'Glioma NOS', 'Adenocarcinoma in situ in tubular adenoma', 'Haemangiosarcoma', 'Acute myeloid leukemia minimal differentiation', 'Adult T-cell lymphoma/leukemia', 'Intraductal papillary adenocarcinoma with invasion', 'Papillotubular adenocarcinoma', 'Adenocarcinoma in situ non-mucinous', 'Carcinoma metastatic NOS', 'Ewing sarcoma', 'Carcinoma in a polyp NOS', 'Liposarcoma differentiated', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Small cell carcinoma NOS', 'Unclassified tumor uncertain whether benign or malignant', 'Malignant melanoma NOS', 'Carcinoma in situ NOS', 'Undifferentiated epithelioid sarcoma', 'Adenocarcinoma in adenomatous polyp', 'Chronic myelomonocytic leukemia NOS', 'Medullary osteosarcoma', 'Neurosarcoma', 'Adenocarcinoma in situ NOS', 'Papillary serous adenocarcinoma', 'Papillary serous cystadenoma NOS', 'Juvenile myelomonocytic leukemia', 'Duct carcinoma NOS', 'Astrocytoma NOS', 'Papillary adenoma NOS', 'Renal cell carcinoma spindle cell', 'Tumorlet benign', 'Sclerosing hemangioma', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Non-lymphocytic leukemia NOS', 'Nevus NOS', 'Acute lymphoblastic leukemia mature B-cell type', 'Tubulolobular carcinoma', 'Precursor T-cell lymphoblastic leukemia', 'Paraganglioma NOS', 'Inflammatory adenocarcinoma', 'Ductal carcinoma in situ NOS', 'Malignant melanoma in congenital melanocytic nevus', 'Malignant melanoma regressing', 'Interstitial cell tumor benign', 'Malignancy', 'Combined small cell-squamous cell carcinoma', 'Pancreatic endocrine tumor benign', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Basal cell adenocarcinoma', 'Chronic myeloproliferative disease NOS', 'T-cell lymphoma NOS', 'Bronchial-associated lymphoid tissue lymphoma', 'Mixed squamous cell and glandular papilloma', 'Sclerosing hepatic carcinoma', 'Hepatocarcinoma', 'Dermal nevus', 'Peripheral T-cell lymphoma large cell', 'Burkitt-like lymphoma', 'Renal carcinoma collecting duct type', 'Precursor B-cell lymphoblastic leukemia', 'Bronchial adenoma carcinoid', 'Pleomorphic carcinoma', 'Inflammatory carcinoma', 'Cerebellar sarcoma NOS', 'Lymphatic leukemic NOS', 'Mixed adenocarcinoma and squamous cell carcinoma', 'B lymphoblastic leukemia/lymphoma NOS', 'Ganglioglioma NOS', 'Undifferentiated leukaemia', 'Micropapillary carcinoma NOS', 'Malignant melanoma in Hutchinson melanotic freckle', 'B-ALL', 'Bronchiolo-alveolar carcinoma NOS', 'Serous surface papillary carcinoma', 'Hodgkin paragranuloma NOS', 'Adenocarcinoma in polypoid adenoma', 'Intraductal carcinoma NOS', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Papillary carcinoma in situ', 'T lymphoblastic leukemia/lymphoma', 'Acute lymphatic leukemia', 'Endometrioid carcinoma NOS', 'Papillary cystadenoma NOS', 'Papillary renal cell carcinoma', 'Bile duct adenoma', 'Pancreatobiliary-type carcinoma', 'Intraepidermal carcinoma NOS', 'Large cell carcinoma NOS', 'Lobular and ductal carcinoma', 'Endometrioid adenocarcinoma NOS', 'Paget disease extramammary', 'Osteoblastoma malignant', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Malignant lymphoma lymphocytic diffuse NOS', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Adenocarcinoma in tubular adenoma', 'Not Reported', 'Glioma malignant', 'Pancreatic endocrine tumor malignant', 'Astrocytoma low grade', 'Medulloblastoma NOS', 'Precursor cell lymphoblastic leukemia NOS', 'Chronic lymphoid leukemia', 'Bronchiolar carcinoma', 'Transitional cell carcinoma', 'Malignant lymphoma mixed cell type diffuse', 'Combined small cell-adenocarcinoma', 'Papillary adenocarcinoma follicular variant', 'Neuroepithelioma NOS', 'Renal medullary carcinoma', 'Myoepithelioma', 'Epidermoid carcinoma NOS', 'Pigmented adenoma', 'Squamous cell carcinoma NOS', 'Chronic granulocytic leukemia BCR/ABL', 'Liposarcoma well differentiated', 'Squamous cell carcinoma clear cell type', 'Melanotic progonoma', 'Chondroma NOS', 'Rodent ulcer', 'Melanoma malignant of soft parts', 'Diffuse melanocytosis', 'Chronic lymphatic leukemia', 'Chronic myelomonocytic leukemia in transformation', 'Papillary adenofibroma', 'Pleomorphic adenoma', 'Carcinoma in pleomorphic adenoma', 'Liver cell adenoma', 'Primary amyloidosis', 'Acute myeloid leukemia NOS', 'Papillary glioneuronal tumor', 'Pleomorphic lobular carcinoma', 'Paget disease of breast', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Epithelial tumor benign', 'Papillary carcinoma NOS', 'Transitional carcinoma', 'Neoplasm metastatic', 'Infiltrating duct carcinoma NOS', 'Combined small cell carcinoma', 'Endometrial sarcoma NOS', 'Adenocarcinoma pancreatobiliary type', 'Tumor malignant NOS', 'Melanotic psammomatous MPNST', 'Cervical intraepithelial neoplasia low grade', 'Undifferentiated round cell sarcoma', 'Hepatoid adenocarcinoma', 'Malignant lymphoma non-Hodgkin NOS', 'Tubulovillous adenoma NOS', 'Hodgkin lymphoma NOS', 'Mixed medullary-follicular carcinoma', 'Lobular carcinoma noninfiltrating', 'Duct adenoma NOS', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Liver cell carcinoma', 'Endometrioid adenoma NOS', 'Melanocytic nevus', 'Papillary tumor of the pineal region', 'Papillary urothelial carcinoma', 'Malignant lymphoma large B-cell diffuse NOS', 'Meningeal melanoma', 'Oat cell carcinoma', 'Central neuroblastoma', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Carcinoma anaplastic NOS', 'Small cell osteosarcoma', 'Adenocarcinoma of anal ducts', 'Tubular carcinoma', 'Melanocytoma eyeball', 'Precursor T-cell lymphoblastic lymphoma', 'Epithelial tumor malignant', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Chronic myelomonocytic leukemia Type 1', 'Tumor secondary', 'Chronic neutrophilic leukemia', 'Liposarcoma NOS', 'Neoplasm benign', 'Pulmonary artery intimal sarcoma', 'Intraductal papillary carcinoma', 'T-cell large granular lymphocytosis', 'Adenocarcinoma NOS', 'Dermatofibroma NOS', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Papillomatosis NOS', 'Splenic diffuse red pulp small B-cell lymphoma', 'Hepatocellular adenoma', 'Rhabdoid tumor NOS', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Astrocytoma anaplastic', 'Mucous adenocarcinoma', 'Tubular androblastoma NOS', 'Pagetoid reticulosis', 'Intraepidermal squamous cell carcinoma Bowen type', 'Tumor embolus', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Infiltrating duct and cribriform carcinoma', 'Prostatic intraepithelial neoplasia grade III', 'Glioblastoma', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Papillary and follicular carcinoma', 'Paraganglioma benign', 'Neurofibromatosis NOS', 'Undifferentiated pleomorphic sarcoma', 'Eosinophil carcinoma', 'Non-invasive low grade serous carcinoma', 'Tumor cells uncertain whether benign or malignant', 'Unclassified tumor borderline malignancy', 'Gastrointestinal stromal tumor malignant', 'Precursor B-cell lymphoblastic lymphoma', 'Gastrin cell tumor', 'Chronic lymphocytic leukemia', 'Adenocarcinoma in a polyp NOS', 'Ependymoma NOS', 'Hodgkin lymphoma nodular sclerosis NOS', 'Malignant lymphoma lymphoblastic NOS', 'Acute leukemia NOS', 'Neuroendocrine carcinoma NOS', 'Diffuse astrocytoma IDH-wildtype', 'Neurofibrosarcoma', 'Lobular carcinoma NOS', 'Malignant lymphoma immunoblastic NOS', 'Bronchiolo-alveolar carcinoma Clara cell', 'Meningioma NOS', 'Diffuse large B-cell lymphoma NOS', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Preleukemic syndrome', 'Gastrin cell tumor malignant', 'Melanoameloblastoma', 'Adenocarcinoma in situ in adenomatous polyp', 'Pleomorphic lobular carcinoma in situ', 'Bronchial adenoma cylindroid', 'Eosinophil adenoma', 'Acute lymphoid leukemia', 'c-ALL', 'Intraductal tubular-papillary neoplasm low grade', 'Infiltrating duct and colloid carcinoma', 'Basal cell tumor', 'Tubular adenoma NOS', 'Mucosal-associated lymphoid tissue lymphoma', 'Combined/mixed carcinoid and adenocarcinoma', 'Renal cell adenocarcinoma', 'Carcinoma in situ in a polyp NOS', 'Carcinoma in situ in adenomatous polyp', 'Malignant lymphoma large B-cell NOS', 'Rhabdoid meningioma', 'Renal cell carcinoma chromophobe type', 'Burkitt cell leukemia', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Tubular adenocarcinoma', 'Renal cell carcinoma NOS', 'Familial adenomatous polyposis', 'Meningioma malignant', 'Burkitt tumor', 'Typical carcinoid', 'Pleomorphic liposarcoma', 'Papillary microcarcinoma', 'Myeloid leukemia NOS', 'Carcinosarcoma NOS', 'Malignant lymphoma lymphocytic nodular NOS', 'Ductal carcinoma NOS', 'Acute promyelocytic leukemia NOS', 'Acinar cell carcinoma', 'Papillotubular adenoma', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Adenocarcinoma combined with other types of carcinoma', 'Duct adenocarcinoma NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Pigmented nevus NOS', 'Carcinoma NOS', 'Chronic myeloproliferative disorder', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Pancreatic microadenoma', 'Secondary carcinoma', 'Paget disease mammary', 'Pancreatic endocrine tumor nonfunctioning', 'Pulmonary adenomatosis', 'Squamous cell carcinoma in situ NOS', 'Chronic myelomonocytic leukemia Type II', 'Combined small cell-large carcinoma', 'Tubulo-papillary adenoma', 'Papilloma NOS', 'Renal cell carcinoma sarcomatoid', 'Malignant lymphoma Hodgkin', 'Hepatocellular carcinoma NOS', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Adenocarcinoma of anal glands', 'Cerebellar liponeurocytoma', 'Mixed medullary-papillary carcinoma', 'Adenocarcinoma metastatic NOS', 'Peripheral T-cell lymphoma NOS', 'Chronic myelocytic leukemia NOS', 'Chronic leukemia NOS', 'Malignant melanoma in giant pigmented nevus', 'Diffuse astrocytoma low grade', 'Lymphoblastic leukemia NOS', 'Papillary transitional cell carcinoma', 'T-cell large granular lymphocytic leukemia', 'Paraganglioma malignant', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Eosinophil adenocarcinoma', 'Rhabdomyosarcoma with ganglionic differentiation', 'Tumor metastatic', 'Small congenital nevus', 'Tumor cells NOS', 'Intraductal tubulopapillary neoplasm', 'Basophil carcinoma', 'Papillary meningioma', 'Acute lymphocytic leukemia']",,Diagnosis +Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['R0', 'Not Reported', 'R1', 'R2', 'RX', 'unknown', '']",,Diagnosis +AJCC Clinical M,AJCC Clinical M,AJCCClinicalM,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['Not Reported', 'M0', 'M1a', 'M1c', 'MX', 'M1', 'cM0 (i+)', 'unknown', 'M1b', '']",,Diagnosis +Precancerous Condition Type,Precancerous Condition Type,PrecancerousConditionType,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,False,,"['Pancreatic Intraepithelial Neoplasia', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma', 'Persistent melanoma in situ', 'Moderate dysplasia', 'No diagnosis possible', 'Normal WDA', 'Ductal Carcinoma In Situ', 'Superficial spreading', 'Mild dysplasia', 'Melanoma in situ arising in a giant congenital nevus', 'Prostatic Intraepithelial Neoplasia', 'Squamous metaplasia - mature', 'Invasive melanoma - nevoid', 'Reserve cell hyperplasia', 'Other', 'Squamous metaplasia - immature', 'Melanocytic hyperplasia', 'Not Applicable', 'Severe dysplasia', 'Squamous carcinoma in situ', 'Melanoma in situ not otherwise classified', 'Melanoma in situ', 'Benign tumor NOS', 'Atypical Adenomatous Lung Hyperplasia', 'Normal', 'Lentigo maligna type', 'Atypical adenomatous hyperplasia', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Invasive melanoma - superficial spreading', 'Invasive melanoma - lentigo maligna', 'Hamartoma', 'Acral-lentiginous', 'Neuroendocrine cell hyperplasia', 'Scar - no residual melanoma', 'Atypical melanocytic proliferation', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - desmoplastic', 'Invasive melanoma - acral lentiginous', 'Carcinoma NOS', 'Invasive melanoma - nodular type', '']",,Diagnosis +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Ventricle NOS', 'Adrenal gland NOS', 'Upper lobe lung', 'Choroid', 'Pleura NOS', 'External lip NOS', 'Overlapping lesion of biliary tract', 'Waldeyer ring', 'Commissure of lip', 'Overlapping lesion of pancreas', 'Vertebral column', 'Overlapping lesion of lung', 'Nervous system NOS', 'Other ill-defined sites', 'Overlapping lesion of eye and adnexa', 'Duodenum', 'Temporal lobe', 'Lymph nodes of multiple regions', 'Head face or neck NOS', 'unknown primary site', 'Extrahepatic bile duct', 'Bone marrow', 'Meninges NOS', 'Bladder neck', 'Head of pancreas', 'Overlapping lesion of vulva', 'Eyelid', 'Brain stem', 'Tonsillar pillar', 'Anterior surface of epiglottis', 'Female genital tract NOS', 'Ascending colon', 'Supraglottis', 'Overlapping lesion of floor of mouth', 'Upper limb NOS', 'Lacrimal gland', 'Tongue NOS', 'Corpus uteri', 'Ileum', 'Mucosa of lower lip', 'Submandibular gland', 'Thymus', 'Descended testis', 'Overlapping lesion of esophagus', 'Spleen', 'Scrotum NOS', 'Posterior wall of nasopharynx', 'Overlapping lesion of palate', 'Orbit NOS', 'Vagina NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Lower lobe lung', 'Pituitary gland', 'Round ligament', 'Nasal cavity', 'Overlapping lesion of skin', 'Male genital organs NOS', 'Bone of limb NOS', 'Overlapping lesion of hypopharynx', 'Sublingual gland', 'Cerebrum', 'Ventral surface of tongue NOS', 'Intestinal tract NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Mandible', 'Pylorus', 'Pancreatic duct', 'External upper lip', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Abdomen NOS', 'Short bones of lower limb and associated joints', 'Overlapping lesion of nasopharynx', 'Mouth NOS', 'Ureteric orifice', 'Colon NOS', 'Cheek mucosa', 'Pancreas NOS', 'Lower-inner quadrant of breast', 'Retina', 'Renal pelvis', 'Posterior wall of bladder', 'Lymph nodes of inguinal region or leg', 'Penis NOS', 'Clitoris', 'Superior wall of nasopharynx', 'Ovary', 'Tail of pancreas', 'Cloacogenic zone', 'Isthmus uteri', 'Retromolar area', 'Undescended testis', 'Eye NOS', 'skin NOS', 'Lesser curvature of stomach NOS', 'Lower-outer quadrant of breast', 'Mucosa of upper lip', 'Skin of lip NOS', 'Gastrointestinal tract NOS', 'Spinal meninges', 'Anterior mediastinum', 'Paraspinal', 'Overlapping lesion of retroperitoneum and peritoneum', 'Floor of mouth NOS', 'unknown', 'Urachus', 'External ear', 'Lymph nodes of head face and neck', 'Specified parts of peritoneum', 'Optic nerve', 'Other specified parts of pancreas', 'Posterior mediastinum', 'Tonsillar fossa', 'Overlapping lesion of tongue', 'Mucosa of lip NOS', 'Kidney NOS', 'Upper-inner quadrant of breast', 'Mediastinum NOS', 'Overlapping lesion of heart mediastinum and pleura', 'Axillary tail of breast', 'Overlapping lesion of corpus uteri', 'Gastric antrum', 'Body of stomach', 'Overlapping lesion of tonsil', 'Uterine adnexa', 'Lateral floor of mouth', 'Labium minus', 'Middle lobe lung', 'Medulla of adrenal gland', 'Lower limb NOS', 'Hard palate', 'Body of penis', 'Overlapping lesion of digestive system', 'Overlapping lesion of other and unspecified parts of mouth', 'Lower gum', 'Overlapping lesion of rectum anus and anal canal', 'Hypopharynx NOS', 'Overlapping lesion of female genital organs', 'Skin of other and unspecified parts of face', 'Glans penis', 'Accessory sinus NOS', 'Overlapping lesion of endocrine glands and related structures', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Bones of skull and face and associated joints', 'Vestibule of mouth', 'Border of tongue', 'Parametrium', 'Ciliary body', 'Soft palate NOS', 'Overlapping lesion of cervix uteri', 'Gum NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Skin of trunk', 'Cranial nerve NOS', 'Ampulla of Vater', 'Palate NOS', 'Pineal gland', 'Lymph nodes of axilla or arm', 'Base of tongue NOS', 'Middle ear', 'Breast NOS', 'Parietal lobe', 'Frontal sinus', 'Overlapping lesion of larynx', 'Retroperitoneum', 'Paraurethral gland', 'Overlapping lesion of urinary organs', 'Connective subcutaneous and other soft tissues NOS', 'Lateral wall of oropharynx', 'Main bronchus', 'Liver', 'Lip NOS', 'Biliary tract NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Anterior 2/3 of tongue NOS', 'Skin of scalp and neck', 'Short bones of upper limb and associated joints', 'Jejunum', 'Overlapping lesion of ill-defined sites', 'Sphenoid sinus', 'Urethra', 'Trachea', 'Hematopoietic system NOS', 'Fallopian tube', 'Cerebellum NOS', 'Carotid body', 'Other specified parts of male genital organs', 'Connective subcutaneous and other soft tissues of abdomen', 'skin of upper limb and shoulder', 'Not Reported', 'Lateral wall of nasopharynx', 'Endocrine gland NOS', 'Heart', 'Dorsal surface of tongue NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Central portion of breast', 'Endometrium', 'Appendix', 'Cerebral meninges', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peritoneum NOS', 'Craniopharyngeal duct', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Ethmoid sinus', 'Exocervix', 'Pharynx NOS', 'Anal canal', 'Aortic body and other paraganglia', 'Labium majus', 'Lingual tonsil', 'Ill-defined sites within respiratory system', 'Lower third of esophagus', 'Overlapping lesion of bones joints and articular cartilage', 'Rectosigmoid junction', 'Placenta', 'Bone NOS', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lateral wall of bladder', 'Cecum', 'Parathyroid gland', 'Cortex of adrenal gland', 'Upper-outer quadrant of breast', 'Vulva NOS', 'Prepuce', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Greater curvature of stomach NOS', 'Autonomic nervous system NOS', 'Nasopharynx NOS', 'Anus NOS', 'Overlapping lesion of male genital organs', 'Descending colon', 'Long bones of lower limb and associated joints', 'Urinary system NOS', 'Cardia NOS', 'Lung NOS', 'Frontal lobe', 'Thoracic esophagus', 'Overlapping lesion of lip', 'Cervical esophagus', 'Uterus NOS', 'Major salivary gland NOS', 'Maxillary sinus', 'Intrathoracic lymph nodes', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Posterior wall of oropharynx', 'Epididymis', 'Spermatic cord', 'Pelvic lymph nodes', 'Dome of bladder', 'Middle third of esophagus', 'Pelvis NOS', 'Tonsil NOS', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cervix uteri', 'Nipple', 'Conjunctiva', 'Olfactory nerve', 'Fundus uteri', 'Anterior floor of mouth', 'Oropharynx NOS', 'Meckel diverticulum', 'Esophagus NOS', 'Intra-abdominal lymph nodes', 'Lymph node NOS', 'Small intestine NOS', 'Brain NOS', 'Overlapping lesion of major salivary glands', 'Vallecula', 'Upper gum', 'Overlapping lesion of small intestine', 'Overlapping lesion of breast', 'Anterior wall of nasopharynx', 'Cauda equina', 'Myometrium', 'skin of lower limb and hip', 'Overlapping lesion of accessory sinuses', 'Hypopharyngeal aspect of aryepiglottic fold', 'Hepatic flexure of colon', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Overlapping lesion of stomach', 'Postcricoid region', 'Uvula', 'Splenic flexure of colon', 'Overlapping lesion of bladder', 'Glottis', 'Pyriform sinus', 'Thorax NOS', 'Trigone of bladder', 'Fundus of stomach', 'Abdominal esophagus', 'Posterior wall of hypopharynx', 'Overlapping lesion of penis', 'Connective subcutaneous and other soft tissues of thorax', 'Blood', 'Body of pancreas', 'Bladder NOS', 'Occipital lobe', 'Intrahepatic bile duct', 'Spinal cord', 'Laryngeal cartilage', 'Transverse colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sigmoid colon', 'Cornea NOS', 'Prostate gland', 'Endocervix', 'Overlapping lesions of oropharynx', 'Overlapping lesion of colon', 'Upper respiratory tract NOS', 'Islets of Langerhans', 'Broad ligament', 'Parotid gland', 'Anterior wall of bladder', 'Rib sternum clavicle and associated joints', 'Long bones of upper limb scapula and associated joints', 'Gallbladder', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Upper third of esophagus', 'Other specified parts of female genital organs', 'Thyroid gland', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of pelvis', 'Reticuloendothelial system NOS', 'Acoustic nerve', 'Larynx NOS', 'Stomach NOS', 'Testis NOS', 'External lower lip', 'Subglottis', 'Ureter', 'Overlapping lesion of brain', 'Rectum NOS']",,Diagnosis +AJCC Pathologic N,AJCC Pathologic N,AJCCPathologicN,The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.,False,,"['N3', 'Not Reported', 'N4', 'N0 (i+)', 'N2', 'N3b', 'N0 (i-)', 'N1bIII', 'N0', 'N1c', 'unknown', 'N2b', 'N3c', 'N2a', 'NX', 'N0 (mol-)', 'N1', 'N1b', 'N2c', 'N1bI', 'N1mi', 'N0 (mol+)', 'N1bIV', 'N1a', 'N1bII', 'N3a', '']",,Diagnosis +AJCC Pathologic T,AJCC Pathologic T,AJCCPathologicT,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).",False,,"['T2a1', 'T1b1', 'Not Reported', 'Tis (DCIS)', 'T0', ""Tis (Paget's)"", 'T1b', 'Tis (LCIS)', 'T1b2', 'T2c', 'T3d', 'T4e', 'T2d', 'T2b', 'T1c', 'Ta', 'T4d', 'T1', 'T4a', 'unknown', 'T3a', 'T1a2', 'T2a', 'T3c', 'TX', 'T1a', 'T3b', 'T2a2', 'T4', 'T1mi', 'T4c', 'Tis', 'T4b', 'T2', 'T1a1', 'T3', '']",,Diagnosis +Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['DU-Disease Unchanged', 'PSR-Pseudoresponse', 'TE-Too Early', 'AJ-Adjuvant Therapy', 'RD-Responsive Disease', 'PB-Palliative Benefit', 'PPD-Pseudoprogression', 'NPB-No Palliative Benefit', 'VGPR-Very Good Partial Response', 'SPD-Surgical Progression', 'PA-Palliative Therapy', 'IMR-Immunoresponse', 'PD-Progressive Disease', 'Non-CR/Non-PD-Non-CR/Non-PD', 'NR-No Response', 'MR-Minimal/Marginal Response', 'sCR-Stringent Complete Response', 'IPD-Immunoprogression', 'PR-Partial Response', 'CR-Complete Response', 'RP-Response', 'CRU-Complete Response Unconfirmed', 'RPD-Radiographic Progressive Disease', 'SD-Stable Disease', 'CPD-Clinical Progression', 'MX-Mixed Response', '']",,Diagnosis +Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Ventricle NOS', 'Adrenal gland NOS', 'Upper lobe lung', 'Choroid', 'Pleura NOS', 'External lip NOS', 'Overlapping lesion of biliary tract', 'Waldeyer ring', 'Commissure of lip', 'Overlapping lesion of pancreas', 'Vertebral column', 'Overlapping lesion of lung', 'Nervous system NOS', 'Other ill-defined sites', 'Overlapping lesion of eye and adnexa', 'Duodenum', 'Temporal lobe', 'Lymph nodes of multiple regions', 'Head face or neck NOS', 'unknown primary site', 'Extrahepatic bile duct', 'Bone marrow', 'Meninges NOS', 'Bladder neck', 'Head of pancreas', 'Overlapping lesion of vulva', 'Eyelid', 'Brain stem', 'Tonsillar pillar', 'Anterior surface of epiglottis', 'Female genital tract NOS', 'Ascending colon', 'Supraglottis', 'Overlapping lesion of floor of mouth', 'Upper limb NOS', 'Lacrimal gland', 'Tongue NOS', 'Corpus uteri', 'Ileum', 'Mucosa of lower lip', 'Submandibular gland', 'Thymus', 'Descended testis', 'Overlapping lesion of esophagus', 'Spleen', 'Scrotum NOS', 'Posterior wall of nasopharynx', 'Overlapping lesion of palate', 'Orbit NOS', 'Vagina NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Lower lobe lung', 'Pituitary gland', 'Round ligament', 'Nasal cavity', 'Overlapping lesion of skin', 'Male genital organs NOS', 'Bone of limb NOS', 'Overlapping lesion of hypopharynx', 'Sublingual gland', 'Cerebrum', 'Ventral surface of tongue NOS', 'Intestinal tract NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Mandible', 'Pylorus', 'Pancreatic duct', 'External upper lip', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Abdomen NOS', 'Short bones of lower limb and associated joints', 'Overlapping lesion of nasopharynx', 'Mouth NOS', 'Ureteric orifice', 'Colon NOS', 'Cheek mucosa', 'Pancreas NOS', 'Lower-inner quadrant of breast', 'Retina', 'Renal pelvis', 'Posterior wall of bladder', 'Lymph nodes of inguinal region or leg', 'Penis NOS', 'Clitoris', 'Superior wall of nasopharynx', 'Ovary', 'Tail of pancreas', 'Cloacogenic zone', 'Isthmus uteri', 'Retromolar area', 'Undescended testis', 'Eye NOS', 'skin NOS', 'Lesser curvature of stomach NOS', 'Lower-outer quadrant of breast', 'Mucosa of upper lip', 'Skin of lip NOS', 'Gastrointestinal tract NOS', 'Spinal meninges', 'Anterior mediastinum', 'Overlapping lesion of retroperitoneum and peritoneum', 'Floor of mouth NOS', 'unknown', 'Urachus', 'External ear', 'Lymph nodes of head face and neck', 'Specified parts of peritoneum', 'Optic nerve', 'Other specified parts of pancreas', 'Posterior mediastinum', 'Tonsillar fossa', 'Overlapping lesion of tongue', 'Mucosa of lip NOS', 'Kidney NOS', 'Upper-inner quadrant of breast', 'Mediastinum NOS', 'Overlapping lesion of heart mediastinum and pleura', 'Axillary tail of breast', 'Overlapping lesion of corpus uteri', 'Gastric antrum', 'Body of stomach', 'Overlapping lesion of tonsil', 'Uterine adnexa', 'Lateral floor of mouth', 'Labium minus', 'Middle lobe lung', 'Medulla of adrenal gland', 'Lower limb NOS', 'Hard palate', 'Body of penis', 'Overlapping lesion of digestive system', 'Overlapping lesion of other and unspecified parts of mouth', 'Lower gum', 'Overlapping lesion of rectum anus and anal canal', 'Hypopharynx NOS', 'Overlapping lesion of female genital organs', 'Skin of other and unspecified parts of face', 'Glans penis', 'Accessory sinus NOS', 'Overlapping lesion of endocrine glands and related structures', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Bones of skull and face and associated joints', 'Vestibule of mouth', 'Border of tongue', 'Parametrium', 'Ciliary body', 'Soft palate NOS', 'Overlapping lesion of cervix uteri', 'Gum NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Skin of trunk', 'Cranial nerve NOS', 'Ampulla of Vater', 'Palate NOS', 'Pineal gland', 'Lymph nodes of axilla or arm', 'Base of tongue NOS', 'Middle ear', 'Breast NOS', 'Parietal lobe', 'Frontal sinus', 'Overlapping lesion of larynx', 'Retroperitoneum', 'Paraurethral gland', 'Overlapping lesion of urinary organs', 'Connective subcutaneous and other soft tissues NOS', 'Lateral wall of oropharynx', 'Main bronchus', 'Liver', 'Lip NOS', 'Biliary tract NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Anterior 2/3 of tongue NOS', 'Skin of scalp and neck', 'Short bones of upper limb and associated joints', 'Jejunum', 'Overlapping lesion of ill-defined sites', 'Sphenoid sinus', 'Urethra', 'Trachea', 'Hematopoietic system NOS', 'Fallopian tube', 'Cerebellum NOS', 'Carotid body', 'Other specified parts of male genital organs', 'Connective subcutaneous and other soft tissues of abdomen', 'skin of upper limb and shoulder', 'Not Reported', 'Lateral wall of nasopharynx', 'Endocrine gland NOS', 'Heart', 'Dorsal surface of tongue NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Central portion of breast', 'Endometrium', 'Appendix', 'Cerebral meninges', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peritoneum NOS', 'Craniopharyngeal duct', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Ethmoid sinus', 'Exocervix', 'Pharynx NOS', 'Anal canal', 'Aortic body and other paraganglia', 'Labium majus', 'Lingual tonsil', 'Ill-defined sites within respiratory system', 'Lower third of esophagus', 'Overlapping lesion of bones joints and articular cartilage', 'Rectosigmoid junction', 'Placenta', 'Bone NOS', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lateral wall of bladder', 'Cecum', 'Parathyroid gland', 'Cortex of adrenal gland', 'Upper-outer quadrant of breast', 'Vulva NOS', 'Prepuce', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Greater curvature of stomach NOS', 'Autonomic nervous system NOS', 'Nasopharynx NOS', 'Anus NOS', 'Overlapping lesion of male genital organs', 'Descending colon', 'Long bones of lower limb and associated joints', 'Urinary system NOS', 'Cardia NOS', 'Lung NOS', 'Frontal lobe', 'Thoracic esophagus', 'Overlapping lesion of lip', 'Cervical esophagus', 'Uterus NOS', 'Major salivary gland NOS', 'Maxillary sinus', 'Intrathoracic lymph nodes', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Posterior wall of oropharynx', 'Epididymis', 'Spermatic cord', 'Pelvic lymph nodes', 'Dome of bladder', 'Middle third of esophagus', 'Pelvis NOS', 'Tonsil NOS', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cervix uteri', 'Nipple', 'Conjunctiva', 'Olfactory nerve', 'Fundus uteri', 'Anterior floor of mouth', 'Oropharynx NOS', 'Meckel diverticulum', 'Esophagus NOS', 'Intra-abdominal lymph nodes', 'Lymph node NOS', 'Small intestine NOS', 'Brain NOS', 'Overlapping lesion of major salivary glands', 'Vallecula', 'Upper gum', 'Overlapping lesion of small intestine', 'Overlapping lesion of breast', 'Anterior wall of nasopharynx', 'Cauda equina', 'Myometrium', 'skin of lower limb and hip', 'Overlapping lesion of accessory sinuses', 'Hypopharyngeal aspect of aryepiglottic fold', 'Hepatic flexure of colon', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Overlapping lesion of stomach', 'Postcricoid region', 'Uvula', 'Splenic flexure of colon', 'Overlapping lesion of bladder', 'Glottis', 'Pyriform sinus', 'Thorax NOS', 'Trigone of bladder', 'Fundus of stomach', 'Abdominal esophagus', 'Posterior wall of hypopharynx', 'Overlapping lesion of penis', 'Connective subcutaneous and other soft tissues of thorax', 'Blood', 'Body of pancreas', 'Bladder NOS', 'Occipital lobe', 'Intrahepatic bile duct', 'Spinal cord', 'Laryngeal cartilage', 'Transverse colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sigmoid colon', 'Cornea NOS', 'Prostate gland', 'Endocervix', 'Overlapping lesions of oropharynx', 'Overlapping lesion of colon', 'Upper respiratory tract NOS', 'Islets of Langerhans', 'Broad ligament', 'Parotid gland', 'Anterior wall of bladder', 'Rib sternum clavicle and associated joints', 'Long bones of upper limb scapula and associated joints', 'Gallbladder', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Upper third of esophagus', 'Other specified parts of female genital organs', 'Thyroid gland', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of pelvis', 'Reticuloendothelial system NOS', 'Acoustic nerve', 'Larynx NOS', 'Stomach NOS', 'Testis NOS', 'External lower lip', 'Subglottis', 'Ureter', 'Overlapping lesion of brain', 'Rectum NOS', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis -Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Not Reported', 'Distant', 'Biochemical', 'Regional', 'Local', 'unknown', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis +Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis +Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Biochemical', 'Not Reported', 'Regional', 'Distant', 'Local', 'unknown', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis Therapeutic Agents,Therapeutic Agents,TherapeuticAgents,Text identification of the individual agent(s) used as part of a treatment regimen.,False,,,,Therapy -Treatment Arm,Treatment Arm,TreatmentArm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,False,,"['EA5142', 'E4512', 'A081105', '']",,Therapy -Treatment Anatomic Site,Treatment Anatomic Site,TreatmentAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']",,Therapy -Days to Treatment Start,Days to Treatment Start,DaystoTreatmentStart,Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable',False,,,,Therapy -Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['Not Reported', 'Partial Response', 'Very Good Partial Response', 'Progressive Disease', 'Mixed Response', 'Complete Response', 'Stable Disease', 'No Response', 'Persistent Disease', 'unknown', 'Treatment Stopped Due to Toxicity', 'No Measurable Disease', 'Treatment Ongoing', '']",,Therapy -Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Other', 'Adverse Therapy Event', 'Death', 'Disease Progression', 'Course of Therapy Completed', 'Withdrawal by Subject', '']",,Therapy +Number of Cycles,Number of Cycles,NumberofCycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,False,,,,Therapy +Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Death', 'Adverse Therapy Event', 'Course of Therapy Completed', 'Disease Progression', 'Other', 'Withdrawal by Subject', '']",,Therapy Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,False,,,,Therapy -Treatment Intent Type,Treatment Intent Type,TreatmentIntentType,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],False,,"['Not Reported', 'Neoadjuvant', 'Prevention', 'Adjuvant', 'Palliative', 'Cancer Control', 'Cure', 'unknown', '']",,Therapy -Initial Disease Status,Initial Disease Status,InitialDiseaseStatus,The text term used to describe the status of the patient's malignancy when the treatment began.,False,,"['Not Reported', 'Recurrent Disease', 'Progressive Disease', 'unknown', 'Initial Diagnosis', 'Residual Disease', '']",,Therapy +Initial Disease Status,Initial Disease Status,InitialDiseaseStatus,The text term used to describe the status of the patient's malignancy when the treatment began.,False,,"['Not Reported', 'Progressive Disease', 'Recurrent Disease', 'Residual Disease', 'unknown', 'Initial Diagnosis', '']",,Therapy +Treatment Effect Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Therapy +Treatment Dose Units,Treatment Dose Units,TreatmentDoseUnits,The text term used to describe the dose units of an agent the patient received.,False,,"['cGy', 'Gy', '']",,Therapy +Treatment or Therapy,Treatment or Therapy,TreatmentorTherapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Therapy +Chemo Concurrent to Radiation,Chemo Concurrent to Radiation,ChemoConcurrenttoRadiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,Therapy +Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['Complete Response', 'Very Good Partial Response', 'Not Reported', 'Mixed Response', 'No Response', 'Stable Disease', 'Progressive Disease', 'Treatment Ongoing', 'No Measurable Disease', 'Partial Response', 'Treatment Stopped Due to Toxicity', 'unknown', 'Persistent Disease', '']",,Therapy Regimen or Line of Therapy,Regimen or Line of Therapy,RegimenorLineofTherapy,The text term used to describe the regimen or line of therapy.,False,,,,Therapy -Chemo Concurrent to Radiation,Chemo Concurrent to Radiation,ChemoConcurrenttoRadiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Therapy -Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Not Reported', 'No Necrosis', 'Complete Necrosis (No Viable Tumor)', 'unknown', 'Incomplete Necrosis (Viable Tumor Present)', '']",,Therapy -Treatment or Therapy,Treatment or Therapy,TreatmentorTherapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Therapy -Number of Cycles,Number of Cycles,NumberofCycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,False,,,,Therapy -Treatment Effect Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,Therapy Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Therapy +Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Incomplete Necrosis (Viable Tumor Present)', 'Not Reported', 'No Necrosis', 'Complete Necrosis (No Viable Tumor)', 'unknown', '']",,Therapy +Treatment Dose,Treatment Dose,TreatmentDose,The numeric value used to describe the dose of an agent the patient received.,False,,,,Therapy Days to Treatment End,Days to Treatment End,DaystoTreatmentEnd,Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable',False,,,,Therapy -Treatment Dose Units,Treatment Dose Units,TreatmentDoseUnits,The text term used to describe the dose units of an agent the patient received.,False,,"['Gy', 'cGy', '']",,Therapy -Treatment Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Not Reported', 'Every Other Day', 'Once Weekly', 'Twice Weekly', 'Four Times Daily', 'Three Times Daily', 'unknown', 'Every Hour', 'Twice Daily', 'Five Times Daily', 'Every 24 Hours', '']",,Therapy +Treatment Intent Type,Treatment Intent Type,TreatmentIntentType,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],False,,"['Not Reported', 'Cancer Control', 'Palliative', 'Prevention', 'Neoadjuvant', 'Cure', 'Adjuvant', 'unknown', '']",,Therapy +Treatment Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Not Reported', 'Twice Weekly', 'Every 24 Hours', 'Five Times Daily', 'Twice Daily', 'Four Times Daily', 'Every Other Day', 'unknown', 'Once Weekly', 'Every Hour', 'Three Times Daily', '']",,Therapy +Treatment Anatomic Site,Treatment Anatomic Site,TreatmentAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,,"['Ventricle NOS', 'Adrenal gland NOS', 'Upper lobe lung', 'Choroid', 'Pleura NOS', 'External lip NOS', 'Overlapping lesion of biliary tract', 'Waldeyer ring', 'Commissure of lip', 'Overlapping lesion of pancreas', 'Vertebral column', 'Overlapping lesion of lung', 'Nervous system NOS', 'Other ill-defined sites', 'Overlapping lesion of eye and adnexa', 'Duodenum', 'Temporal lobe', 'Lymph nodes of multiple regions', 'Head face or neck NOS', 'unknown primary site', 'Extrahepatic bile duct', 'Bone marrow', 'Meninges NOS', 'Bladder neck', 'Head of pancreas', 'Overlapping lesion of vulva', 'Eyelid', 'Brain stem', 'Tonsillar pillar', 'Anterior surface of epiglottis', 'Female genital tract NOS', 'Ascending colon', 'Supraglottis', 'Overlapping lesion of floor of mouth', 'Upper limb NOS', 'Lacrimal gland', 'Tongue NOS', 'Corpus uteri', 'Ileum', 'Mucosa of lower lip', 'Submandibular gland', 'Thymus', 'Descended testis', 'Overlapping lesion of esophagus', 'Spleen', 'Scrotum NOS', 'Posterior wall of nasopharynx', 'Overlapping lesion of palate', 'Orbit NOS', 'Vagina NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Lower lobe lung', 'Pituitary gland', 'Round ligament', 'Nasal cavity', 'Overlapping lesion of skin', 'Male genital organs NOS', 'Bone of limb NOS', 'Overlapping lesion of hypopharynx', 'Sublingual gland', 'Cerebrum', 'Ventral surface of tongue NOS', 'Intestinal tract NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Mandible', 'Pylorus', 'Pancreatic duct', 'External upper lip', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Abdomen NOS', 'Short bones of lower limb and associated joints', 'Overlapping lesion of nasopharynx', 'Mouth NOS', 'Ureteric orifice', 'Colon NOS', 'Cheek mucosa', 'Pancreas NOS', 'Lower-inner quadrant of breast', 'Retina', 'Renal pelvis', 'Posterior wall of bladder', 'Lymph nodes of inguinal region or leg', 'Penis NOS', 'Clitoris', 'Superior wall of nasopharynx', 'Ovary', 'Tail of pancreas', 'Cloacogenic zone', 'Isthmus uteri', 'Retromolar area', 'Undescended testis', 'Eye NOS', 'skin NOS', 'Lesser curvature of stomach NOS', 'Lower-outer quadrant of breast', 'Mucosa of upper lip', 'Skin of lip NOS', 'Gastrointestinal tract NOS', 'Spinal meninges', 'Anterior mediastinum', 'Overlapping lesion of retroperitoneum and peritoneum', 'Floor of mouth NOS', 'unknown', 'Urachus', 'External ear', 'Lymph nodes of head face and neck', 'Specified parts of peritoneum', 'Optic nerve', 'Other specified parts of pancreas', 'Posterior mediastinum', 'Tonsillar fossa', 'Overlapping lesion of tongue', 'Mucosa of lip NOS', 'Kidney NOS', 'Upper-inner quadrant of breast', 'Mediastinum NOS', 'Overlapping lesion of heart mediastinum and pleura', 'Axillary tail of breast', 'Overlapping lesion of corpus uteri', 'Gastric antrum', 'Body of stomach', 'Overlapping lesion of tonsil', 'Uterine adnexa', 'Lateral floor of mouth', 'Labium minus', 'Middle lobe lung', 'Medulla of adrenal gland', 'Lower limb NOS', 'Hard palate', 'Body of penis', 'Overlapping lesion of digestive system', 'Overlapping lesion of other and unspecified parts of mouth', 'Lower gum', 'Overlapping lesion of rectum anus and anal canal', 'Hypopharynx NOS', 'Overlapping lesion of female genital organs', 'Skin of other and unspecified parts of face', 'Glans penis', 'Accessory sinus NOS', 'Overlapping lesion of endocrine glands and related structures', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Bones of skull and face and associated joints', 'Vestibule of mouth', 'Border of tongue', 'Parametrium', 'Ciliary body', 'Soft palate NOS', 'Overlapping lesion of cervix uteri', 'Gum NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Skin of trunk', 'Cranial nerve NOS', 'Ampulla of Vater', 'Palate NOS', 'Pineal gland', 'Lymph nodes of axilla or arm', 'Base of tongue NOS', 'Middle ear', 'Breast NOS', 'Parietal lobe', 'Frontal sinus', 'Overlapping lesion of larynx', 'Retroperitoneum', 'Paraurethral gland', 'Overlapping lesion of urinary organs', 'Connective subcutaneous and other soft tissues NOS', 'Lateral wall of oropharynx', 'Main bronchus', 'Liver', 'Lip NOS', 'Biliary tract NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Anterior 2/3 of tongue NOS', 'Skin of scalp and neck', 'Short bones of upper limb and associated joints', 'Jejunum', 'Overlapping lesion of ill-defined sites', 'Sphenoid sinus', 'Urethra', 'Trachea', 'Hematopoietic system NOS', 'Fallopian tube', 'Cerebellum NOS', 'Carotid body', 'Other specified parts of male genital organs', 'Connective subcutaneous and other soft tissues of abdomen', 'skin of upper limb and shoulder', 'Not Reported', 'Lateral wall of nasopharynx', 'Endocrine gland NOS', 'Heart', 'Dorsal surface of tongue NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Central portion of breast', 'Endometrium', 'Appendix', 'Cerebral meninges', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peritoneum NOS', 'Craniopharyngeal duct', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Ethmoid sinus', 'Exocervix', 'Pharynx NOS', 'Anal canal', 'Aortic body and other paraganglia', 'Labium majus', 'Lingual tonsil', 'Ill-defined sites within respiratory system', 'Lower third of esophagus', 'Overlapping lesion of bones joints and articular cartilage', 'Rectosigmoid junction', 'Placenta', 'Bone NOS', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lateral wall of bladder', 'Cecum', 'Parathyroid gland', 'Cortex of adrenal gland', 'Upper-outer quadrant of breast', 'Vulva NOS', 'Prepuce', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Greater curvature of stomach NOS', 'Autonomic nervous system NOS', 'Nasopharynx NOS', 'Anus NOS', 'Overlapping lesion of male genital organs', 'Descending colon', 'Long bones of lower limb and associated joints', 'Urinary system NOS', 'Cardia NOS', 'Lung NOS', 'Frontal lobe', 'Thoracic esophagus', 'Overlapping lesion of lip', 'Cervical esophagus', 'Uterus NOS', 'Major salivary gland NOS', 'Maxillary sinus', 'Intrathoracic lymph nodes', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Posterior wall of oropharynx', 'Epididymis', 'Spermatic cord', 'Pelvic lymph nodes', 'Dome of bladder', 'Middle third of esophagus', 'Pelvis NOS', 'Tonsil NOS', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cervix uteri', 'Nipple', 'Conjunctiva', 'Olfactory nerve', 'Fundus uteri', 'Anterior floor of mouth', 'Oropharynx NOS', 'Meckel diverticulum', 'Esophagus NOS', 'Intra-abdominal lymph nodes', 'Lymph node NOS', 'Small intestine NOS', 'Brain NOS', 'Overlapping lesion of major salivary glands', 'Vallecula', 'Upper gum', 'Overlapping lesion of small intestine', 'Overlapping lesion of breast', 'Anterior wall of nasopharynx', 'Cauda equina', 'Myometrium', 'skin of lower limb and hip', 'Overlapping lesion of accessory sinuses', 'Hypopharyngeal aspect of aryepiglottic fold', 'Hepatic flexure of colon', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Overlapping lesion of stomach', 'Postcricoid region', 'Uvula', 'Splenic flexure of colon', 'Overlapping lesion of bladder', 'Glottis', 'Pyriform sinus', 'Thorax NOS', 'Trigone of bladder', 'Fundus of stomach', 'Abdominal esophagus', 'Posterior wall of hypopharynx', 'Overlapping lesion of penis', 'Connective subcutaneous and other soft tissues of thorax', 'Blood', 'Body of pancreas', 'Bladder NOS', 'Occipital lobe', 'Intrahepatic bile duct', 'Spinal cord', 'Laryngeal cartilage', 'Transverse colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sigmoid colon', 'Cornea NOS', 'Prostate gland', 'Endocervix', 'Overlapping lesions of oropharynx', 'Overlapping lesion of colon', 'Upper respiratory tract NOS', 'Islets of Langerhans', 'Broad ligament', 'Parotid gland', 'Anterior wall of bladder', 'Rib sternum clavicle and associated joints', 'Long bones of upper limb scapula and associated joints', 'Gallbladder', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Upper third of esophagus', 'Other specified parts of female genital organs', 'Thyroid gland', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of pelvis', 'Reticuloendothelial system NOS', 'Acoustic nerve', 'Larynx NOS', 'Stomach NOS', 'Testis NOS', 'External lower lip', 'Subglottis', 'Ureter', 'Overlapping lesion of brain', 'Rectum NOS', '']",,Therapy HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Therapy -Treatment Dose,Treatment Dose,TreatmentDose,The numeric value used to describe the dose of an agent the patient received.,False,,,,Therapy -Chromosome,Chromosome,Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Not Reported', 'chrM', 'chr16', 'chr10', 'chr20', 'chr1', 'unknown', 'chrY', 'chr17', 'chr3', 'chr11', 'chr6', 'chr7', 'chr21', 'chr22', 'chr5', 'chr18', 'chr2', 'chr8', 'chr13', 'chr9', 'chr15', 'chr19', 'chrX', 'chr14', 'chr4', 'chr12', 'chr23', '']",,MolecularTest +Days to Treatment Start,Days to Treatment Start,DaystoTreatmentStart,Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable',False,,,,Therapy +Treatment Arm,Treatment Arm,TreatmentArm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,False,,"['A081105', 'E4512', 'EA5142', '']",,Therapy +Clinical Biospecimen Type,Clinical Biospecimen Type,ClinicalBiospecimenType,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Urine', 'Soft Tissue', 'Not Reported', 'Pleural Fluid', 'Bone Marrow', 'Serum', 'Tissue NOS', 'Muscle Tissue', 'Feces', 'Plasma', 'Skin', 'Granulocyte', 'Embryonic Tissue', 'Blood', 'unknown', 'Buffy Coat', 'Saliva', 'Connective Tissue', 'Nerve Tissue', 'Peritoneal Fluid', 'Embryonic Fluid', 'Cerebrospinal Fluid', 'Buccal Mucosa', 'Uninvolved Tissue NOS', '']",,MolecularTest +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MolecularTest Test Units,Test Units,TestUnits,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Intron,Intron,Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",False,,,,MolecularTest -Cytoband,Cytoband,Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -Mismatch Repair Mutation,Mismatch Repair Mutation,MismatchRepairMutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Not Reported', 'no', 'unknown', 'yes', '']",,MolecularTest +Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Non-clonal', 'Clonal', '']",,MolecularTest +Cell Count,Cell Count,CellCount,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Second Gene Symbol,Second Gene Symbol,SecondGeneSymbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Molecular Consequence,Molecular Consequence,MolecularConsequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['NMD Transcript Variant', 'Transcript Amplification', 'Synonymous Variant', 'TFBS Amplification', 'Downstream Gene Variant', 'Inframe Deletion', 'Regulatory Region Amplification', 'Regulatory Region Variant', 'Protein Altering Variant', 'Start Lost', 'Transcript Ablation', 'Stop Retained Variant', 'Frameshift Variant', 'Stop Gain', 'TFBS Ablation', 'Intron Variant', '3 Prime UTR Variant', 'Non-coding Transcript Exon Variant', 'Mature miRNA Variant', 'Splice Region Variant', 'Splice Donor Variant', 'Stop Lost', 'Feature Elongation', 'Splice Acceptor Variant', 'Inframe Insertion', 'Coding Sequence Variant', 'Missense Variant', 'Incomplete Terminal Codon Variant', 'Intergenic Variant', 'Upstream Gene Variant', 'Feature Truncation', 'TF Binding Site Variant', 'Regulatory Region Ablation', '5 Prime UTR Variant', 'Non-coding Transcript Variant', '']",,MolecularTest Specialized Molecular Test,Specialized Molecular Test,SpecializedMolecularTest,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Not Reported', 'Copy Number Reported', 'Low', 'Not Applicable', 'Intermediate', 'Overexpressed', 'Test Value Reported', 'Normal', 'unknown', 'positive', 'negative', 'Equivocal', 'High', 'Loss of Expression', 'Abnormal NOS']",,MolecularTest -Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['Not Reported', 'Hypodiploid', 'Diploid', 'Hyperdiploid', 'Tetraploid', 'Near Diploid', 'unknown', 'Aneuploid', '']",,MolecularTest -Molecular Consequence,Molecular Consequence,MolecularConsequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Inframe Insertion', 'Inframe Deletion', 'Missense Variant', 'Upstream Gene Variant', 'Regulatory Region Ablation', 'TFBS Ablation', 'Start Lost', 'Splice Acceptor Variant', 'Synonymous Variant', 'Transcript Amplification', 'Stop Lost', 'TF Binding Site Variant', 'Regulatory Region Amplification', 'NMD Transcript Variant', 'Feature Truncation', 'Incomplete Terminal Codon Variant', 'TFBS Amplification', 'Transcript Ablation', '3 Prime UTR Variant', 'Feature Elongation', 'Regulatory Region Variant', 'Splice Region Variant', 'Intergenic Variant', 'Protein Altering Variant', 'Stop Retained Variant', 'Frameshift Variant', '5 Prime UTR Variant', 'Coding Sequence Variant', 'Non-coding Transcript Variant', 'Mature miRNA Variant', 'Splice Donor Variant', 'Non-coding Transcript Exon Variant', 'Intron Variant', 'Stop Gain', 'Downstream Gene Variant', '']",,MolecularTest +Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,MolecularTest +Second Exon,Second Exon,SecondExon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.",False,,,,MolecularTest +Copy Number,Copy Number,CopyNumber,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Nullizygous', 'Not Reported', 'Hemizygous', 'Homozygous', 'Heterozygous', 'unknown', '']",,MolecularTest +Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['negative', 'positive', 'Equivocal', 'Not Reported', 'Low', 'Copy Number Reported', 'Overexpressed', 'Normal', 'Intermediate', 'High', 'Loss of Expression', 'Abnormal NOS', 'unknown', 'Not Applicable', 'Test Value Reported']",,MolecularTest +Antigen,Antigen,Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Not Reported', 'CD30', 'CD7', 'CA-125', 'CD23', 'CD14', 'CD33', 'CD5', 'NSE', 'Squamous Cell Carcinoma Antigen', 'CD15', 'unknown', 'CD45', 'BCL6', 'CD56', 'CD34', 'CCND1', 'CD138', 'CD19', 'HLA-DR', 'CD22', 'CA19-9', 'CEA', 'CD10', 'CD25', 'Mesothelin', 'CD20', 'CD3', 'CD79A', 'CD117', '']",,MolecularTest Blood Test Normal Range Upper,Blood Test Normal Range Upper,BloodTestNormalRangeUpper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest -Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Not Reported', 'Translocation', 'Alleles', 'unknown', 'Hypermethylation', 'Repeated Sequences', 'Deletion', 'Mosaicism', 'Loss', 'Other', 'Inversion', 'Splice', 'Chrimerism', 'Gain', 'Amplification', 'Deletion-Insertion', 'Extension', 'Duplication', 'Conversion', 'Substitution', 'Insertion', 'Rearrangement', 'Methylation', 'Partial Methylation', '']",,MolecularTest -Loci Count,Loci Count,LociCount,Numeric value used to describe the number of loci tested.,False,,,,MolecularTest -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MolecularTest -Variant Origin,Variant Origin,VariantOrigin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Somatic', 'unknown', 'Germline', '']",,MolecularTest -Cell Count,Cell Count,CellCount,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MolecularTest +Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Nuclear Staining', 'FISH', 'Southern Blotting', 'Not Reported', 'Microarray', 'Microsatellite Analysis', 'ISH', 'WXS', 'Flow Cytometry', 'Karyotype', 'unknown', 'Other', 'Not Applicable', 'WGS', 'Targeted Sequencing', 'Comparative Genomic Hybridization', 'RNA Sequencing', 'RT-PCR', 'Cytogenetics NOS', 'Sequencing NOS', 'IHC']",,MolecularTest +AA Change,AA Change,AAChange,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest Loci Abnormal Count,Loci Abnormal Count,LociAbnormalCount,Numeric value used to describe the number of loci determined to be abnormal.,False,,,,MolecularTest -Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Not Reported', 'Comparative Genomic Hybridization', 'Microarray', 'Microsatellite Analysis', 'Not Applicable', 'Southern Blotting', 'unknown', 'Flow Cytometry', 'Nuclear Staining', 'Other', 'WXS', 'WGS', 'ISH', 'FISH', 'Cytogenetics NOS', 'Karyotype', 'RNA Sequencing', 'Sequencing NOS', 'Targeted Sequencing', 'IHC', 'RT-PCR']",,MolecularTest +Chromosome,Chromosome,Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Not Reported', 'chr15', 'chr23', 'chr4', 'chr18', 'chr1', 'chr17', 'chr11', 'unknown', 'chr9', 'chr16', 'chrM', 'chr3', 'chr7', 'chr21', 'chr22', 'chr13', 'chr10', 'chr2', 'chr5', 'chrX', 'chr6', 'chr12', 'chr20', 'chr8', 'chrY', 'chr14', 'chr19', '']",,MolecularTest +Pathogenicity,Pathogenicity,Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,False,,"['Likely Benign', 'Pathogenic', 'Benign', 'Likely Pathogenic', 'Uncertain Significance', '']",,MolecularTest Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,MolecularTest -AA Change,AA Change,AAChange,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Laboratory Test,Laboratory Test,LaboratoryTest,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.",False,,"['Not Reported', 'Segmented Neutrophil', 'Myeloblasts', 'Epstein-Barr Virus', 'Glucose', 'Lymphoblasts', 'unknown', 'Basophil', 'Myelocytes', 'Platelets', 'Kappa', 'Alpha Fetoprotein', 'Lactate Dehydrogenase', 'Luteinizing Hormone', 'Eosinophil', 'Lymphocytes', 'Hematocrit', 'Prolymphocytes', 'Human Chorionic Gonadotropin', 'Immunoglobulin A', 'Albumin', 'Beta 2 Microglobulin', 'Total Bilirubin', 'M Protein', 'Blood Urea Nitrogen', 'Calcium', 'NOS', 'B-cell genotyping', 'Serum Free Immunoglobulin Light Chain', 'Promonocytes', 'Leukocytes', 'Promyelocytes', 'Total Protein', 'Metamyelocytes', 'Hemoglobin', 'Creatinine', 'Human Papillomavirus', 'Immunoglobulin G', 'Immunoglobulin M', 'Neutrophil Bands', 'Lambda', 'C-Reactive Protein', 'Circulating Tumor Cells', 'Testosterone', 'HPV-E6/E7', 'Absolute Neutrophil', 'Cellularity', '']",,MolecularTest Blood Test Normal Range Lower,Blood Test Normal Range Lower,BloodTestNormalRangeLower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest -Pathogenicity,Pathogenicity,Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,False,,"['Likely Benign', 'Benign', 'Likely Pathogenic', 'Uncertain Significance', 'Pathogenic', '']",,MolecularTest -Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Not Reported', 'Heterozygous', 'Hemizygous', 'Nullizygous', 'unknown', 'Homozygous', '']",,MolecularTest -Second Exon,Second Exon,SecondExon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.",False,,,,MolecularTest -Test Analyte Type,Test Analyte Type,TestAnalyteType,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Not Reported', 'Total RNA', 'DNA', 'miRNA', 'unknown', 'Protein Analyte', 'mRNA', '']",,MolecularTest -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MolecularTest -Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,MolecularTest -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MolecularTest -Antigen,Antigen,Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Not Reported', 'CD138', 'CD25', 'CCND1', 'unknown', 'CD19', 'CD5', 'CA-125', 'CD30', 'BCL6', 'CD20', 'Squamous Cell Carcinoma Antigen', 'CD7', 'CD79A', 'CD14', 'CD56', 'NSE', 'CD33', 'CD3', 'CD23', 'CA19-9', 'CD34', 'Mesothelin', 'CD10', 'CD117', 'HLA-DR', 'CD45', 'CD15', 'CD22', 'CEA', '']",,MolecularTest -Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,MolecularTest -Histone Variant,Histone Variant,HistoneVariant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Not Reported', 'H2A.Z.2.2', 'unknown', 'H2A.Z.1', 'H3.5', 'H3t (H3.4)', 'H3.X', 'H2A.Z.2', 'mH2A.1', 'H2A.Z', 'H3.1', 'H2A.X', 'H3.2', 'mH2A', 'mH2A.2', 'CENP-A', 'H3.3', 'H3.Y', 'H2A-Bbd', '']",,MolecularTest -Clinical Biospecimen Type,Clinical Biospecimen Type,ClinicalBiospecimenType,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Not Reported', 'Embryonic Fluid', 'Blood', 'unknown', 'Soft Tissue', 'Connective Tissue', 'Muscle Tissue', 'Skin', 'Peritoneal Fluid', 'Tissue NOS', 'Plasma', 'Bone Marrow', 'Saliva', 'Nerve Tissue', 'Cerebrospinal Fluid', 'Embryonic Tissue', 'Uninvolved Tissue NOS', 'Granulocyte', 'Serum', 'Pleural Fluid', 'Feces', 'Urine', 'Buffy Coat', 'Buccal Mucosa', '']",,MolecularTest -Exon,Exon,Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Intron,Intron,Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",False,,,,MolecularTest +Test Analyte Type,Test Analyte Type,TestAnalyteType,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['DNA', 'Not Reported', 'Protein Analyte', 'mRNA', 'Total RNA', 'unknown', 'miRNA', '']",,MolecularTest +Histone Variant,Histone Variant,HistoneVariant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['H3t (H3.4)', 'CENP-A', 'Not Reported', 'H3.3', 'H3.2', 'H3.5', 'H2A-Bbd', 'H2A.Z.2.2', 'unknown', 'H2A.Z.1', 'H2A.Z', 'H2A.Z.2', 'H3.Y', 'mH2A.2', 'mH2A', 'H3.X', 'H3.1', 'mH2A.1', 'H2A.X', '']",,MolecularTest Test Value,Test Value,TestValue,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,False,,,,MolecularTest -Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,MolecularTest -Copy Number,Copy Number,CopyNumber,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -Second Gene Symbol,Second Gene Symbol,SecondGeneSymbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -Histone Family,Histone Family,HistoneFamily,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.",False,,"['Not Reported', 'H3', 'H2A', 'H2B', 'H1', 'unknown', 'H4', '']",,MolecularTest +Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,MolecularTest +Laboratory Test,Laboratory Test,LaboratoryTest,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.",False,,"['Hematocrit', 'Not Reported', 'C-Reactive Protein', 'Human Chorionic Gonadotropin', 'Glucose', 'Hemoglobin', 'Absolute Neutrophil', 'Human Papillomavirus', 'Leukocytes', 'Immunoglobulin G', 'Promonocytes', 'Lymphoblasts', 'Epstein-Barr Virus', 'Luteinizing Hormone', 'Lactate Dehydrogenase', 'Myeloblasts', 'Platelets', 'Promyelocytes', 'Immunoglobulin A', 'NOS', 'Total Bilirubin', 'Basophil', 'unknown', 'Kappa', 'Myelocytes', 'Albumin', 'Neutrophil Bands', 'Alpha Fetoprotein', 'Total Protein', 'Serum Free Immunoglobulin Light Chain', 'Creatinine', 'Testosterone', 'Calcium', 'Cellularity', 'Lymphocytes', 'B-cell genotyping', 'M Protein', 'Circulating Tumor Cells', 'Blood Urea Nitrogen', 'HPV-E6/E7', 'Immunoglobulin M', 'Eosinophil', 'Metamyelocytes', 'Beta 2 Microglobulin', 'Segmented Neutrophil', 'Prolymphocytes', 'Lambda', '']",,MolecularTest Transcript,Transcript,Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Loci Count,Loci Count,LociCount,Numeric value used to describe the number of loci tested.,False,,,,MolecularTest +Cytoband,Cytoband,Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Not Reported', 'Loss', 'Translocation', 'Mosaicism', 'Duplication', 'Rearrangement', 'Alleles', 'Extension', 'Hypermethylation', 'Insertion', 'Inversion', 'Substitution', 'unknown', 'Other', 'Conversion', 'Deletion-Insertion', 'Chrimerism', 'Repeated Sequences', 'Deletion', 'Methylation', 'Partial Methylation', 'Splice', 'Gain', 'Amplification', '']",,MolecularTest HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MolecularTest -Site Data Source,Site Data Source,SiteDataSource,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",False,,,,Biospecimen -Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,Biospecimen -Percent Lymphocyte Infiltration,Percent Lymphocyte Infiltration,PercentLymphocyteInfiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,False,,,,Biospecimen -Percent Eosinophil Infiltration,Percent Eosinophil Infiltration,PercentEosinophilInfiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,False,,,,Biospecimen +Mismatch Repair Mutation,Mismatch Repair Mutation,MismatchRepairMutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['unknown', 'no', 'yes', 'Not Reported', '']",,MolecularTest +Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['Diploid', 'Not Reported', 'Hyperdiploid', 'Near Diploid', 'Hypodiploid', 'Tetraploid', 'unknown', 'Aneuploid', '']",,MolecularTest +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MolecularTest +Exon,Exon,Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Histone Family,Histone Family,HistoneFamily,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.",False,,"['Not Reported', 'H2B', 'H3', 'H4', 'H1', 'unknown', 'H2A', '']",,MolecularTest +Variant Origin,Variant Origin,VariantOrigin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['unknown', 'Somatic', 'Germline', '']",,MolecularTest Dysplasia Fraction,Dysplasia Fraction,DysplasiaFraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],False,,,,Biospecimen -Mounting Medium,Mounting Medium,MountingMedium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media",False,,"['Not Reported', 'Aqueous water based', 'PBS', 'Antifade without DAPI', 'Antifade with DAPI', 'Non-Aqueous Solvent based', 'unknown', 'Xylene', 'Toluene', '']",,Biospecimen -Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Mouth Rinse Biospecimen Type', 'Urine Biospecimen Type', 'Analyte Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Ascites Biospecimen Type', 'Cells Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Fluids Biospecimen Type', 'Stool Biospecimen Type']",,Biospecimen -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Biospecimen -HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,Biospecimen -Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['Digital', 'Microscopy', 'Other', 'unknown', '']",,Biospecimen +Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Forceps biopsy', 'Biopsy', 'Endoscopic biopsy', 'Other Acquisition Method', 'Not specified', 'Sentinel Node Biopsy', 'Excision', 'Shave Biopsy', 'Non induced sputum', 'Re-excision', 'Fluid collection', 'Blood draw', 'Autopsy', 'Surgical Resection', 'Punch Biopsy', 'Lymphadenectomy - Regional Nodes', 'BAL (bronchial alveolar lavage)', 'Fine Needle Aspirate', 'Cytobrush', 'Core needle biopsy', 'Induced sputum']",,Biospecimen +Number Proliferating Cells,Number Proliferating Cells,NumberProliferatingCells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,False,,,,Biospecimen +Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['PAXgene tissue', 'Unfixed', ""Carnoy's Fixative"", 'Formalin', 'TCL lysis buffer', 'Acetone', 'Dimethylacetamide', 'Glutaraldehyde', 'unknown', 'Other', 'None', 'Carbodiimide', 'Dimidoester', 'Para-benzoquinone', '95% Ethanol', 'Cryo-store', 'NP40 lysis buffer', 'OCT media', 'Alcohol', 'Saline', 'Polaxamer', 'RNAlater', 'Methacarn']",,Biospecimen +Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',True,,,,Biospecimen +Percent Tumor Cells,Percent Tumor Cells,PercentTumorCells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,False,,,,Biospecimen +Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,Biospecimen +Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,Biospecimen +Mounting Medium,Mounting Medium,MountingMedium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media",False,,"['Xylene', 'Not Reported', 'PBS', 'Aqueous water based', 'Antifade with DAPI', 'Non-Aqueous Solvent based', 'Toluene', 'Antifade without DAPI', 'unknown', '']",,Biospecimen Lysis Buffer,Lysis Buffer,LysisBuffer,scRNA-seq specific: Type of lysis buffer used,False,,,,Biospecimen -Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,False,,,,Biospecimen +Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['4C in vacuum chamber', 'Ambient temperature', 'Frozen at -70C', 'Paraffin block', 'Desiccant at 4C', 'Frozen at -20C', 'RNAlater at -20C', 'unknown', 'Not Applicable', 'RNAlater at 4C', 'Refrigerated at 4 degrees', 'Frozen in vapor phase', 'Cut slide', 'Frozen in liquid nitrogen', 'RNAlater at 25C', 'Frozen at -80C', 'Refrigerated vacuum chamber', 'Fresh', 'Frozen at -150C']",,Biospecimen +Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Grid Slides - Hemocytometer', 'Not Reported', 'Adhesive Markers', 'Nuclear Stain - DAPI', 'unknown', 'Other', 'Fluorescent Beads', '']",,Biospecimen +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Biospecimen +Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,Biospecimen +Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['RPMI+Serum', 'PBS+Serum', 'RPMI', 'PBS', 'DMEM', 'DMEM+Serum', 'None', '']",,Biospecimen +Percent Tumor Nuclei,Percent Tumor Nuclei,PercentTumorNuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,False,,,,Biospecimen +Percent Neutrophil Infiltration,Percent Neutrophil Infiltration,PercentNeutrophilInfiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,False,,,,Biospecimen +Percent Lymphocyte Infiltration,Percent Lymphocyte Infiltration,PercentLymphocyteInfiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,False,,,,Biospecimen Percent Normal Cells,Percent Normal Cells,PercentNormalCells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,False,,,,Biospecimen -Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Not Reported', 'Other', 'Sliding microtome', 'Cryosectioning', 'Tissue molds', 'Sectioning', 'unknown', 'Vibratome', '']",,Biospecimen -Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Not Applicable', 'Refrigerated vacuum chamber', 'unknown', 'Ambient temperature', 'Cut slide', 'Frozen at -20C', 'Frozen at -70C', 'RNAlater at -20C', 'Desiccant at 4C', 'Frozen at -150C', '4C in vacuum chamber', 'Paraffin block', 'RNAlater at 25C', 'Fresh', 'Frozen in liquid nitrogen', 'Frozen at -80C', 'Frozen in vapor phase', 'RNAlater at 4C', 'Refrigerated at 4 degrees']",,Biospecimen -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,Biospecimen +Percent Stromal Cells,Percent Stromal Cells,PercentStromalCells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",False,,,,Biospecimen Percent Granulocyte Infiltration,Percent Granulocyte Infiltration,PercentGranulocyteInfiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,False,,,,Biospecimen -Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Not Reported', 'Other', 'Grid Slides - Hemocytometer', 'Fluorescent Beads', 'unknown', 'Nuclear Stain - DAPI', 'Adhesive Markers', '']",,Biospecimen -Percent Tumor Cells,Percent Tumor Cells,PercentTumorCells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,False,,,,Biospecimen +Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Adenocarcinoma in situ - mucinous', 'Persistent melanoma in situ', 'Moderate dysplasia', 'Invasive melanoma - other', 'Melanoma in situ - acral-lentiginous', 'Melanoma in situ - arising in a giant congenital nevus', 'No diagnosis possible', 'Normal WDA', 'Melanoma in situ - superficial spreading', 'Mild dysplasia', 'Squamous metaplasia - mature', 'Invasive melanoma - nevoid', 'Reserve cell hyperplasia', 'Melanoma in situ - lentigo maligna type', 'Severe dysplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Benign tumor NOS', 'Melanoma in situ - not otherwise classified', 'Atypical adenomatous hyperplasia', 'Invasive melanoma - superficial spreading', 'Invasive melanoma - lentigo maligna', 'Squamous Carcinoma in situ', 'Hamartoma', 'Scar - no residual melanoma', 'Atypical melanocytic proliferation', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - desmoplastic', 'Invasive melanoma - acral lentiginous', 'Carcinoma NOS', 'Invasive melanoma - nodular type', '']",,Biospecimen +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,Biospecimen +Site Data Source,Site Data Source,SiteDataSource,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",False,,,,Biospecimen Method of Nucleic Acid Isolation,Method of Nucleic Acid Isolation,MethodofNucleicAcidIsolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",False,,,,Biospecimen -Percent Stromal Cells,Percent Stromal Cells,PercentStromalCells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",False,,,,Biospecimen -Percent Neutrophil Infiltration,Percent Neutrophil Infiltration,PercentNeutrophilInfiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,False,,,,Biospecimen -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Biospecimen -Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',True,,,,Biospecimen +Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,False,,,,Biospecimen +Processing Location,Processing Location,ProcessingLocation,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",False,,,,Biospecimen Percent Inflam Infiltration,Percent Inflam Infiltration,PercentInflamInfiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.",False,,,,Biospecimen -Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,Biospecimen -Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['PBS+Serum', 'PBS', 'RPMI', 'DMEM+Serum', 'None', 'RPMI+Serum', 'DMEM', '']",,Biospecimen -Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,Biospecimen +Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Fluids Biospecimen Type', 'Analyte Biospecimen Type', 'Stool Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Urine Biospecimen Type', 'Blood Biospecimen Type', 'Ascites Biospecimen Type', 'Sputum Biospecimen Type', 'Tissue Biospecimen Type', 'Cells Biospecimen Type', 'Mouth Rinse Biospecimen Type']",,Biospecimen +Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,Biospecimen +Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['unknown', 'Microscopy', 'Other', 'Digital', '']",,Biospecimen +HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,Biospecimen +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Biospecimen +Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['unknown', 'Pathologist', 'Other', 'Research Scientist', '']",,Biospecimen +Percent Eosinophil Infiltration,Percent Eosinophil Infiltration,PercentEosinophilInfiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,False,,,,Biospecimen +Degree of Dysplasia,Degree of Dysplasia,DegreeofDysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,False,,"['Mild dysplasia', 'Moderate dysplasia', 'Carcinoma in Situ', 'unknown', 'Severe dysplasia', 'Normal or basal cell hyperplasia or metaplasia', '']",,Biospecimen +Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Not Reported', 'Tissue molds', 'Sliding microtome', 'Cryosectioning', 'Sectioning', 'unknown', 'Other', 'Vibratome', '']",,Biospecimen Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Biospecimen -Number Proliferating Cells,Number Proliferating Cells,NumberProliferatingCells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,False,,,,Biospecimen -Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['No diagnosis possible', 'Invasive melanoma - superficial spreading', 'Severe dysplasia', 'Invasive melanoma - lentigo maligna', 'Atypical melanocytic proliferation', 'Squamous metaplasia - immature', 'Adenocarcinoma in situ - mucinous', 'Mild dysplasia', 'Atypical adenomatous hyperplasia', 'Scar - no residual melanoma', 'Invasive melanoma - other', 'Squamous metaplasia - mature', 'Melanocytic hyperplasia', 'Invasive melanoma - acral lentiginous', 'Invasive melanoma - desmoplastic', 'Melanoma in situ - acral-lentiginous', 'Reserve cell hyperplasia', 'Benign tumor NOS', 'Invasive melanoma - nevoid', 'Normal WDA', 'Squamous Carcinoma in situ', 'Melanoma in situ - arising in a giant congenital nevus', 'Persistent melanoma in situ', 'Hamartoma', 'Adenocarcinoma in situ - non mucinous', 'Melanoma in situ - not otherwise classified', 'Carcinoma NOS', 'Melanoma in situ - lentigo maligna type', 'Melanoma in situ - superficial spreading', 'Invasive melanoma - nodular type', 'Moderate dysplasia', '']",,Biospecimen -Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Endoscopic biopsy', 'Re-excision', 'Surgical Resection', 'Cytobrush', 'Shave Biopsy', 'Fine Needle Aspirate', 'Autopsy', 'Forceps biopsy', 'Induced sputum', 'BAL (bronchial alveolar lavage)', 'Non induced sputum', 'Core needle biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Lymphadenectomy - Regional Nodes', 'Not specified', 'Biopsy', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Excision']",,Biospecimen -Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['Methacarn', 'unknown', 'Carbodiimide', 'NP40 lysis buffer', 'Other', 'Cryo-store', '95% Ethanol', 'Dimidoester', 'Alcohol', 'Formalin', 'Saline', 'PAXgene tissue', 'Dimethylacetamide', 'Unfixed', 'Acetone', 'OCT media', 'Para-benzoquinone', ""Carnoy's Fixative"", 'Glutaraldehyde', 'Polaxamer', 'None', 'RNAlater', 'TCL lysis buffer']",,Biospecimen -Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,Biospecimen -Percent Tumor Nuclei,Percent Tumor Nuclei,PercentTumorNuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,False,,,,Biospecimen -Degree of Dysplasia,Degree of Dysplasia,DegreeofDysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,False,,"['Severe dysplasia', 'Mild dysplasia', 'unknown', 'Moderate dysplasia', 'Carcinoma in Situ', 'Normal or basal cell hyperplasia or metaplasia', '']",,Biospecimen -Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,Biospecimen -Processing Location,Processing Location,ProcessingLocation,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",False,,,,Biospecimen -Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['Pathologist', 'Other', 'unknown', 'Research Scientist', '']",,Biospecimen -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['Liquid Nitrogen', 'Warm Ischemia', 'Negative -20C', 'Cold Ischemia', 'Dry Ice', 'unknown', 'Ambient air', '4C wet ice', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Metastatic', 'Normal adjacent', 'Recurrent', 'Post therapy', 'Normal distant', 'Primary', 'Post therapy adjuvant', 'Not analyzed', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Premalignant - in situ', 'Normal', 'Premalignant', 'Post therapy neoadjuvant', 'Additional Primary', 'Local recurrence', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Not Reported', 'OCT', 'Negative 80 Deg C', 'Cryopreservation in liquid nitrogen - live cells', 'unknown', 'Formalin fixed-buffered', 'Liquid Nitrogen', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Cryopreservation in liquid nitrogen - dead tissue', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed paraffin embedded - FFPE', 'Cryopreserved', 'Fresh dissociated', 'Fresh', 'Cryopreservation in dry ice - dead tissue', 'Fresh dissociated and single cell sorted', 'Formalin fixed-unbuffered', 'Snap Frozen', 'Methacarn fixed paraffin embedded - MFPE', 'Frozen', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Not Applicable', 'unknown', 'Bilateral', 'Right', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen -Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Liquid Nitrogen', 'Cold Pack', 'Ambient Pack', 'Ice Pack', 'Not Shipped', 'Dry Ice', 'Other Shipping Environment', 'Specimen at Room Temperature', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",Biospecimen -Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen +Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,Biospecimen +Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",Biospecimen +Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Dry Ice', 'Not Shipped', 'Other Shipping Environment', 'Liquid Nitrogen', 'Ambient Pack', 'Specimen at Room Temperature', 'Ice Pack', 'Cold Pack', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",Biospecimen +Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Uncharged', 'Not applicable', 'Charged', 'Coverslip', 'Other', '']","['Biospecimen is ""Analyte""']",Biospecimen +Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,True,,"['Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",Biospecimen -Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Coverslip', 'Other', 'Not applicable', 'Uncharged', 'Charged', '']","['Biospecimen is ""Analyte""']",Biospecimen -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['cDNA Libraries Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'cfDNA Analyte', 'Plasma', 'DNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'Serum Analyte', 'protein', 'PBMCs', 'lipid', 'metabolite', 'RNA Analyte', 'Tissue Section Analyte', '']","['Biospecimen is ""Analyte""']",Biospecimen -Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['Tissue Block Analyte', 'metabolite', 'lipid', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'cDNA Libraries Analyte', 'Serum Analyte', 'PBMCs', 'protein', 'DNA Analyte', 'Tissue Section Analyte', 'Plasma', '']","['Biospecimen is ""Analyte""']",Biospecimen +Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen +Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['Dry Ice', '4C wet ice', 'Warm Ischemia', 'Liquid Nitrogen', 'Ambient air', 'Negative -20C', 'unknown', 'Cold Ischemia', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Ventricle NOS', 'Adrenal gland NOS', 'Upper lobe lung', 'Choroid', 'Pleura NOS', 'External lip NOS', 'Overlapping lesion of biliary tract', 'Waldeyer ring', 'Commissure of lip', 'Overlapping lesion of pancreas', 'Vertebral column', 'Overlapping lesion of lung', 'Nervous system NOS', 'Other ill-defined sites', 'Overlapping lesion of eye and adnexa', 'Duodenum', 'Temporal lobe', 'Lymph nodes of multiple regions', 'Head face or neck NOS', 'unknown primary site', 'Extrahepatic bile duct', 'Bone marrow', 'Meninges NOS', 'Bladder neck', 'Head of pancreas', 'Overlapping lesion of vulva', 'Eyelid', 'Brain stem', 'Tonsillar pillar', 'Anterior surface of epiglottis', 'Female genital tract NOS', 'Ascending colon', 'Supraglottis', 'Overlapping lesion of floor of mouth', 'Upper limb NOS', 'Lacrimal gland', 'Tongue NOS', 'Corpus uteri', 'Ileum', 'Mucosa of lower lip', 'Submandibular gland', 'Thymus', 'Descended testis', 'Overlapping lesion of esophagus', 'Spleen', 'Scrotum NOS', 'Posterior wall of nasopharynx', 'Overlapping lesion of palate', 'Orbit NOS', 'Vagina NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Lower lobe lung', 'Pituitary gland', 'Round ligament', 'Nasal cavity', 'Overlapping lesion of skin', 'Male genital organs NOS', 'Bone of limb NOS', 'Overlapping lesion of hypopharynx', 'Sublingual gland', 'Cerebrum', 'Ventral surface of tongue NOS', 'Intestinal tract NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Mandible', 'Pylorus', 'Pancreatic duct', 'External upper lip', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Abdomen NOS', 'Short bones of lower limb and associated joints', 'Overlapping lesion of nasopharynx', 'Mouth NOS', 'Ureteric orifice', 'Colon NOS', 'Cheek mucosa', 'Pancreas NOS', 'Lower-inner quadrant of breast', 'Retina', 'Renal pelvis', 'Posterior wall of bladder', 'Lymph nodes of inguinal region or leg', 'Penis NOS', 'Clitoris', 'Superior wall of nasopharynx', 'Ovary', 'Tail of pancreas', 'Cloacogenic zone', 'Isthmus uteri', 'Retromolar area', 'Undescended testis', 'Eye NOS', 'skin NOS', 'Lesser curvature of stomach NOS', 'Lower-outer quadrant of breast', 'Mucosa of upper lip', 'Skin of lip NOS', 'Gastrointestinal tract NOS', 'Spinal meninges', 'Anterior mediastinum', 'Paraspinal', 'Overlapping lesion of retroperitoneum and peritoneum', 'Floor of mouth NOS', 'unknown', 'Urachus', 'External ear', 'Lymph nodes of head face and neck', 'Specified parts of peritoneum', 'Optic nerve', 'Other specified parts of pancreas', 'Posterior mediastinum', 'Tonsillar fossa', 'Overlapping lesion of tongue', 'Mucosa of lip NOS', 'Kidney NOS', 'Upper-inner quadrant of breast', 'Mediastinum NOS', 'Overlapping lesion of heart mediastinum and pleura', 'Axillary tail of breast', 'Overlapping lesion of corpus uteri', 'Gastric antrum', 'Body of stomach', 'Overlapping lesion of tonsil', 'Uterine adnexa', 'Lateral floor of mouth', 'Labium minus', 'Middle lobe lung', 'Medulla of adrenal gland', 'Lower limb NOS', 'Hard palate', 'Body of penis', 'Overlapping lesion of digestive system', 'Overlapping lesion of other and unspecified parts of mouth', 'Lower gum', 'Overlapping lesion of rectum anus and anal canal', 'Hypopharynx NOS', 'Overlapping lesion of female genital organs', 'Skin of other and unspecified parts of face', 'Glans penis', 'Accessory sinus NOS', 'Overlapping lesion of endocrine glands and related structures', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Bones of skull and face and associated joints', 'Vestibule of mouth', 'Border of tongue', 'Parametrium', 'Ciliary body', 'Soft palate NOS', 'Overlapping lesion of cervix uteri', 'Gum NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Skin of trunk', 'Cranial nerve NOS', 'Ampulla of Vater', 'Palate NOS', 'Pineal gland', 'Lymph nodes of axilla or arm', 'Base of tongue NOS', 'Middle ear', 'Breast NOS', 'Parietal lobe', 'Frontal sinus', 'Overlapping lesion of larynx', 'Retroperitoneum', 'Paraurethral gland', 'Overlapping lesion of urinary organs', 'Connective subcutaneous and other soft tissues NOS', 'Lateral wall of oropharynx', 'Main bronchus', 'Liver', 'Lip NOS', 'Biliary tract NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Anterior 2/3 of tongue NOS', 'Skin of scalp and neck', 'Short bones of upper limb and associated joints', 'Jejunum', 'Overlapping lesion of ill-defined sites', 'Sphenoid sinus', 'Urethra', 'Trachea', 'Hematopoietic system NOS', 'Fallopian tube', 'Cerebellum NOS', 'Carotid body', 'Other specified parts of male genital organs', 'Connective subcutaneous and other soft tissues of abdomen', 'skin of upper limb and shoulder', 'Not Reported', 'Lateral wall of nasopharynx', 'Endocrine gland NOS', 'Heart', 'Dorsal surface of tongue NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Central portion of breast', 'Endometrium', 'Appendix', 'Cerebral meninges', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peritoneum NOS', 'Craniopharyngeal duct', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Ethmoid sinus', 'Exocervix', 'Pharynx NOS', 'Anal canal', 'Aortic body and other paraganglia', 'Labium majus', 'Lingual tonsil', 'Ill-defined sites within respiratory system', 'Lower third of esophagus', 'Overlapping lesion of bones joints and articular cartilage', 'Rectosigmoid junction', 'Placenta', 'Bone NOS', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lateral wall of bladder', 'Cecum', 'Parathyroid gland', 'Cortex of adrenal gland', 'Upper-outer quadrant of breast', 'Vulva NOS', 'Prepuce', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Greater curvature of stomach NOS', 'Autonomic nervous system NOS', 'Nasopharynx NOS', 'Anus NOS', 'Overlapping lesion of male genital organs', 'Descending colon', 'Long bones of lower limb and associated joints', 'Urinary system NOS', 'Cardia NOS', 'Lung NOS', 'Frontal lobe', 'Thoracic esophagus', 'Overlapping lesion of lip', 'Cervical esophagus', 'Uterus NOS', 'Major salivary gland NOS', 'Maxillary sinus', 'Intrathoracic lymph nodes', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Posterior wall of oropharynx', 'Epididymis', 'Spermatic cord', 'Pelvic lymph nodes', 'Dome of bladder', 'Middle third of esophagus', 'Pelvis NOS', 'Tonsil NOS', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cervix uteri', 'Nipple', 'Conjunctiva', 'Olfactory nerve', 'Fundus uteri', 'Anterior floor of mouth', 'Oropharynx NOS', 'Meckel diverticulum', 'Esophagus NOS', 'Intra-abdominal lymph nodes', 'Lymph node NOS', 'Small intestine NOS', 'Brain NOS', 'Overlapping lesion of major salivary glands', 'Vallecula', 'Upper gum', 'Overlapping lesion of small intestine', 'Overlapping lesion of breast', 'Anterior wall of nasopharynx', 'Cauda equina', 'Myometrium', 'skin of lower limb and hip', 'Overlapping lesion of accessory sinuses', 'Hypopharyngeal aspect of aryepiglottic fold', 'Hepatic flexure of colon', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Overlapping lesion of stomach', 'Postcricoid region', 'Uvula', 'Splenic flexure of colon', 'Overlapping lesion of bladder', 'Glottis', 'Pyriform sinus', 'Thorax NOS', 'Trigone of bladder', 'Fundus of stomach', 'Abdominal esophagus', 'Posterior wall of hypopharynx', 'Overlapping lesion of penis', 'Connective subcutaneous and other soft tissues of thorax', 'Blood', 'Body of pancreas', 'Bladder NOS', 'Occipital lobe', 'Intrahepatic bile duct', 'Spinal cord', 'Laryngeal cartilage', 'Transverse colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sigmoid colon', 'Cornea NOS', 'Prostate gland', 'Endocervix', 'Overlapping lesions of oropharynx', 'Overlapping lesion of colon', 'Upper respiratory tract NOS', 'Islets of Langerhans', 'Broad ligament', 'Parotid gland', 'Anterior wall of bladder', 'Rib sternum clavicle and associated joints', 'Long bones of upper limb scapula and associated joints', 'Gallbladder', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Upper third of esophagus', 'Other specified parts of female genital organs', 'Thyroid gland', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of pelvis', 'Reticuloendothelial system NOS', 'Acoustic nerve', 'Larynx NOS', 'Stomach NOS', 'Testis NOS', 'External lower lip', 'Subglottis', 'Ureter', 'Overlapping lesion of brain', 'Rectum NOS', '']","['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen +Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Fresh dissociated and single cell sorted', 'Not Reported', 'Cryopreservation in liquid nitrogen - live cells', 'Formalin fixed-unbuffered', 'OCT', 'Cryopreservation in dry ice - dead tissue', 'unknown', 'Formalin fixed paraffin embedded - FFPE', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Frozen', 'Liquid Nitrogen', 'Cryopreserved', 'Snap Frozen', 'Formalin fixed-buffered', 'Fresh dissociated', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE', 'Cryopreservation in liquid nitrogen - dead tissue', 'Fresh', 'Fresh dissociated and single cell sorted into plates', '']","['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",Biospecimen -Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'mL', 'square centimeter', '']",,Biospecimen -Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['mm', 'cm', '']",,Biospecimen -Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,SRRSBiospecimen -Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Mouth Rinse Biospecimen Type', 'Urine Biospecimen Type', 'Analyte Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Ascites Biospecimen Type', 'Cells Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Fluids Biospecimen Type', 'Stool Biospecimen Type']",,SRRSBiospecimen -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSBiospecimen -HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,SRRSBiospecimen -Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Not Applicable', 'Refrigerated vacuum chamber', 'unknown', 'Ambient temperature', 'Cut slide', 'Frozen at -20C', 'Frozen at -70C', 'RNAlater at -20C', 'Desiccant at 4C', 'Frozen at -150C', '4C in vacuum chamber', 'Paraffin block', 'RNAlater at 25C', 'Fresh', 'Frozen in liquid nitrogen', 'Frozen at -80C', 'Frozen in vapor phase', 'RNAlater at 4C', 'Refrigerated at 4 degrees']",,SRRSBiospecimen -Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSBiospecimen -Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Not Reported', 'OCT', 'Negative 80 Deg C', 'Cryopreservation in liquid nitrogen - live cells', 'unknown', 'Formalin fixed-buffered', 'Liquid Nitrogen', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Cryopreservation in liquid nitrogen - dead tissue', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed paraffin embedded - FFPE', 'Cryopreserved', 'Fresh dissociated', 'Fresh', 'Cryopreservation in dry ice - dead tissue', 'Fresh dissociated and single cell sorted', 'Formalin fixed-unbuffered', 'Snap Frozen', 'Methacarn fixed paraffin embedded - MFPE', 'Frozen']",,SRRSBiospecimen -Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['C25.0', 'C31.9', 'C11.3', 'C53.0', 'C51.2', 'C68.8', 'C38.2', 'C57.9', 'C71.5', 'C02.3', 'C57.3', 'C74.1', 'C11.8', 'C03.9', 'C62.1', 'C38.8', 'C31.3', 'C05.2', 'C08.0', 'C21.2', 'C69.8', 'C49.1', 'C57.2', 'C24.9', 'C72.8', 'C51.0', 'C51.1', 'C42.3', 'C62.9', 'C56.9', 'C71.1', 'C75.3', 'C02.8', 'C70.0', 'C34.3', 'C49.2', 'C17.2', 'C69.0', 'C73.9', 'C39.0', 'C69.1', 'C00.5', 'C49.5', 'C50.1', 'C60.9', 'C75.8', 'C16.4', 'C06.9', 'C11.9', 'C09.8', 'C00.1', 'C60.2', 'C41.2', 'C69.6', 'C12.9', 'C68.9', 'C22.0', 'C02.1', 'C74.0', 'C68.0', 'C47.0', 'C38.3', 'C54.0', 'C24.8', 'C20.9', 'C32.3', 'C71.6', 'C08.1', 'C63.1', 'C41.3', 'C53.1', 'C32.8', 'C48.1', 'C54.8', 'C02.9', 'C40.3', 'C76.3', 'C25.8', 'C76.8', 'C50.8', 'C44.5', 'C30.1', 'C70.9', 'C71.7', 'C38.1', 'C18.1', 'C50.6', 'C13.9', 'C25.7', 'C00.0', 'C11.0', 'C00.2', 'C54.3', 'C13.0', 'C77.0', 'C26.9', 'C40.8', 'C47.9', 'C00.4', 'C77.4', 'C00.8', 'C75.2', 'C41.9', 'C74.9', 'C69.9', 'C52.9', 'C39.9', 'C72.5', 'C18.0', 'C47.6', 'C76.4', 'C10.0', 'C16.6', 'C10.9', 'C76.1', 'C47.1', 'C67.1', 'C48.0', 'C49.8', 'C05.8', 'C34.0', 'C15.4', 'C14.2', 'C16.9', 'C00.6', 'C04.9', 'C51.8', 'C72.1', 'C11.1', 'C49.4', 'C72.4', 'C50.4', 'C63.2', 'C14.8', 'C18.8', 'C50.5', 'C34.1', 'C67.8', 'C19.9', 'C49.6', 'C04.8', 'C18.3', 'C60.8', 'C16.5', 'C75.9', 'C17.8', 'C32.2', 'C67.2', 'C21.1', 'C18.4', 'C08.9', 'C77.2', 'C62.0', 'C16.0', 'C65.9', 'C04.0', 'C25.9', 'C18.6', 'C47.5', 'C15.8', 'C75.4', 'C40.1', 'C13.2', 'C03.1', 'C71.4', 'C31.8', 'C49.3', 'C25.1', 'C06.1', 'C41.0', 'C75.1', 'C67.4', 'C05.9', 'C18.5', 'C01.9', 'C63.8', 'C72.9', 'C47.4', 'C25.3', 'C38.0', 'C60.0', 'C14.0', 'C77.5', 'C44.2', 'C18.7', 'C26.8', 'C39.8', 'C10.4', 'C76.7', 'C50.2', 'C44.1', 'C71.0', 'C63.9', 'C17.0', 'C05.1', 'C44.3', 'C71.2', 'C53.8', 'C26.0', 'C72.3', 'C71.9', 'C17.1', 'C24.0', 'C77.1', 'C44.4', 'C25.2', 'C42.0', 'C04.1', 'C15.5', 'C69.5', 'C40.0', 'C18.9', 'C38.4', 'C17.9', 'C49.0', 'C49.9', 'C76.0', 'C31.1', 'C40.9', 'C17.3', 'C47.3', 'C44.7', 'C09.1', 'C68.1', 'Not Reported', 'C13.8', 'C57.8', 'C50.0', 'C03.0', 'C44.0', 'unknown', 'C21.0', 'C69.2', 'C50.3', 'C32.1', 'C77.9', 'C34.8', 'C09.9', 'C64.9', 'C71.8', 'C57.0', 'C24.1', 'C16.2', 'C11.2', 'C77.8', 'C63.7', 'C77.3', 'C21.8', 'C02.0', 'C08.8', 'C67.7', 'C70.1', 'C41.4', 'C41.8', 'C53.9', 'C06.8', 'C15.3', 'C15.1', 'C32.0', 'C37.9', 'C60.1', 'C25.4', 'C34.2', 'C10.2', 'C47.2', 'C57.7', 'C33.9', 'C05.0', 'C69.4', 'C72.0', 'C06.2', 'C15.2', 'C75.0', 'C67.0', 'C22.1', 'C16.3', 'C42.2', 'C09.0', 'C13.1', 'C54.1', 'C47.8', 'C67.9', 'C72.2', 'C42.4', 'C10.1', 'C41.1', 'C32.9', 'C54.2', 'C76.2', 'C15.9', 'C23.9', 'C80.9', 'C76.5', 'C69.3', 'C10.8', 'C63.0', 'C51.9', 'C57.4', 'C02.2', 'C15.0', 'C34.9', 'C48.8', 'C44.6', 'C71.3', 'C54.9', 'C31.0', 'C48.2', 'C50.9', 'C07.9', 'C06.0', 'C67.6', 'C57.1', 'C00.3', 'C42.1', 'C02.4', 'C16.1', 'C75.5', 'C31.2', 'C61.9', 'C10.3', 'C18.2', 'C30.0', 'C55.9', 'C16.8', 'C66.9', '']",,SRRSBiospecimen -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSBiospecimen +Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Right', 'Bilateral', 'unknown', 'Left', 'Not Applicable', '']","['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen +Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen +Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Not analyzed', 'Primary', 'Metastatic', 'Normal distant', 'Premalignant - in situ', 'Local recurrence', 'Recurrent', 'Normal adjacent', 'Normal', 'Post therapy adjuvant', 'Not Otherwise Specified', 'Post therapy', 'Additional Primary', 'Atypia - hyperplasia', 'Post therapy neoadjuvant', 'Premalignant', '']","['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen +Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen +Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",Biospecimen +Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['cm', 'mm', '']",,Biospecimen +Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'square centimeter', 'mL', '']",,Biospecimen +Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['Not Reported', 'skin of palm', 'Peri-tumoral Airway', 'skin of abdomen', 'skin of sole', 'skin of chest', 'Hilar Airway', 'skin of lip', 'skin of nose', 'skin of lower limb and hip', 'skin of scrotum', 'skin of other parts of face', 'Skin of trunk', 'skin of vulva', 'skin of neck', 'skin of eye lid', 'skin of breast', 'skin of back', 'skin of penis', 'skin of ear', 'skin NOS', 'skin of upper limb and shoulder', 'skin of scalp', '']",,SRRSBiospecimen +Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Forceps biopsy', 'Biopsy', 'Endoscopic biopsy', 'Other Acquisition Method', 'Not specified', 'Sentinel Node Biopsy', 'Excision', 'Shave Biopsy', 'Non induced sputum', 'Re-excision', 'Fluid collection', 'Blood draw', 'Autopsy', 'Surgical Resection', 'Punch Biopsy', 'Lymphadenectomy - Regional Nodes', 'BAL (bronchial alveolar lavage)', 'Fine Needle Aspirate', 'Cytobrush', 'Core needle biopsy', 'Induced sputum']",,SRRSBiospecimen +Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['PAXgene tissue', 'Unfixed', ""Carnoy's Fixative"", 'Formalin', 'TCL lysis buffer', 'Acetone', 'Dimethylacetamide', 'Glutaraldehyde', 'unknown', 'Other', 'None', 'Carbodiimide', 'Dimidoester', 'Para-benzoquinone', '95% Ethanol', 'Cryo-store', 'NP40 lysis buffer', 'OCT media', 'Alcohol', 'Saline', 'Polaxamer', 'RNAlater', 'Methacarn']",,SRRSBiospecimen Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',True,,,,SRRSBiospecimen -Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,SRRSBiospecimen -Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['PBS+Serum', 'PBS', 'RPMI', 'DMEM+Serum', 'None', 'RPMI+Serum', 'DMEM', '']",,SRRSBiospecimen -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSBiospecimen -Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",True,,,,SRRSBiospecimen -Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['No diagnosis possible', 'Invasive melanoma - superficial spreading', 'Severe dysplasia', 'Invasive melanoma - lentigo maligna', 'Atypical melanocytic proliferation', 'Squamous metaplasia - immature', 'Adenocarcinoma in situ - mucinous', 'Mild dysplasia', 'Atypical adenomatous hyperplasia', 'Scar - no residual melanoma', 'Invasive melanoma - other', 'Squamous metaplasia - mature', 'Melanocytic hyperplasia', 'Invasive melanoma - acral lentiginous', 'Invasive melanoma - desmoplastic', 'Melanoma in situ - acral-lentiginous', 'Reserve cell hyperplasia', 'Benign tumor NOS', 'Invasive melanoma - nevoid', 'Normal WDA', 'Squamous Carcinoma in situ', 'Melanoma in situ - arising in a giant congenital nevus', 'Persistent melanoma in situ', 'Hamartoma', 'Adenocarcinoma in situ - non mucinous', 'Melanoma in situ - not otherwise classified', 'Carcinoma NOS', 'Melanoma in situ - lentigo maligna type', 'Melanoma in situ - superficial spreading', 'Invasive melanoma - nodular type', 'Moderate dysplasia', '']",,SRRSBiospecimen -Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Endoscopic biopsy', 'Re-excision', 'Surgical Resection', 'Cytobrush', 'Shave Biopsy', 'Fine Needle Aspirate', 'Autopsy', 'Forceps biopsy', 'Induced sputum', 'BAL (bronchial alveolar lavage)', 'Non induced sputum', 'Core needle biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Lymphadenectomy - Regional Nodes', 'Not specified', 'Biopsy', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Excision']",,SRRSBiospecimen -Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['Methacarn', 'unknown', 'Carbodiimide', 'NP40 lysis buffer', 'Other', 'Cryo-store', '95% Ethanol', 'Dimidoester', 'Alcohol', 'Formalin', 'Saline', 'PAXgene tissue', 'Dimethylacetamide', 'Unfixed', 'Acetone', 'OCT media', 'Para-benzoquinone', ""Carnoy's Fixative"", 'Glutaraldehyde', 'Polaxamer', 'None', 'RNAlater', 'TCL lysis buffer']",,SRRSBiospecimen Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,SRRSBiospecimen -Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['Liquid Nitrogen', 'Warm Ischemia', 'Negative -20C', 'Cold Ischemia', 'Dry Ice', 'unknown', 'Ambient air', '4C wet ice', '']",,SRRSBiospecimen +Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['4C in vacuum chamber', 'Ambient temperature', 'Frozen at -70C', 'Paraffin block', 'Desiccant at 4C', 'Frozen at -20C', 'RNAlater at -20C', 'unknown', 'Not Applicable', 'RNAlater at 4C', 'Refrigerated at 4 degrees', 'Frozen in vapor phase', 'Cut slide', 'Frozen in liquid nitrogen', 'RNAlater at 25C', 'Frozen at -80C', 'Refrigerated vacuum chamber', 'Fresh', 'Frozen at -150C']",,SRRSBiospecimen +Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",True,,,,SRRSBiospecimen +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSBiospecimen +Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,SRRSBiospecimen +Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['RPMI+Serum', 'PBS+Serum', 'RPMI', 'PBS', 'DMEM', 'DMEM+Serum', 'None', '']",,SRRSBiospecimen +Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['Dry Ice', '4C wet ice', 'Warm Ischemia', 'Liquid Nitrogen', 'Ambient air', 'Negative -20C', 'unknown', 'Cold Ischemia', '']",,SRRSBiospecimen Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,,,,SRRSBiospecimen -Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['Not Reported', 'skin of penis', 'skin of nose', 'skin of neck', 'skin of breast', 'skin of upper limb and shoulder', 'skin of vulva', 'skin NOS', 'skin of back', 'skin of abdomen', 'Peri-tumoral Airway', 'Skin of trunk', 'skin of palm', 'skin of eye lid', 'skin of sole', 'skin of chest', 'skin of lower limb and hip', 'skin of lip', 'Hilar Airway', 'skin of scalp', 'skin of other parts of face', 'skin of scrotum', 'skin of ear', '']",,SRRSBiospecimen -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Spinal meninges', 'Palate NOS', 'Body of pancreas', 'Biliary tract NOS', 'Small intestine NOS', 'Bone marrow', 'Lower limb NOS', 'Trigone of bladder', 'Liver', 'Intestinal tract NOS', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Waldeyer ring', 'Lung NOS', 'External lip NOS', 'Connective subcutaneous and other soft tissues of abdomen', 'Cervix uteri', 'Overlapping lesion of endocrine glands and related structures', 'Thoracic esophagus', 'Round ligament', 'Greater curvature of stomach NOS', 'Ileum', 'Connective subcutaneous and other soft tissues of thorax', 'Cortex of adrenal gland', 'Splenic flexure of colon', 'Endometrium', 'Intrathoracic lymph nodes', 'Lateral wall of oropharynx', 'Pharynx NOS', 'Blood', 'Overlapping lesion of breast', 'Overlapping lesion of biliary tract', 'Paraurethral gland', 'Glans penis', 'Anus NOS', 'Posterior wall of nasopharynx', 'Parietal lobe', 'unknown primary site', 'Anterior wall of nasopharynx', 'Ampulla of Vater', 'Lateral wall of nasopharynx', 'Subglottis', 'Head face or neck NOS', 'Anterior wall of bladder', 'Head of pancreas', 'Lip NOS', 'Myometrium', 'Cerebrum', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Peripheral nerves and autonomic nervous system of thorax', 'Overlapping lesion of small intestine', 'Other specified parts of female genital organs', 'Overlapping lesion of rectum anus and anal canal', 'Pineal gland', 'Lymph node NOS', 'Acoustic nerve', 'Middle ear', 'External ear', 'Overlapping lesion of penis', 'Long bones of upper limb scapula and associated joints', 'Anterior surface of epiglottis', 'Overlapping lesion of skin', 'Overlapping lesion of eye and adnexa', 'Pelvic bones sacrum coccyx and associated joints', 'Body of penis', 'Lower-inner quadrant of breast', 'Central portion of breast', 'Vertebral column', 'Thymus', 'Overlapping lesion of larynx', 'Female genital tract NOS', 'Penis NOS', 'Pancreatic duct', 'Anterior mediastinum', 'Overlapping lesion of esophagus', 'Pyriform sinus', 'Gastrointestinal tract NOS', 'Axillary tail of breast', 'Retina', 'Extrahepatic bile duct', 'Lower third of esophagus', 'Tongue NOS', 'Orbit NOS', 'Overlapping lesion of vulva', 'Frontal sinus', 'Connective subcutaneous and other soft tissues NOS', 'Lower gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cornea NOS', 'Bladder NOS', 'Overlapping lesion of brain and central nervous system', 'Long bones of lower limb and associated joints', 'Sphenoid sinus', 'Main bronchus', 'Bladder neck', 'Lateral wall of bladder', 'Major salivary gland NOS', 'Overlapping lesion of cervix uteri', 'Overlapping lesion of tongue', 'Upper gum', 'Intra-abdominal lymph nodes', 'Oropharynx NOS', 'Tail of pancreas', 'Autonomic nervous system NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Body of stomach', 'Trachea', 'Overlapping lesion of brain', 'Vestibule of mouth', 'Prostate gland', 'Breast NOS', 'Epididymis', 'Overlapping lesion of stomach', 'Pelvic lymph nodes', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Urachus', 'Aortic body and other paraganglia', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Mucosa of lower lip', 'Tonsil NOS', 'Fundus uteri', 'Choroid', 'Other specified parts of pancreas', 'Overlapping lesion of palate', 'Cerebral meninges', 'External upper lip', 'Uvula', 'Gum NOS', 'Bone NOS', 'Lymph nodes of multiple regions', 'Cranial nerve NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Brain NOS', 'Abdominal esophagus', 'Pancreas NOS', 'Descending colon', 'Anterior 2/3 of tongue NOS', 'Branchial cleft', 'Peritoneum NOS', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Rectum NOS', 'Cloacogenic zone', 'Submandibular gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Cheek mucosa', 'Retromolar area', 'Anterior floor of mouth', 'Lesser curvature of stomach NOS', 'Temporal lobe', 'Mandible', 'Vagina NOS', 'Thorax NOS', 'Lymph nodes of head face and neck', 'Abdomen NOS', 'Urethra', 'Optic nerve', 'Labium majus', 'Overlapping lesion of pancreas', 'skin of upper limb and shoulder', 'Tonsillar pillar', 'Overlapping lesion of digestive system', 'Parathyroid gland', 'Craniopharyngeal duct', 'Overlapping lesion of corpus uteri', 'Lingual tonsil', 'Ovary', 'Undescended testis', 'Endocervix', 'Lymph nodes of axilla or arm', 'Hypopharyngeal aspect of aryepiglottic fold', 'Dome of bladder', 'Thyroid gland', 'Ascending colon', 'Overlapping lesion of floor of mouth', 'Spermatic cord', 'Pelvis NOS', 'Cervical esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Broad ligament', 'Nasopharynx NOS', 'Parametrium', 'Nipple', 'Occipital lobe', 'Bone of limb NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Eyelid', 'Gallbladder', 'Dorsal surface of tongue NOS', 'Skin of scalp and neck', 'Carotid body', 'Upper lobe lung', 'Cerebellum NOS', 'Hypopharynx NOS', 'Overlapping lesion of colon', 'Male genital organs NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Accessory sinus NOS', 'Hard palate', 'Overlapping lesion of retroperitoneum and peritoneum', 'Mucosa of upper lip', 'Colon NOS', 'Upper limb NOS', 'Ventral surface of tongue NOS', 'Middle third of esophagus', 'Laryngeal cartilage', 'Adrenal gland NOS', 'Olfactory nerve', 'Gastric antrum', 'Mucosa of lip NOS', 'Overlapping lesion of tonsil', 'Overlapping lesions of oropharynx', 'Ureter', 'Maxillary sinus', 'Posterior wall of oropharynx', 'skin of lower limb and hip', 'Paraspinal', 'Overlapping lesion of heart mediastinum and pleura', 'Connective subcutaneous and other soft tissues of head face and neck', 'Not Reported', 'Other ill-defined sites', 'External lower lip', 'unknown', 'Cauda equina', 'Base of tongue NOS', 'Rib sternum clavicle and associated joints', 'Descended testis', 'Lateral floor of mouth', 'Conjunctiva', 'Peripheral nerves and autonomic nervous system of pelvis', 'Clitoris', 'Hepatic flexure of colon', 'Parotid gland', 'Other specified parts of male genital organs', 'Overlapping lesion of ill-defined sites', 'Lower-outer quadrant of breast', 'Nervous system NOS', 'Overlapping lesion of accessory sinuses', 'Endocrine gland NOS', 'Superior wall of nasopharynx', 'Exocervix', 'Labium minus', 'Tonsillar fossa', 'Spinal cord', 'Frontal lobe', 'Overlapping lesion of hypopharynx', 'Stomach NOS', 'Posterior mediastinum', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Glottis', 'Pleura NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Esophagus NOS', 'Jejunum', 'Bones of skull and face and associated joints', 'Placenta', 'Ethmoid sinus', 'Fundus of stomach', 'Pylorus', 'Larynx NOS', 'Medulla of adrenal gland', 'Transverse colon', 'Uterus NOS', 'Soft palate NOS', 'Cardia NOS', 'Corpus uteri', 'skin NOS', 'Short bones of lower limb and associated joints', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sublingual gland', 'Scrotum NOS', 'Appendix', 'Hematopoietic system NOS', 'Rectosigmoid junction', 'Islets of Langerhans', 'Lacrimal gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Posterior wall of bladder', 'Posterior wall of hypopharynx', 'Commissure of lip', 'Short bones of upper limb and associated joints', 'Floor of mouth NOS', 'Mediastinum NOS', 'Overlapping lesion of bladder', 'Ventricle NOS', 'Lower lobe lung', 'Skin of lip NOS', 'Kidney NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of major salivary glands', 'Vulva NOS', 'Upper third of esophagus', 'Sigmoid colon', 'Duodenum', 'Ureteric orifice', 'Lymph nodes of inguinal region or leg', 'Overlapping lesion of urinary organs', 'Upper respiratory tract NOS', 'Intrahepatic bile duct', 'Retroperitoneum', 'Vallecula', 'Middle lobe lung', 'Urinary system NOS', 'Postcricoid region', 'Supraglottis', 'Eye NOS', 'Anal canal', 'Meninges NOS', 'Upper-inner quadrant of breast', 'Spleen', 'Overlapping lesion of lung', 'Uterine adnexa', 'Specified parts of peritoneum', 'Prepuce', 'Upper-outer quadrant of breast', 'Nasal cavity', 'Cecum', 'Isthmus uteri', 'Testis NOS', 'Fallopian tube', 'Overlapping lesion of lip', 'Skin of other and unspecified parts of face', 'Mouth NOS', 'Renal pelvis', 'Overlapping lesion of male genital organs', 'Meckel diverticulum', 'Reticuloendothelial system NOS', 'Skin of trunk', 'Brain stem', 'Ill-defined sites within respiratory system', 'Border of tongue', 'Heart', 'Ciliary body', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Metastatic', 'Normal adjacent', 'Recurrent', 'Post therapy', 'Normal distant', 'Primary', 'Post therapy adjuvant', 'Not analyzed', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Premalignant - in situ', 'Normal', 'Premalignant', 'Post therapy neoadjuvant', 'Additional Primary', 'Local recurrence', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Not Applicable', 'unknown', 'Bilateral', 'Right', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen -Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Liquid Nitrogen', 'Cold Pack', 'Ambient Pack', 'Ice Pack', 'Not Shipped', 'Dry Ice', 'Other Shipping Environment', 'Specimen at Room Temperature', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",SRRSBiospecimen -Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen +Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Adenocarcinoma in situ - mucinous', 'Persistent melanoma in situ', 'Moderate dysplasia', 'Invasive melanoma - other', 'Melanoma in situ - acral-lentiginous', 'Melanoma in situ - arising in a giant congenital nevus', 'No diagnosis possible', 'Normal WDA', 'Melanoma in situ - superficial spreading', 'Mild dysplasia', 'Squamous metaplasia - mature', 'Invasive melanoma - nevoid', 'Reserve cell hyperplasia', 'Melanoma in situ - lentigo maligna type', 'Severe dysplasia', 'Melanocytic hyperplasia', 'Squamous metaplasia - immature', 'Benign tumor NOS', 'Melanoma in situ - not otherwise classified', 'Atypical adenomatous hyperplasia', 'Invasive melanoma - superficial spreading', 'Invasive melanoma - lentigo maligna', 'Squamous Carcinoma in situ', 'Hamartoma', 'Scar - no residual melanoma', 'Atypical melanocytic proliferation', 'Adenocarcinoma in situ - non mucinous', 'Invasive melanoma - desmoplastic', 'Invasive melanoma - acral lentiginous', 'Carcinoma NOS', 'Invasive melanoma - nodular type', '']",,SRRSBiospecimen +Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['C64.9', 'C18.0', 'C06.0', 'C12.9', 'C22.1', 'C44.2', 'C77.0', 'C15.2', 'C05.0', 'C41.4', 'C62.0', 'C69.9', 'C18.3', 'C26.9', 'C49.6', 'C04.1', 'C15.5', 'C26.8', 'C40.3', 'C40.9', 'C02.0', 'C15.9', 'C51.9', 'C63.1', 'C47.0', 'C54.0', 'C04.9', 'C06.2', 'C49.5', 'C10.2', 'C18.2', 'C77.1', 'C67.9', 'C50.1', 'C57.0', 'C62.1', 'C00.0', 'C38.2', 'C18.5', 'C72.8', 'C49.1', 'C69.1', 'C10.1', 'C16.6', 'C62.9', 'C17.8', 'C07.9', 'C69.8', 'C15.8', 'C34.3', 'C16.4', 'C38.8', 'C08.0', 'C11.3', 'C49.3', 'C14.8', 'C25.4', 'C15.3', 'C25.7', 'C42.3', 'C75.0', 'C03.1', 'C57.8', 'C70.9', 'C72.1', 'C25.0', 'C76.5', 'C50.4', 'C60.2', 'C48.2', 'C44.7', 'C18.8', 'C72.5', 'C75.2', 'C31.1', 'C39.8', 'C14.2', 'C77.9', 'C18.6', 'C06.8', 'C32.3', 'C44.0', 'C04.0', 'C11.2', 'C05.1', 'C44.3', 'C57.4', 'C77.5', 'C51.2', 'C70.0', 'C57.3', 'C02.9', 'C24.0', 'C24.1', 'C76.7', 'C25.9', 'C68.8', 'C54.1', 'C77.4', 'C57.7', 'C50.0', 'C14.0', 'C42.1', 'C11.8', 'C47.5', 'C41.1', 'C53.1', 'C02.1', 'C60.1', 'C67.7', 'C47.3', 'C67.2', 'C13.0', 'C16.5', 'C00.6', 'C50.2', 'unknown', 'C16.2', 'C32.2', 'C50.6', 'C76.4', 'C71.1', 'C76.8', 'C68.0', 'C57.1', 'C69.0', 'C69.4', 'C53.8', 'C05.8', 'C49.9', 'C75.9', 'C00.1', 'C10.9', 'C61.9', 'C17.1', 'C48.8', 'C30.0', 'C13.8', 'C00.8', 'C44.4', 'C06.9', 'C16.0', 'C60.0', 'C69.3', 'C74.1', 'C69.6', 'C13.1', 'C02.8', 'C00.4', 'C18.9', 'C47.2', 'C48.1', 'C39.9', 'C63.2', 'C70.1', 'C50.5', 'C02.3', 'C18.1', 'C41.9', 'C39.0', 'C75.3', 'C49.2', 'C54.3', 'C09.9', 'C40.1', 'C17.9', 'C54.8', 'C69.2', 'C31.9', 'C08.8', 'C25.2', 'C16.9', 'C67.4', 'C71.0', 'C47.6', 'C67.1', 'C54.9', 'C50.8', 'C24.8', 'Not Reported', 'C69.5', 'C54.2', 'C57.2', 'C41.8', 'C50.3', 'C13.2', 'C31.8', 'C32.9', 'C21.8', 'C63.9', 'C25.8', 'C47.1', 'C10.0', 'C16.3', 'C15.0', 'C41.3', 'C72.2', 'C18.4', 'C42.4', 'C06.1', 'C30.1', 'C32.0', 'C66.9', 'C34.9', 'C05.9', 'C25.3', 'C57.9', 'C38.0', 'C63.8', 'C75.1', 'C18.7', 'C71.4', 'C34.2', 'C72.9', 'C55.9', 'C71.9', 'C02.2', 'C47.9', 'C22.0', 'C63.0', 'C21.0', 'C49.8', 'C77.3', 'C63.7', 'C08.1', 'C71.6', 'C74.0', 'C47.8', 'C71.5', 'C47.4', 'C26.0', 'C37.9', 'C71.2', 'C31.3', 'C10.4', 'C51.0', 'C16.1', 'C44.5', 'C52.9', 'C53.0', 'C44.1', 'C33.9', 'C38.3', 'C68.1', 'C32.8', 'C08.9', 'C01.9', 'C75.4', 'C51.8', 'C09.1', 'C60.8', 'C34.0', 'C31.2', 'C60.9', 'C67.0', 'C24.9', 'C71.3', 'C00.3', 'C17.0', 'C03.0', 'C09.8', 'C11.9', 'C74.9', 'C76.2', 'C73.9', 'C10.3', 'C23.9', 'C20.9', 'C16.8', 'C02.4', 'C00.5', 'C03.9', 'C15.1', 'C21.2', 'C72.0', 'C42.2', 'C56.9', 'C77.8', 'C40.0', 'C49.0', 'C17.2', 'C67.8', 'C13.9', 'C76.3', 'C31.0', 'C77.2', 'C67.6', 'C09.0', 'C11.0', 'C65.9', 'C50.9', 'C51.1', 'C41.2', 'C15.4', 'C41.0', 'C21.1', 'C71.7', 'C75.8', 'C68.9', 'C11.1', 'C34.1', 'C38.4', 'C80.9', 'C19.9', 'C04.8', 'C48.0', 'C71.8', 'C44.6', 'C42.0', 'C00.2', 'C38.1', 'C40.8', 'C49.4', 'C10.8', 'C05.2', 'C72.4', 'C76.1', 'C75.5', 'C32.1', 'C72.3', 'C53.9', 'C25.1', 'C17.3', 'C76.0', 'C34.8', '']",,SRRSBiospecimen +Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSBiospecimen +Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Fluids Biospecimen Type', 'Analyte Biospecimen Type', 'Stool Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Urine Biospecimen Type', 'Blood Biospecimen Type', 'Ascites Biospecimen Type', 'Sputum Biospecimen Type', 'Tissue Biospecimen Type', 'Cells Biospecimen Type', 'Mouth Rinse Biospecimen Type']",,SRRSBiospecimen +Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Fresh dissociated and single cell sorted', 'Not Reported', 'Cryopreservation in liquid nitrogen - live cells', 'Formalin fixed-unbuffered', 'OCT', 'Cryopreservation in dry ice - dead tissue', 'unknown', 'Formalin fixed paraffin embedded - FFPE', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Frozen', 'Liquid Nitrogen', 'Cryopreserved', 'Snap Frozen', 'Formalin fixed-buffered', 'Fresh dissociated', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE', 'Cryopreservation in liquid nitrogen - dead tissue', 'Fresh', 'Fresh dissociated and single cell sorted into plates']",,SRRSBiospecimen +Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,SRRSBiospecimen +HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,SRRSBiospecimen +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSBiospecimen +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSBiospecimen +Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",SRRSBiospecimen +Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Dry Ice', 'Not Shipped', 'Other Shipping Environment', 'Liquid Nitrogen', 'Ambient Pack', 'Specimen at Room Temperature', 'Ice Pack', 'Cold Pack', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",SRRSBiospecimen +Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Uncharged', 'Not applicable', 'Charged', 'Coverslip', 'Other', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen -Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Coverslip', 'Other', 'Not applicable', 'Uncharged', 'Charged', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['cDNA Libraries Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'cfDNA Analyte', 'Plasma', 'DNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'Serum Analyte', 'protein', 'PBMCs', 'lipid', 'metabolite', 'RNA Analyte', 'Tissue Section Analyte', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen -Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['Tissue Block Analyte', 'metabolite', 'lipid', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'cDNA Libraries Analyte', 'Serum Analyte', 'PBMCs', 'protein', 'DNA Analyte', 'Tissue Section Analyte', 'Plasma', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen +Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Ventricle NOS', 'Adrenal gland NOS', 'Upper lobe lung', 'Choroid', 'Pleura NOS', 'External lip NOS', 'Overlapping lesion of biliary tract', 'Waldeyer ring', 'Commissure of lip', 'Overlapping lesion of pancreas', 'Vertebral column', 'Overlapping lesion of lung', 'Nervous system NOS', 'Other ill-defined sites', 'Overlapping lesion of eye and adnexa', 'Duodenum', 'Temporal lobe', 'Lymph nodes of multiple regions', 'Head face or neck NOS', 'unknown primary site', 'Extrahepatic bile duct', 'Bone marrow', 'Meninges NOS', 'Bladder neck', 'Head of pancreas', 'Overlapping lesion of vulva', 'Eyelid', 'Brain stem', 'Tonsillar pillar', 'Anterior surface of epiglottis', 'Female genital tract NOS', 'Ascending colon', 'Supraglottis', 'Overlapping lesion of floor of mouth', 'Upper limb NOS', 'Lacrimal gland', 'Tongue NOS', 'Corpus uteri', 'Ileum', 'Mucosa of lower lip', 'Submandibular gland', 'Thymus', 'Descended testis', 'Overlapping lesion of esophagus', 'Spleen', 'Scrotum NOS', 'Posterior wall of nasopharynx', 'Overlapping lesion of palate', 'Orbit NOS', 'Vagina NOS', 'Peripheral nerves and autonomic nervous system of thorax', 'Lower lobe lung', 'Pituitary gland', 'Round ligament', 'Nasal cavity', 'Overlapping lesion of skin', 'Male genital organs NOS', 'Bone of limb NOS', 'Overlapping lesion of hypopharynx', 'Sublingual gland', 'Cerebrum', 'Ventral surface of tongue NOS', 'Intestinal tract NOS', 'Peripheral nerves and autonomic nervous system of abdomen', 'Mandible', 'Pylorus', 'Pancreatic duct', 'External upper lip', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Abdomen NOS', 'Short bones of lower limb and associated joints', 'Overlapping lesion of nasopharynx', 'Mouth NOS', 'Ureteric orifice', 'Colon NOS', 'Cheek mucosa', 'Pancreas NOS', 'Lower-inner quadrant of breast', 'Retina', 'Renal pelvis', 'Posterior wall of bladder', 'Lymph nodes of inguinal region or leg', 'Penis NOS', 'Clitoris', 'Superior wall of nasopharynx', 'Ovary', 'Tail of pancreas', 'Cloacogenic zone', 'Isthmus uteri', 'Retromolar area', 'Undescended testis', 'Eye NOS', 'skin NOS', 'Lesser curvature of stomach NOS', 'Lower-outer quadrant of breast', 'Mucosa of upper lip', 'Skin of lip NOS', 'Gastrointestinal tract NOS', 'Spinal meninges', 'Anterior mediastinum', 'Paraspinal', 'Overlapping lesion of retroperitoneum and peritoneum', 'Floor of mouth NOS', 'unknown', 'Urachus', 'External ear', 'Lymph nodes of head face and neck', 'Specified parts of peritoneum', 'Optic nerve', 'Other specified parts of pancreas', 'Posterior mediastinum', 'Tonsillar fossa', 'Overlapping lesion of tongue', 'Mucosa of lip NOS', 'Kidney NOS', 'Upper-inner quadrant of breast', 'Mediastinum NOS', 'Overlapping lesion of heart mediastinum and pleura', 'Axillary tail of breast', 'Overlapping lesion of corpus uteri', 'Gastric antrum', 'Body of stomach', 'Overlapping lesion of tonsil', 'Uterine adnexa', 'Lateral floor of mouth', 'Labium minus', 'Middle lobe lung', 'Medulla of adrenal gland', 'Lower limb NOS', 'Hard palate', 'Body of penis', 'Overlapping lesion of digestive system', 'Overlapping lesion of other and unspecified parts of mouth', 'Lower gum', 'Overlapping lesion of rectum anus and anal canal', 'Hypopharynx NOS', 'Overlapping lesion of female genital organs', 'Skin of other and unspecified parts of face', 'Glans penis', 'Accessory sinus NOS', 'Overlapping lesion of endocrine glands and related structures', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Bones of skull and face and associated joints', 'Vestibule of mouth', 'Border of tongue', 'Parametrium', 'Ciliary body', 'Soft palate NOS', 'Overlapping lesion of cervix uteri', 'Gum NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Skin of trunk', 'Cranial nerve NOS', 'Ampulla of Vater', 'Palate NOS', 'Pineal gland', 'Lymph nodes of axilla or arm', 'Base of tongue NOS', 'Middle ear', 'Breast NOS', 'Parietal lobe', 'Frontal sinus', 'Overlapping lesion of larynx', 'Retroperitoneum', 'Paraurethral gland', 'Overlapping lesion of urinary organs', 'Connective subcutaneous and other soft tissues NOS', 'Lateral wall of oropharynx', 'Main bronchus', 'Liver', 'Lip NOS', 'Biliary tract NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Anterior 2/3 of tongue NOS', 'Skin of scalp and neck', 'Short bones of upper limb and associated joints', 'Jejunum', 'Overlapping lesion of ill-defined sites', 'Sphenoid sinus', 'Urethra', 'Trachea', 'Hematopoietic system NOS', 'Fallopian tube', 'Cerebellum NOS', 'Carotid body', 'Other specified parts of male genital organs', 'Connective subcutaneous and other soft tissues of abdomen', 'skin of upper limb and shoulder', 'Not Reported', 'Lateral wall of nasopharynx', 'Endocrine gland NOS', 'Heart', 'Dorsal surface of tongue NOS', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Central portion of breast', 'Endometrium', 'Appendix', 'Cerebral meninges', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peritoneum NOS', 'Craniopharyngeal duct', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Ethmoid sinus', 'Exocervix', 'Pharynx NOS', 'Anal canal', 'Aortic body and other paraganglia', 'Labium majus', 'Lingual tonsil', 'Ill-defined sites within respiratory system', 'Lower third of esophagus', 'Overlapping lesion of bones joints and articular cartilage', 'Rectosigmoid junction', 'Placenta', 'Bone NOS', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lateral wall of bladder', 'Cecum', 'Parathyroid gland', 'Cortex of adrenal gland', 'Upper-outer quadrant of breast', 'Vulva NOS', 'Prepuce', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Greater curvature of stomach NOS', 'Autonomic nervous system NOS', 'Nasopharynx NOS', 'Anus NOS', 'Overlapping lesion of male genital organs', 'Descending colon', 'Long bones of lower limb and associated joints', 'Urinary system NOS', 'Cardia NOS', 'Lung NOS', 'Frontal lobe', 'Thoracic esophagus', 'Overlapping lesion of lip', 'Cervical esophagus', 'Uterus NOS', 'Major salivary gland NOS', 'Maxillary sinus', 'Intrathoracic lymph nodes', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of brain and central nervous system', 'Posterior wall of oropharynx', 'Epididymis', 'Spermatic cord', 'Pelvic lymph nodes', 'Dome of bladder', 'Middle third of esophagus', 'Pelvis NOS', 'Tonsil NOS', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Cervix uteri', 'Nipple', 'Conjunctiva', 'Olfactory nerve', 'Fundus uteri', 'Anterior floor of mouth', 'Oropharynx NOS', 'Meckel diverticulum', 'Esophagus NOS', 'Intra-abdominal lymph nodes', 'Lymph node NOS', 'Small intestine NOS', 'Brain NOS', 'Overlapping lesion of major salivary glands', 'Vallecula', 'Upper gum', 'Overlapping lesion of small intestine', 'Overlapping lesion of breast', 'Anterior wall of nasopharynx', 'Cauda equina', 'Myometrium', 'skin of lower limb and hip', 'Overlapping lesion of accessory sinuses', 'Hypopharyngeal aspect of aryepiglottic fold', 'Hepatic flexure of colon', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Overlapping lesion of stomach', 'Postcricoid region', 'Uvula', 'Splenic flexure of colon', 'Overlapping lesion of bladder', 'Glottis', 'Pyriform sinus', 'Thorax NOS', 'Trigone of bladder', 'Fundus of stomach', 'Abdominal esophagus', 'Posterior wall of hypopharynx', 'Overlapping lesion of penis', 'Connective subcutaneous and other soft tissues of thorax', 'Blood', 'Body of pancreas', 'Bladder NOS', 'Occipital lobe', 'Intrahepatic bile duct', 'Spinal cord', 'Laryngeal cartilage', 'Transverse colon', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Sigmoid colon', 'Cornea NOS', 'Prostate gland', 'Endocervix', 'Overlapping lesions of oropharynx', 'Overlapping lesion of colon', 'Upper respiratory tract NOS', 'Islets of Langerhans', 'Broad ligament', 'Parotid gland', 'Anterior wall of bladder', 'Rib sternum clavicle and associated joints', 'Long bones of upper limb scapula and associated joints', 'Gallbladder', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Upper third of esophagus', 'Other specified parts of female genital organs', 'Thyroid gland', 'Branchial cleft', 'Connective subcutaneous and other soft tissues of pelvis', 'Reticuloendothelial system NOS', 'Acoustic nerve', 'Larynx NOS', 'Stomach NOS', 'Testis NOS', 'External lower lip', 'Subglottis', 'Ureter', 'Overlapping lesion of brain', 'Rectum NOS', '']","['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",SRRSBiospecimen -Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'mL', 'square centimeter', '']",,SRRSBiospecimen -Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['mm', 'cm', '']",,SRRSBiospecimen -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,OtherAssay +Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Reported', 'Right', 'Bilateral', 'unknown', 'Left', 'Not Applicable', '']","['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Not analyzed', 'Primary', 'Metastatic', 'Normal distant', 'Premalignant - in situ', 'Local recurrence', 'Recurrent', 'Normal adjacent', 'Normal', 'Post therapy adjuvant', 'Not Otherwise Specified', 'Post therapy', 'Additional Primary', 'Atypia - hyperplasia', 'Post therapy neoadjuvant', 'Premalignant', '']","['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['cm', 'mm', '']",,SRRSBiospecimen +Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'square centimeter', 'mL', '']",,SRRSBiospecimen HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,OtherAssay -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OtherAssay -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,OtherAssay Filename,Filename,Filename,Name of a file,True,,,,OtherAssay +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,OtherAssay Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,OtherAssay -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ExSeqMinimal +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OtherAssay +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,OtherAssay HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ExSeqMinimal -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ExSeqMinimal -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ExSeqMinimal Filename,Filename,Filename,Name of a file,True,,,,ExSeqMinimal +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ExSeqMinimal Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,ExSeqMinimal -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel1 -Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 -Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,ScRNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScRNA-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,ScRNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,ScRNA-seqLevel1 -Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,ScRNA-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScRNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScRNA-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ExSeqMinimal +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ExSeqMinimal +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,ScRNA-seqLevel1 Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Microfluidics Chip', 'Droplets', '10x', 'Nuclei Isolation', 'FACS']",,ScRNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['R1&R2', 'I1', 'R1', 'R2', 'Other']",,ScRNA-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel1 Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,ScRNA-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,ScRNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,ScRNA-seqLevel1 -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScRNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScRNA-seqLevel1 Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,ScRNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,ScRNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScRNA-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['5 Prime', 'Full Length Transcript', '3 Prime']",,ScRNA-seqLevel1 +Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 +Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,ScRNA-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10x Multiome', '10xV1.0', '10xV3', ""10x GEM 5'"", '10xV1.1', '10xV2', '10x FLEX', 'Nextera XT', 'Drop-seq', 'CEL-seq2', 'inDropsV3', 'TruDrop', 'sci-ATAC-seq', 'inDropsV2', '10xV3.1', ""10x GEM 3'"", 'Smart-seq2', 'Smart-SeqV4']",,ScRNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,ScRNA-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScRNA-seqLevel1 +Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Oligo-dT', 'Random', 'Poly-dT']",,ScRNA-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'ERCC', 'No Spike In', 'PhiX']",,ScRNA-seqLevel1 Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Dounce', 'gentleMACS', 'Not Applicable', 'Enzymatic Digestion']",,ScRNA-seqLevel1 +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScRNA-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['Nextera XT', 'Drop-seq', 'CEL-seq2', '10xV2', '10xV1.1', 'inDropsV2', 'sci-ATAC-seq', '10x Multiome', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', ""10x GEM 3'"", '10xV3.1', 'Smart-SeqV4', ""10x GEM 5'"", '10x FLEX']",,ScRNA-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Enzymatic Digestion', 'Not Applicable', 'Dounce']",,ScRNA-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,ScRNA-seqLevel1 -Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,ScRNA-seqLevel1 -Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 -Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 -Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 +Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,ScRNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,ScRNA-seqLevel1 +Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 +Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 +Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 -Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",ScRNA-seqLevel1 +Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",ScRNA-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",ScRNA-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",ScRNA-seqLevel1 Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,,"['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",ScRNA-seqLevel1 Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",ScRNA-seqLevel1 -Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,ScRNA-seqLevel2 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,ScRNA-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel2 +Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,ScRNA-seqLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScRNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScRNA-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,ScRNA-seqLevel2 +Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,ScRNA-seqLevel2 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,ScRNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel2 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,ScRNA-seqLevel2 -Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,ScRNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScRNA-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,ScRNA-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,ScRNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScRNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel2 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,ScRNA-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,ScRNA-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel2 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel2 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STARsolo', 'dropEST', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'Differentiation trajectory analysis', 'Cell annotation', 'HTSeq - FPKM', 'SEQC', 'DEXSeq', 'Other']",,ScRNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScRNA-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,ScRNA-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",ScRNA-seqLevel2 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,ScRNA-seqLevel3 -Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,ScRNA-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,ScRNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel3 Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,ScRNA-seqLevel3 -scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel3 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,ScRNA-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScRNA-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel3 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STARsolo', 'dropEST', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'Differentiation trajectory analysis', 'Cell annotation', 'HTSeq - FPKM', 'SEQC', 'DEXSeq', 'Other']",,ScRNA-seqLevel3 Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,ScRNA-seqLevel3 +scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScRNA-seqLevel3 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Transcript Expression', 'Gene Expression', 'Isoform Expression Quantification', 'Gene Expression Quantification', 'Splice Junction Quantification', 'Exon Expression Quantification', 'Other']",,ScRNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel3 +Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,ScRNA-seqLevel3 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel3 Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,ScRNA-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Batch Corrected Counts', 'Scaled Counts', 'Normalized Counts']",,ScRNA-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel4 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel4 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,ScRNA-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScRNA-seqLevel4 Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScRNA-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel4 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel4 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel4 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STARsolo', 'dropEST', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'Differentiation trajectory analysis', 'Cell annotation', 'HTSeq - FPKM', 'SEQC', 'DEXSeq', 'Other']",,ScRNA-seqLevel4 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,Slide-seqLevel1 +Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,Slide-seqLevel1 +Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,Slide-seqLevel1 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['R1&R2', 'I1', 'R1', 'R2', 'Other']",,Slide-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,Slide-seqLevel1 Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,True,,,,Slide-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,Slide-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,Slide-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,Slide-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Slide-seqLevel1 -Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['Nextera XT', 'Drop-seq', '10xV2', '10xV1.1', 'inDropsV2', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', '10xV3.1', 'Smart-SeqV4']",,Slide-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,Slide-seqLevel1 -Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1 +Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,Slide-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['5 Prime', 'Full Length Transcript', '3 Prime']",,Slide-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,Slide-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Slide-seqLevel1 +Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV1.0', '10xV3', '10xV1.1', '10xV2', 'Nextera XT', 'Drop-seq', 'inDropsV3', 'TruDrop', 'inDropsV2', '10xV3.1', 'Smart-seq2', 'Smart-SeqV4']",,Slide-seqLevel1 Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,Slide-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,Slide-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Oligo-dT', 'Random', 'Poly-dT']",,Slide-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'ERCC', 'No Spike In', 'PhiX']",,Slide-seqLevel1 Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,Slide-seqLevel1 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,Slide-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,Slide-seqLevel1 -Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel1 -Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,Slide-seqLevel1 -Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,Slide-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,Slide-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,Slide-seqLevel1 -UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 +Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1 Spatial Barcode Length,Spatial Barcode Length,SpatialBarcodeLength,Length of spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",Slide-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 +UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",Slide-seqLevel1 Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",Slide-seqLevel1 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,Slide-seqLevel2 +Matched Spatial Barcode Tag,Matched Spatial Barcode Tag,MatchedSpatialBarcodeTag,SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific),True,,,,Slide-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel2 +Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,Slide-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,Slide-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,Slide-seqLevel2 -Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,Slide-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,Slide-seqLevel2 -Matched Spatial Barcode Tag,Matched Spatial Barcode Tag,MatchedSpatialBarcodeTag,SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific),True,,,,Slide-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,Slide-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,Slide-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,Slide-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,Slide-seqLevel2 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel2 -Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,Slide-seqLevel2 Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,Slide-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel2 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel2 +Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,Slide-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,Slide-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,Slide-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",Slide-seqLevel2 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,Slide-seqLevel3 -Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,Slide-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,Slide-seqLevel3 -Beads Total,Beads Total,BeadsTotal,Number of sequenced beads. Applies to raw counts matrix only. Integer,False,,,,Slide-seqLevel3 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,Slide-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel3 +Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel3 Slide-seq Fragment Size,Slide-seq Fragment Size,Slide-seqFragmentSize,Average cDNA length associated with the experiemtn. Integer,False,,,,Slide-seqLevel3 -Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,Slide-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,Slide-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,Slide-seqLevel3 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel3 -Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel3 Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel3 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,Slide-seqLevel3 Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,Slide-seqLevel3 -Slide-seq Bead File Type,Slide-seq Bead File Type,Slide-seqBeadFileType,The type of Level 3 file submitted as part of the Slide-seq workflow.,True,,"['All Bead Locations', 'Not Applicable', 'Matched Bead Locations', 'Matched Bead Barcodes', 'All Bead Barcodes', 'Matrix Barcodes', 'Matrix Features']",,Slide-seqLevel3 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,BulkRNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel1 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Transcript Expression', 'Gene Expression', 'Isoform Expression Quantification', 'Gene Expression Quantification', 'Splice Junction Quantification', 'Exon Expression Quantification', 'Other']",,Slide-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel3 +Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,Slide-seqLevel3 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel3 +Slide-seq Bead File Type,Slide-seq Bead File Type,Slide-seqBeadFileType,The type of Level 3 file submitted as part of the Slide-seq workflow.,True,,"['All Bead Barcodes', 'Matrix Barcodes', 'All Bead Locations', 'Matrix Features', 'Matched Bead Barcodes', 'Matched Bead Locations', 'Not Applicable']",,Slide-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel3 +Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,Slide-seqLevel3 +Beads Total,Beads Total,BeadsTotal,Number of sequenced beads. Applies to raw counts matrix only. Integer,False,,,,Slide-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Batch Corrected Counts', 'Scaled Counts', 'Normalized Counts']",,Slide-seqLevel3 +Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,BulkRNA-seqLevel1 +Transcript Integrity Number,Transcript Integrity Number,TranscriptIntegrityNumber,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",False,,,,BulkRNA-seqLevel1 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkRNA-seqLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkRNA-seqLevel1 +Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkRNA-seqLevel1 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkRNA-seqLevel1 +Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,BulkRNA-seqLevel1 +Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 -Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'Random', 'Other', 'PCR', 'Affinity Enrichment', 'miRNA Size Fractionation', 'Hybrid Selection', 'Poly-T Enrichment']",,BulkRNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkRNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,BulkRNA-seqLevel1 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkRNA-seqLevel1 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['R1&R2', 'I1', 'R1', 'R2', 'Other']",,BulkRNA-seqLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkRNA-seqLevel1 -Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkRNA-seqLevel1 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel1 +Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Second Stranded', 'Not Applicable', 'First Stranded', 'Unstranded', '']",,BulkRNA-seqLevel1 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkRNA-seqLevel1 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkRNA-seqLevel1 Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkRNA-seqLevel1 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel1 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkRNA-seqLevel1 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkRNA-seqLevel1 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkRNA-seqLevel1 +RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,BulkRNA-seqLevel1 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Hybrid Selection', 'PCR', 'Poly-T Enrichment', 'rRNA Depletion', 'Other', 'Affinity Enrichment']",,BulkRNA-seqLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Long Read', 'Mid-length', 'Single Read']",,BulkRNA-seqLevel1 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,BulkRNA-seqLevel1 +DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,BulkRNA-seqLevel1 QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkRNA-seqLevel1 -Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1 -Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,BulkRNA-seqLevel1 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkRNA-seqLevel1 +Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkRNA-seqLevel1 Micro-region Seq Platform,Micro-region Seq Platform,Micro-regionSeqPlatform,The platform used for micro-regional RNA sequencing (if applicable),False,,"['Laser Capture Microdissection', 'Rarecyte Pick-Seq', '']",,BulkRNA-seqLevel1 -Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkRNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkRNA-seqLevel1 Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkRNA-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel1 -Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,BulkRNA-seqLevel1 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 ROI Tag,ROI Tag,ROITag,The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.,False,,,,BulkRNA-seqLevel1 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,BulkRNA-seqLevel1 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkRNA-seqLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 -Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 -Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 -Transcript Integrity Number,Transcript Integrity Number,TranscriptIntegrityNumber,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",False,,,,BulkRNA-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,BulkRNA-seqLevel1 -Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkRNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,BulkRNA-seqLevel1 -Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Second Stranded', 'Not Applicable', 'First Stranded', '']",,BulkRNA-seqLevel1 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkRNA-seqLevel1 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkRNA-seqLevel1 -RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,BulkRNA-seqLevel1 +Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkRNA-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'ERCC', 'No Spike In', 'PhiX']",,BulkRNA-seqLevel1 +Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkRNA-seqLevel1 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkRNA-seqLevel1 +Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel1 +Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkRNA-seqLevel1 Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",BulkRNA-seqLevel1 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkRNA-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkRNA-seqLevel2 +MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkRNA-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkRNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkRNA-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkRNA-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkRNA-seqLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel2 -MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkRNA-seqLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkRNA-seqLevel2 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkRNA-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BSMAP', 'BS-Seeker2', 'STAR 2-Pass Genome', 'BSmooth', 'Pash', 'RMAP', 'BS-Seeker', 'GSNAP', 'BWA', 'BWA-aln', 'BWA with Mark Duplicates and BQSR', 'STAR 2-Pass Transcriptome', 'None', 'BWA with BQSR', 'Other Alignment Workflow', 'BWA-meth', 'Bisulfighter', 'Bowtie', 'BatMeth', 'ERNE-BS5', 'BWA-mem', 'SOCS-B', 'STAR 2-Pass Chimeric', 'B-SOLANA', 'Bismark', 'BRAT-BW', 'MethylCoder', 'Segemehl', 'STAR 2-Pass', 'LAST']",,BulkRNA-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkRNA-seqLevel2 Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,BulkRNA-seqLevel2 +MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-high', 'MSI-low', 'MSS', 'MSI', '']",,BulkRNA-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkRNA-seqLevel2 -MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSI-low', 'MSS', 'MSI-high', '']",,BulkRNA-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkRNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkRNA-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkRNA-seqLevel2 -Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkRNA-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkRNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkRNA-seqLevel2 Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkRNA-seqLevel2 -Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkRNA-seqLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,False,True,,"['Is lowest level is ""Yes - Is lowest level""']",BulkRNA-seqLevel2 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,BulkRNA-seqLevel3 -Pseudo Alignment Used,Pseudo Alignment Used,PseudoAlignmentUsed,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,True,,"['Yes - Pseudo Alignment Used', 'no']",,BulkRNA-seqLevel3 -Fusion Gene Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['Yes - Fusion Gene Detected', 'unknown', 'no', '']",,BulkRNA-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,BulkRNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel3 +Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkRNA-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel3 -Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['Other', 'RPKM', 'FPKM', 'TPM', 'NA', 'Counts']",,BulkRNA-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel3 -Fusion Gene Identity,Fusion Gene Identity,FusionGeneIdentity,The gene symbols of fused genes.,False,,,,BulkRNA-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkRNA-seqLevel3 +Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['FPKM', 'NA', 'TPM', 'Counts', 'RPKM', 'Other']",,BulkRNA-seqLevel3 +Fusion Gene Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['unknown', 'no', 'Yes - Fusion Gene Detected', '']",,BulkRNA-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkRNA-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Transcript Expression', 'Gene Expression', 'Isoform Expression Quantification', 'Gene Expression Quantification', 'Splice Junction Quantification', 'Exon Expression Quantification', 'Other']",,BulkRNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel3 +Pseudo Alignment Used,Pseudo Alignment Used,PseudoAlignmentUsed,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,True,,"['no', 'Yes - Pseudo Alignment Used']",,BulkRNA-seqLevel3 +Fusion Gene Identity,Fusion Gene Identity,FusionGeneIdentity,The gene symbols of fused genes.,False,,,,BulkRNA-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Batch Corrected Counts', 'Scaled Counts', 'Normalized Counts']",,BulkRNA-seqLevel3 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 Specify Other Fusion Gene,Specify Other Fusion Gene,SpecifyOtherFusionGene,"Specify fusion gene detected, if not in list",False,True,,"['Fusion Gene Identity is ""Other Fusion Gene""']",BulkRNA-seqLevel3 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,BulkWESLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel1 +Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkWESLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkWESLevel1 +Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkWESLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,BulkWESLevel1 +Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkWESLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['R1&R2', 'I1', 'R1', 'R2', 'Other']",,BulkWESLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'Random', 'Other', 'PCR', 'Affinity Enrichment', 'miRNA Size Fractionation', 'Hybrid Selection', 'Poly-T Enrichment']",,BulkWESLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkWESLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,BulkWESLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkWESLevel1 Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkWESLevel1 +Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkWESLevel1 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkWESLevel1 Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 +Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkWESLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Hybrid Selection', 'PCR', 'Poly-T Enrichment', 'rRNA Depletion', 'Other', 'Affinity Enrichment']",,BulkWESLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Long Read', 'Mid-length', 'Single Read']",,BulkWESLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,BulkWESLevel1 Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkWESLevel1 +Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkWESLevel1 +Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkWESLevel1 Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkWESLevel1 Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkWESLevel1 -Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkWESLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,BulkWESLevel1 -Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkWESLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkWESLevel1 -Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkWESLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkWESLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel1 -Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel1 -Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkWESLevel1 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,BulkWESLevel1 -Target Capture Kit,Target Capture Kit,TargetCaptureKit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.",True,,"['SureSelect Human All Exon v3', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'TruSeq Exome Enrichment - 62 Mb', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Not Applicable', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', '25 rxn xGen Universal Blocking Oligo – TS HT-i7', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb', 'Custom Twist Broad Exome v1.0 - 35.0 Mb', 'unknown', 'Nextera Rapid Capture Exome v1.2', 'SureSelect Human All Exon v5 + UTR', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'SeqCap EZ Human Exome v3.0', 'xGen Exome Research Panel v1.0', 'Custom SureSelect GENIE-UHN Panel - 555 Genes', 'Custom Targets File Provided', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'Custom MSK IMPACT Panel - 410 Genes', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'Custom MSK IMPACT Panel - 341 Genes', 'Nextera DNA Exome', 'SeqCap EZ HGSC VCRome v2.1', 'SureSelect Human All Exon v5', 'TruSight Myeloid Sequencing Panel', 'TruSeq RNA Exome', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2', 'Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', 'Foundation Medicine T5a Panel - 322 Genes', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes', 'xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn', 'Ion AmpliSeq Comprehensive Cancer Panel', 'SureSelect Human All Exon v6', 'Foundation Medicine T7 Panel - 429 Genes', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'SeqCap EZ Human Exome v2.0', 'TruSeq Amplicon Cancer Panel', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'Custom GENIE-DFCI OncoPanel - 275 Genes', 'SureSelect Human All Exon v4', 'Custom MSK IMPACT Panel - 468 Genes', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Ion AmpliSeq Cancer Hotspot Panel v2']",,BulkWESLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 -Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 -Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkWESLevel1 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkWESLevel2 +Target Capture Kit,Target Capture Kit,TargetCaptureKit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.",True,,"['Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', 'Custom MSK IMPACT Panel - 410 Genes', 'Custom MSK IMPACT Panel - 468 Genes', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'Nextera DNA Exome', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2', 'SeqCap EZ HGSC VCRome v2.1', 'SeqCap EZ Human Exome v3.0', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'SureSelect Human All Exon v4', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Custom SureSelect GENIE-UHN Panel - 555 Genes', 'xGen Exome Research Panel v1.0', 'unknown', 'Not Applicable', 'TruSeq RNA Exome', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'Custom Twist Broad Exome v1.0 - 35.0 Mb', 'SeqCap EZ Human Exome v2.0', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes', 'TruSeq Exome Enrichment - 62 Mb', '25 rxn xGen Universal Blocking Oligo – TS HT-i7', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'Ion AmpliSeq Cancer Hotspot Panel v2', 'xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn', 'Ion AmpliSeq Comprehensive Cancer Panel', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'TruSeq Amplicon Cancer Panel', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Custom Targets File Provided', 'TruSight Myeloid Sequencing Panel', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'Foundation Medicine T5a Panel - 322 Genes', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Foundation Medicine T7 Panel - 429 Genes', 'SureSelect Human All Exon v3', 'SureSelect Human All Exon v5 + UTR', 'SureSelect Human All Exon v6', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'SureSelect Human All Exon v5', 'Nextera Rapid Capture Exome v1.2', 'Custom MSK IMPACT Panel - 341 Genes', 'Custom GENIE-DFCI OncoPanel - 275 Genes']",,BulkWESLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkWESLevel1 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkWESLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkWESLevel2 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkWESLevel2 +MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkWESLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkWESLevel2 +Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkWESLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkWESLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkWESLevel2 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkWESLevel2 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkWESLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel2 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel2 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkWESLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkWESLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel2 -MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkWESLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkWESLevel2 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkWESLevel2 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkWESLevel2 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkWESLevel2 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkWESLevel2 -QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkWESLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BSMAP', 'BS-Seeker2', 'STAR 2-Pass Genome', 'BSmooth', 'Pash', 'RMAP', 'BS-Seeker', 'GSNAP', 'BWA', 'BWA-aln', 'BWA with Mark Duplicates and BQSR', 'STAR 2-Pass Transcriptome', 'None', 'BWA with BQSR', 'Other Alignment Workflow', 'BWA-meth', 'Bisulfighter', 'Bowtie', 'BatMeth', 'ERNE-BS5', 'BWA-mem', 'SOCS-B', 'STAR 2-Pass Chimeric', 'B-SOLANA', 'Bismark', 'BRAT-BW', 'MethylCoder', 'Segemehl', 'STAR 2-Pass', 'LAST']",,BulkWESLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkWESLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkWESLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel2 -Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel2 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,BulkWESLevel2 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkWESLevel2 +MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2 +MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-high', 'MSI-low', 'MSS', 'MSI', '']",,BulkWESLevel2 +QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkWESLevel2 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkWESLevel2 -MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI', 'MSI-low', 'MSS', 'MSI-high', '']",,BulkWESLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkWESLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkWESLevel2 Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel2 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkWESLevel2 -Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkWESLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 -Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkWESLevel2 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkWESLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkWESLevel2 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel2 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,BulkWESLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel2 Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkWESLevel2 -MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkWESLevel2 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,BulkWESLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2 -Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkWESLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,False,True,,"['Is lowest level is ""Yes - Is lowest level""']",BulkWESLevel2 -Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['MuTect2', 'Pindel', 'SomaticSniper', 'CaVEMan', 'VarScan2', 'Other Somatic Variants Workflow Type', 'None', 'MuSE', 'GATK4', '']",,BulkWESLevel3 -Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['BRASS', 'CNVkit', 'Other Structural Variant Workflow Type', 'None', 'CNV', 'GATK4', '']",,BulkWESLevel3 -Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,BulkWESLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel3 +Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkWESLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel3 +Germline Variants Workflow Type,Germline Variants Workflow Type,GermlineVariantsWorkflowType,Generic name for the workflow used to analyze a data set,False,,"['Other Germline Variants Workflow Type', 'None', 'GATK4', '']",,BulkWESLevel3 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel3 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel3 -Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Case Sample', 'Not Applicable', 'Control Sample']",,BulkWESLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel3 -Germline Variants Workflow URL,Germline Variants Workflow URL,GermlineVariantsWorkflowURL,"Link to workflow document, e.g. Github, DockStore.org recommended",True,,,,BulkWESLevel3 -Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkWESLevel3 +Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,BulkWESLevel3 Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel3 -Germline Variants Workflow Type,Germline Variants Workflow Type,GermlineVariantsWorkflowType,Generic name for the workflow used to analyze a data set,False,,"['Other Germline Variants Workflow Type', 'None', 'GATK4', '']",,BulkWESLevel3 -Custom Somatic Variants Workflow Type,Custom Somatic Variants Workflow Type,CustomSomaticVariantsWorkflowType,Specify the name of a custom workflow name,False,True,,"['Somatic is ""Other""']",BulkWESLevel3 -Custom Structural Variant Workflow Type,Custom Structural Variant Workflow Type,CustomStructuralVariantWorkflowType,Specify the name of a custom workflow name,False,True,,"['Structural is ""Other""']",BulkWESLevel3 -Custom Germline Variants Workflow Type,Custom Germline Variants Workflow Type,CustomGermlineVariantsWorkflowType,Specify the name of a custom alignment workflow,False,True,,"['Germline is ""Other""']",BulkWESLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkWESLevel3 +Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Case Sample', 'Control Sample', 'Not Applicable']",,BulkWESLevel3 +Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['GATK4', 'Other Somatic Variants Workflow Type', 'SomaticSniper', 'MuSE', 'MuTect2', 'Pindel', 'CaVEMan', 'VarScan2', 'None', '']",,BulkWESLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel3 +Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3 +Germline Variants Workflow URL,Germline Variants Workflow URL,GermlineVariantsWorkflowURL,"Link to workflow document, e.g. Github, DockStore.org recommended",True,,,,BulkWESLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel3 +Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['CNV', 'CNVkit', 'GATK4', 'Other Structural Variant Workflow Type', 'BRASS', 'None', '']",,BulkWESLevel3 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel3 +Custom Germline Variants Workflow Type,Custom Germline Variants Workflow Type,CustomGermlineVariantsWorkflowType,Specify the name of a custom alignment workflow,False,True,,"['Germline is ""Other""']",BulkWESLevel3 +Custom Somatic Variants Workflow Type,Custom Somatic Variants Workflow Type,CustomSomaticVariantsWorkflowType,Specify the name of a custom workflow name,False,True,,"['Somatic is ""Other""']",BulkWESLevel3 +Custom Structural Variant Workflow Type,Custom Structural Variant Workflow Type,CustomStructuralVariantWorkflowType,Specify the name of a custom workflow name,False,True,,"['Structural is ""Other""']",BulkWESLevel3 +Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel1 Microarray Protocol Auxiliary File,Microarray Protocol Auxiliary File,MicroarrayProtocolAuxiliaryFile,"Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).",True,,,,MicroarrayLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MicroarrayLevel1 -Microarray Molecule,Microarray Molecule,MicroarrayMolecule,Microarray is measuring this kind of molecule,True,,"['RNA', 'DNA']",,MicroarrayLevel1 -Microarray Value Definition,Microarray Value Definition,MicroarrayValueDefinition,What the provided value signifies,True,,,,MicroarrayLevel1 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,MicroarrayLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MicroarrayLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,MicroarrayLevel1 Filename,Filename,Filename,Name of a file,True,,,,MicroarrayLevel1 -Microarray Label,Microarray Label,MicroarrayLabel,Microarray used this kind of label,True,,,,MicroarrayLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MicroarrayLevel1 HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel1 -Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MicroarrayLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MicroarrayLevel2 +Microarray Molecule,Microarray Molecule,MicroarrayMolecule,Microarray is measuring this kind of molecule,True,,"['DNA', 'RNA']",,MicroarrayLevel1 +Microarray Label,Microarray Label,MicroarrayLabel,Microarray used this kind of label,True,,,,MicroarrayLevel1 +Microarray Value Definition,Microarray Value Definition,MicroarrayValueDefinition,What the provided value signifies,True,,,,MicroarrayLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MicroarrayLevel1 +Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel2 Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,MicroarrayLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MicroarrayLevel2 Filename,Filename,Filename,Name of a file,True,,,,MicroarrayLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MicroarrayLevel2 HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel2 -Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MicroarrayLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MicroarrayLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel2 -HTAN RPPA Antibody Table,HTAN RPPA Antibody Table,HTANRPPAAntibodyTable,A table containing antibody level metadata for RPPA,True,,,,RPPALevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel2 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am', '']",,RPPALevel2 -Filename,Filename,Filename,Name of a file,False,,,,RPPALevel2 -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel2 +Filename,Filename,Filename,Name of a file,True,,,,RPPALevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,RPPALevel2 HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel2 +HTAN RPPA Antibody Table,HTAN RPPA Antibody Table,HTANRPPAAntibodyTable,A table containing antibody level metadata for RPPA,True,,,,RPPALevel2 +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel2 Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,RPPALevel2 -Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['true', 'false', '']",,RPPALevel2 -Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2 +Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['false', 'true', '']",,RPPALevel2 Antibody Notes,Antibody Notes,AntibodyNotes,Notes on antibodies replacements and antibody recognition observations.,False,,,,RPPALevel2 -Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2 -GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,RPPALevel2 -HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,False,,,,RPPALevel2 -Species,Species,Species,Host animal.,False,,"['Rabbit', 'Mouse', 'Goat', '']",,RPPALevel2 -Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,RPPALevel2 +RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2 +Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,RPPALevel2 +Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,RPPALevel2 Clone,Clone,Clone,Clone,False,,,,RPPALevel2 +Species,Species,Species,Host animal.,False,,"['Goat', 'Rabbit', 'Mouse', '']",,RPPALevel2 +GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,RPPALevel2 +Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2 UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,The comma separated list of UNIPROT IDs targeted by the antibody.,False,,,,RPPALevel2 +RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Under Evaluation', 'Used for QC', 'Use with Caution', 'Valid', '']",,RPPALevel2 +HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,False,,,,RPPALevel2 +Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2 +Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Non-clonal', 'Clonal', '']",,RPPALevel2 Internal Ab ID,Internal Ab ID,InternalAbID,Internal lab ID for an antibody.,False,,,,RPPALevel2 -RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2 -Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,RPPALevel2 -Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,RPPALevel2 -RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Used for QC', 'Under Evaluation', 'Valid', 'Use with Caution', '']",,RPPALevel2 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,ScATAC-seqLevel1 +Median Fraction of Reads in Annotated cis DNA Elements,Median Fraction of Reads in Annotated cis DNA Elements,MedianFractionofReadsinAnnotatedcisDNAElements,Median fraction of reads in annotated cis-DNA elements (FRIADE),True,,,,ScATAC-seqLevel1 +Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScATAC-seqLevel1 +Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1 +scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Microfluidics Chip', 'Droplets', '10x', 'Nuclei Isolation', 'FACS']",,ScATAC-seqLevel1 +Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['NIB', '10x', 'TST', 'Omni']",,ScATAC-seqLevel1 Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScATAC-seqLevel1 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel1 -scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['Sample Index', 'Cell Barcode and DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'DNA Insert']",,ScATAC-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScATAC-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScATAC-seqLevel1 -scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1 -scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['Sample Index', 'Cell Barcode and DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'DNA Insert', '']",,ScATAC-seqLevel1 -Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScATAC-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScATAC-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,ScATAC-seqLevel1 -scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['Sample Index', 'Cell Barcode and DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'DNA Insert']",,ScATAC-seqLevel1 -Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScATAC-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1 -Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScATAC-seqLevel1 -Median Fraction of Reads in Annotated cis DNA Elements,Median Fraction of Reads in Annotated cis DNA Elements,MedianFractionofReadsinAnnotatedcisDNAElements,Median fraction of reads in annotated cis-DNA elements (FRIADE),True,,,,ScATAC-seqLevel1 -Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'Omni', 'TST', 'NIB']",,ScATAC-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,ScATAC-seqLevel1 -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScATAC-seqLevel1 Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScATAC-seqLevel1 +Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScATAC-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScATAC-seqLevel1 +scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['Cell Barcode and DNA Insert', 'Sample Index', 'DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode']",,ScATAC-seqLevel1 Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScATAC-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['Nextera XT', 'Drop-seq', 'CEL-seq2', '10xV2', '10xV1.1', 'inDropsV2', 'sci-ATAC-seq', '10x Multiome', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', ""10x GEM 3'"", '10xV3.1', 'Smart-SeqV4', ""10x GEM 5'"", '10x FLEX']",,ScATAC-seqLevel1 -Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Nextera Tn5', 'Tn5-059', 'In-House', 'Diagenode-unloaded Apex-Bio', 'Tn5', 'EZ-Tn5', 'Diagenode-loaded Apex-Bio']",,ScATAC-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Enzymatic Digestion', 'Not Applicable', 'Dounce']",,ScATAC-seqLevel1 -Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,ScATAC-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1 +Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScATAC-seqLevel1 +Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Tn5-059', 'Nextera Tn5', 'EZ-Tn5', 'Diagenode-unloaded Apex-Bio', 'In-House', 'Diagenode-loaded Apex-Bio', 'Tn5']",,ScATAC-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10x Multiome', '10xV1.0', '10xV3', ""10x GEM 5'"", '10xV1.1', '10xV2', '10x FLEX', 'Nextera XT', 'Drop-seq', 'CEL-seq2', 'inDropsV3', 'TruDrop', 'sci-ATAC-seq', 'inDropsV2', '10xV3.1', ""10x GEM 3'"", 'Smart-seq2', 'Smart-SeqV4']",,ScATAC-seqLevel1 +scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['Cell Barcode and DNA Insert', 'Sample Index', 'DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', '']",,ScATAC-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,ScATAC-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScATAC-seqLevel1 +scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['Cell Barcode and DNA Insert', 'Sample Index', 'DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode']",,ScATAC-seqLevel1 Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScATAC-seqLevel1 +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Dounce', 'gentleMACS', 'Not Applicable', 'Enzymatic Digestion']",,ScATAC-seqLevel1 +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScATAC-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel1 Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,ScATAC-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1 Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,,"['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScATAC-seqLevel2 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScATAC-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScATAC-seqLevel2 Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScATAC-seqLevel2 +MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2 +Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScATAC-seqLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScATAC-seqLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScATAC-seqLevel2 Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScATAC-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BSMAP', 'BS-Seeker2', 'STAR 2-Pass Genome', 'BSmooth', 'Pash', 'RMAP', 'BS-Seeker', 'GSNAP', 'BWA', 'BWA-aln', 'BWA with Mark Duplicates and BQSR', 'STAR 2-Pass Transcriptome', 'None', 'BWA with BQSR', 'Other Alignment Workflow', 'BWA-meth', 'Bisulfighter', 'Bowtie', 'BatMeth', 'ERNE-BS5', 'BWA-mem', 'SOCS-B', 'STAR 2-Pass Chimeric', 'B-SOLANA', 'Bismark', 'BRAT-BW', 'MethylCoder', 'Segemehl', 'STAR 2-Pass', 'LAST']",,ScATAC-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScATAC-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScATAC-seqLevel2 Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 -MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 -Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,ScATAC-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScATAC-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScATAC-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScATAC-seqLevel2 Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScATAC-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScATAC-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScATAC-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScATAC-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScATAC-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScATAC-seqLevel2 Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScATAC-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScATAC-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScATAC-seqLevel2 -MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,False,,,,ScATAC-seqLevel3 +nCount Peaks,nCount Peaks,NCountPeaks,Total number of fragments in peaks,False,,,,ScATAC-seqLevel3 +Seurat Clusters,Seurat Clusters,SeuratClusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,False,,,,ScATAC-seqLevel3 +TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,False,,,,ScATAC-seqLevel3 +Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3 +TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3 MACS2 Fold Change,MACS2 Fold Change,MACS2FoldChange,Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2,False,,,,ScATAC-seqLevel3 -MACS2 Score,MACS2 Score,MACS2Score,Peak score (proportional to q-value) in MACS2,False,,,,ScATAC-seqLevel3 -nFeature Peaks,nFeature Peaks,NFeaturePeaks,Number of peaks with at least one read,False,,,,ScATAC-seqLevel3 +Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3 +MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel3 -MACS2 Start,MACS2 Start,MACS2Start,Genomic starting position in MACS2,False,,,,ScATAC-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScATAC-seqLevel3 -Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,ScATAC-seqLevel3 -MACS2 Neg Log10 qvalue Summit,MACS2 Neg Log10 qvalue Summit,MACS2NegLog10qvalueSummit,Negative log10 q-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 -Blacklist Ratio,Blacklist Ratio,BlacklistRatio,Ratio of reads in blacklist regions,False,,,,ScATAC-seqLevel3 -MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3 Chimeric Read-Pairs,Chimeric Read-Pairs,ChimericRead-Pairs,Number of chimerically mapped read-pairs,False,,,,ScATAC-seqLevel3 +Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel3 scATAC-seq Object ID,scATAC-seq Object ID,ScATAC-seqObjectID,Orig.Ident or scATAC-seq Object ID,False,,,,ScATAC-seqLevel3 -DNase Sensitive Region Fragments,DNase Sensitive Region Fragments,DNaseSensitiveRegionFragments,Number of fragments overlapping with DNase sensitive regions,False,,,,ScATAC-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScATAC-seqLevel3 MACS2 End,MACS2 End,MACS2End,Genomic ending position in MACS2,False,,,,ScATAC-seqLevel3 +MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3 +MACS2 Neg Log10 qvalue Summit,MACS2 Neg Log10 qvalue Summit,MACS2NegLog10qvalueSummit,Negative log10 q-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel3 -Nucleosome Signal,Nucleosome Signal,NucleosomeSignal,"Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))",False,,,,ScATAC-seqLevel3 -On Target Fragments,On Target Fragments,OnTargetFragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",False,,,,ScATAC-seqLevel3 -nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3 -Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter regions,False,,,,ScATAC-seqLevel3 -Seurat Clusters,Seurat Clusters,SeuratClusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,False,,,,ScATAC-seqLevel3 -nCount RNA,nCount RNA,NCountRNA,Total number of fragments in genes,False,,,,ScATAC-seqLevel3 -Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3 -MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3 -Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3 -TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3 +Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3 +Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,False,,,,ScATAC-seqLevel3 Pct Reads in Peaks,Pct Reads in Peaks,PctReadsinPeaks,Percentage of reads in peaks,False,,,,ScATAC-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel3 -Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel3 -TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,False,,,,ScATAC-seqLevel3 Unmapped Read-Pairs,Unmapped Read-Pairs,UnmappedRead-Pairs,Number of read-pairs with at least one end not mapped,False,,,,ScATAC-seqLevel3 -MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3 -Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3 -Peak Region Fragments,Peak Region Fragments,PeakRegionFragments,Number of fragments overlapping peaks,False,,,,ScATAC-seqLevel3 -Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3 +Blacklist Ratio,Blacklist Ratio,BlacklistRatio,Ratio of reads in blacklist regions,False,,,,ScATAC-seqLevel3 +Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,ScATAC-seqLevel3 +MACS2 Score,MACS2 Score,MACS2Score,Peak score (proportional to q-value) in MACS2,False,,,,ScATAC-seqLevel3 Nucleosome Percentile,Nucleosome Percentile,NucleosomePercentile,Percentile rank of nucleosome score,False,,,,ScATAC-seqLevel3 -Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3 -nCount Peaks,nCount Peaks,NCountPeaks,Total number of fragments in peaks,False,,,,ScATAC-seqLevel3 LowMapQ,LowMapQ,LowMapQ,Number of read-pairs with <30 mapq on at least one end,False,,,,ScATAC-seqLevel3 -MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3 -Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,False,,,,ScATAC-seqLevel3 -MACS2 Neg Log10 pvalue Summit,MACS2 Neg Log10 pvalue Summit,MACS2NegLog10pvalueSummit,Negative log10 p-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 +nFeature Peaks,nFeature Peaks,NFeaturePeaks,Number of peaks with at least one read,False,,,,ScATAC-seqLevel3 +Peak Region Fragments,Peak Region Fragments,PeakRegionFragments,Number of fragments overlapping peaks,False,,,,ScATAC-seqLevel3 TSS Enrichment,TSS Enrichment,TSSEnrichment,Transcription start site (TSS) enrichment score,False,,,,ScATAC-seqLevel3 +Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter regions,False,,,,ScATAC-seqLevel3 +MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3 +On Target Fragments,On Target Fragments,OnTargetFragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",False,,,,ScATAC-seqLevel3 +nCount RNA,nCount RNA,NCountRNA,Total number of fragments in genes,False,,,,ScATAC-seqLevel3 +MACS2 Start,MACS2 Start,MACS2Start,Genomic starting position in MACS2,False,,,,ScATAC-seqLevel3 +DNase Sensitive Region Fragments,DNase Sensitive Region Fragments,DNaseSensitiveRegionFragments,Number of fragments overlapping with DNase sensitive regions,False,,,,ScATAC-seqLevel3 +MACS2 Neg Log10 pvalue Summit,MACS2 Neg Log10 pvalue Summit,MACS2NegLog10pvalueSummit,Negative log10 p-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 +Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3 +MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,False,,,,ScATAC-seqLevel3 +nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3 +Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3 +Nucleosome Signal,Nucleosome Signal,NucleosomeSignal,"Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))",False,,,,ScATAC-seqLevel3 +MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel3 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,ScmC-seqLevel1 +Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScmC-seqLevel1 +Single Nucleus Capture,Single Nucleus Capture,SingleNucleusCapture,Nuclei isolation method,False,,"['Plates', 'droplet', '10x', '']",,ScmC-seqLevel1 +scmCseq Read3,scmCseq Read3,ScmCseqRead3,Read 3 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 +scmCseq Read2,scmCseq Read2,ScmCseqRead2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Microfluidics Chip', 'Droplets', '10x', 'Nuclei Isolation', 'FACS']",,ScmC-seqLevel1 +Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['NIB', '10x', 'TST', 'Omni']",,ScmC-seqLevel1 Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScmC-seqLevel1 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,ScmC-seqLevel1 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScmC-seqLevel1 -Single Nucleus Capture,Single Nucleus Capture,SingleNucleusCapture,Nuclei isolation method,False,,"['10x', 'droplet', 'Plates', '']",,ScmC-seqLevel1 -Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScmC-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScmC-seqLevel1 -scmCseq Read2,scmCseq Read2,ScmCseqRead2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,ScmC-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel1 -scmCseq Read3,scmCseq Read3,ScmCseqRead3,Read 3 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 -Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScmC-seqLevel1 -Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'Omni', 'TST', 'NIB']",,ScmC-seqLevel1 -Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,True,,,,ScmC-seqLevel1 -scmCseq Read1,scmCseq Read1,ScmCseqRead1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,ScmC-seqLevel1 -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScmC-seqLevel1 Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScmC-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScmC-seqLevel1 +Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['NEBNext Enzymatic Methyl-seq Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Zimo EZ DNA Methylation Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit']",,ScmC-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScmC-seqLevel1 Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScmC-seqLevel1 -Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Zimo EZ-96 DNA Methylation Deep Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit']",,ScmC-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,ScmC-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel1 +Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScmC-seqLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Long Read', 'Mid-length', 'Single Read']",,ScmC-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,ScmC-seqLevel1 Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScmC-seqLevel1 -Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScmC-seqLevel1 -Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScmC-seqLevel1 -Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScmC-seqLevel1 +scmCseq Read1,scmCseq Read1,ScmCseqRead1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel1 +Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,ScmC-seqLevel1 +Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1 +Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkMethylation-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,BulkMethylation-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1 +Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScmC-seqLevel1 +Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScmC-seqLevel1 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel1 Total DNA Input,Total DNA Input,TotalDNAInput,"Overall number of reads for a given sample in digits (microgram, nanogram).",False,,,,BulkMethylation-seqLevel1 -Replicate Type,Replicate Type,ReplicateType,A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.,True,,"['Technical replicate', 'Not Applicable', 'Biological replicate']",,BulkMethylation-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel1 -Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Zimo EZ-96 DNA Methylation Deep Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit']",,BulkMethylation-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,BulkMethylation-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkMethylation-seqLevel1 -Bulk Methylation Assay Type,Bulk Methylation Assay Type,BulkMethylationAssayType,Assay types normally determine genomic coverage,True,,"['Beadchip Array', 'Whole genome', 'Targeted Genome']",,BulkMethylation-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,BulkMethylation-seqLevel1 +Replicate Type,Replicate Type,ReplicateType,A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.,True,,"['Technical replicate', 'Biological replicate', 'Not Applicable']",,BulkMethylation-seqLevel1 +Bulk Methylation Assay Type,Bulk Methylation Assay Type,BulkMethylationAssayType,Assay types normally determine genomic coverage,True,,"['Whole genome', 'Beadchip Array', 'Targeted Genome']",,BulkMethylation-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkMethylation-seqLevel1 +Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['NEBNext Enzymatic Methyl-seq Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Zimo EZ DNA Methylation Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit']",,BulkMethylation-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,BulkMethylation-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkMethylation-seqLevel1 Beadchip Array,Beadchip Array,BeadchipArray,Assay that uses beads to target a specific locus on the genome.,False,,"['HM27K', 'HM450K', '']",,BulkMethylation-seqLevel1 Targeted Genome,Targeted Genome,TargetedGenome,Assay for analyzing specific mutations in a given sample,False,,"['MeDIP', 'RRBS', '']",,BulkMethylation-seqLevel1 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScmC-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScmC-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScmC-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScmC-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScmC-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScmC-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScmC-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScmC-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScmC-seqLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScmC-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScmC-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScmC-seqLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScmC-seqLevel2 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScmC-seqLevel2 Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScmC-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScmC-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BSMAP', 'BS-Seeker2', 'STAR 2-Pass Genome', 'BSmooth', 'Pash', 'RMAP', 'BS-Seeker', 'GSNAP', 'BWA', 'BWA-aln', 'BWA with Mark Duplicates and BQSR', 'STAR 2-Pass Transcriptome', 'None', 'BWA with BQSR', 'Other Alignment Workflow', 'BWA-meth', 'Bisulfighter', 'Bowtie', 'BatMeth', 'ERNE-BS5', 'BWA-mem', 'SOCS-B', 'STAR 2-Pass Chimeric', 'B-SOLANA', 'Bismark', 'BRAT-BW', 'MethylCoder', 'Segemehl', 'STAR 2-Pass', 'LAST']",,ScmC-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScmC-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScmC-seqLevel2 Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScmC-seqLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScmC-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,ScmC-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScmC-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScmC-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScmC-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScmC-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScmC-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScmC-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScmC-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScmC-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScmC-seqLevel2 Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScmC-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScmC-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScmC-seqLevel2 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScATAC-seqLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel4 -scATACseq Workflow Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,,,ScATAC-seqLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel4 scATACseq Workflow Parameters Description,scATACseq Workflow Parameters Description,ScATACseqWorkflowParametersDescription,Parameters used to run the scATAC-seq workflow.,True,,,,ScATAC-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScATAC-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel4 Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScATAC-seqLevel4 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScATAC-seqLevel4 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,ScDNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel1 -Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 -Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['rRNA Depletion', 'Random', 'Other', 'PCR', 'Affinity Enrichment', 'miRNA Size Fractionation', 'Hybrid Selection', 'Poly-T Enrichment']",,ScDNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScDNA-seqLevel1 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScDNA-seqLevel1 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,ScDNA-seqLevel1 +scATACseq Workflow Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,,,ScATAC-seqLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel4 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScATAC-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel4 +Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,ScDNA-seqLevel1 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,ScDNA-seqLevel1 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,ScDNA-seqLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,ScDNA-seqLevel1 Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,ScDNA-seqLevel1 -Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,ScDNA-seqLevel1 +Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,ScDNA-seqLevel1 +Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 +Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 +Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,ScDNA-seqLevel1 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel1 +Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Second Stranded', 'Not Applicable', 'First Stranded', 'Unstranded', '']",,ScDNA-seqLevel1 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScDNA-seqLevel1 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScDNA-seqLevel1 +Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,ScDNA-seqLevel1 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,ScDNA-seqLevel1 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel1 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Hybrid Selection', 'PCR', 'Poly-T Enrichment', 'rRNA Depletion', 'Other', 'Affinity Enrichment']",,ScDNA-seqLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Long Read', 'Mid-length', 'Single Read']",,ScDNA-seqLevel1 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,ScDNA-seqLevel1 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'Not Reported', 'WARN', 'unknown', 'PASS', '']",,ScDNA-seqLevel1 Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,ScDNA-seqLevel1 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,ScDNA-seqLevel1 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 +Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 +Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,ScDNA-seqLevel1 Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,ScDNA-seqLevel1 -QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,ScDNA-seqLevel1 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,ScDNA-seqLevel1 Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,ScDNA-seqLevel1 -Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,ScDNA-seqLevel1 -Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,ScDNA-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScDNA-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel1 -Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,ScDNA-seqLevel1 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['Yes - Trim Adapter Sequence', 'no', '']",,ScDNA-seqLevel1 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,ScDNA-seqLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 -Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 -Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,ScDNA-seqLevel1 -Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,ScDNA-seqLevel1 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,ScDNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,ScDNA-seqLevel1 -Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Second Stranded', 'Not Applicable', 'First Stranded', '']",,ScDNA-seqLevel1 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['Not Reported', 'FAIL', 'WARN', 'PASS', 'unknown', '']",,ScDNA-seqLevel1 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScDNA-seqLevel2 +Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1 +Proportion Mitochondrial Reads,Proportion Mitochondrial Reads,ProportionMitochondrialReads,Proportion of reads mapping to mitochondria.,False,,,,ScDNA-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScDNA-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScDNA-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScDNA-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScDNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ScDNA-seqLevel2 Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScDNA-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScDNA-seqLevel2 +MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScDNA-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ScDNA-seqLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScDNA-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScDNA-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScDNA-seqLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScDNA-seqLevel2 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScDNA-seqLevel2 Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScDNA-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScDNA-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BSMAP', 'BS-Seeker2', 'STAR 2-Pass Genome', 'BSmooth', 'Pash', 'RMAP', 'BS-Seeker', 'GSNAP', 'BWA', 'BWA-aln', 'BWA with Mark Duplicates and BQSR', 'STAR 2-Pass Transcriptome', 'None', 'BWA with BQSR', 'Other Alignment Workflow', 'BWA-meth', 'Bisulfighter', 'Bowtie', 'BatMeth', 'ERNE-BS5', 'BWA-mem', 'SOCS-B', 'STAR 2-Pass Chimeric', 'B-SOLANA', 'Bismark', 'BRAT-BW', 'MethylCoder', 'Segemehl', 'STAR 2-Pass', 'LAST']",,ScDNA-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScDNA-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScDNA-seqLevel2 Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2 -MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScDNA-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScDNA-seqLevel2 -Proportion Mitochondrial Reads,Proportion Mitochondrial Reads,ProportionMitochondrialReads,Proportion of reads mapping to mitochondria.,False,,,,ScDNA-seqLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScDNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScDNA-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,ScDNA-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScDNA-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScDNA-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScDNA-seqLevel2 Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScDNA-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScDNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScDNA-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScDNA-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScDNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScDNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScDNA-seqLevel2 Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScDNA-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScDNA-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScDNA-seqLevel2 -Single Cell Barcode Method Applied,Single Cell Barcode Method Applied,SingleCellBarcodeMethodApplied,The method by which cells are multiplex or labeled with cell surface markers or probes,True,,"['Hashtag- multiplex', 'Cite-seq custom panel', 'Other', 'Biolegend Total seq B Human Universal cocktail V1.0', 'Nuclear Hashtag- multiplex', 'Biolegend Total seq A Custom', 'Biolegend Total seq C Custom', 'Biolegend Total seq B Custom', 'Biolegend Total seq A Human', 'Biolegend Total seq C Human Universal cocktail V1.0', 'Cell', 'Universal cocktail V1.0']",,MultiplexedCITE-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 -Barcode Folder File List,Barcode Folder File List,BarcodeFolderFileList,A comma separated list of filenames in the gzipped folder detailing what barcodes are specific to demultiplexing samples versus providing surface protein data,True,,,,MultiplexedCITE-seqLevel1 -Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 -Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],True,,,,MultiplexedCITE-seqLevel1 -Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,MultiplexedCITE-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MultiplexedCITE-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,MultiplexedCITE-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,MultiplexedCITE-seqLevel1 -Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,MultiplexedCITE-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,,"['no', 'yes', '']",,MultiplexedCITE-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",True,,,,MultiplexedCITE-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,MultiplexedCITE-seqLevel1 Barcode Folder Synapse ID,Barcode Folder Synapse ID,BarcodeFolderSynapseID,Synapse ID of the folder containing the barcode lists,True,,,,MultiplexedCITE-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MultiplexedCITE-seqLevel1 -Feature Barcode Library Type,Feature Barcode Library Type,FeatureBarcodeLibraryType,The library construction methods for the feature barcode library,True,,"['10x ADT – citeseq/hashing', '10x TCR', '10x BCR']",,MultiplexedCITE-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel1 +Single Cell Barcode Method Applied,Single Cell Barcode Method Applied,SingleCellBarcodeMethodApplied,The method by which cells are multiplex or labeled with cell surface markers or probes,True,,"['Nuclear Hashtag- multiplex', 'Biolegend Total seq A Human', 'Biolegend Total seq C Custom', 'Biolegend Total seq B Human Universal cocktail V1.0', 'Hashtag- multiplex', 'Biolegend Total seq B Custom', 'Cite-seq custom panel', 'Biolegend Total seq A Custom', 'Universal cocktail V1.0', 'Biolegend Total seq C Human Universal cocktail V1.0', 'Other', 'Cell']",,MultiplexedCITE-seqLevel1 Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",True,,,,MultiplexedCITE-seqLevel1 -Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,True,,,,MultiplexedCITE-seqLevel1 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,,"['no', 'yes', '']",,MultiplexedCITE-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Microfluidics Chip', 'Droplets', '10x', 'Nuclei Isolation', 'FACS']",,MultiplexedCITE-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['R1&R2', 'I1', 'R1', 'R2', 'Other']",,MultiplexedCITE-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel1 Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,MultiplexedCITE-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Microfluidics Chip', '10x', 'Nuclei Isolation', 'Droplets', 'Plates', 'FACS']",,MultiplexedCITE-seqLevel1 -Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,MultiplexedCITE-seqLevel1 -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,MultiplexedCITE-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MultiplexedCITE-seqLevel1 Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,MultiplexedCITE-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,MultiplexedCITE-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['5 Prime', 'Full Length Transcript', '3 Prime']",,MultiplexedCITE-seqLevel1 +Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1 +Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,True,,,,MultiplexedCITE-seqLevel1 +Feature Barcode Library Type,Feature Barcode Library Type,FeatureBarcodeLibraryType,The library construction methods for the feature barcode library,True,,"['10x ADT – citeseq/hashing', '10x BCR', '10x TCR']",,MultiplexedCITE-seqLevel1 +Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,MultiplexedCITE-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10x Multiome', '10xV1.0', '10xV3', ""10x GEM 5'"", '10xV1.1', '10xV2', '10x FLEX', 'Nextera XT', 'Drop-seq', 'CEL-seq2', 'inDropsV3', 'TruDrop', 'sci-ATAC-seq', 'inDropsV2', '10xV3.1', ""10x GEM 3'"", 'Smart-seq2', 'Smart-SeqV4']",,MultiplexedCITE-seqLevel1 +Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],True,,,,MultiplexedCITE-seqLevel1 +Barcode Folder File List,Barcode Folder File List,BarcodeFolderFileList,A comma separated list of filenames in the gzipped folder detailing what barcodes are specific to demultiplexing samples versus providing surface protein data,True,,,,MultiplexedCITE-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,MultiplexedCITE-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MultiplexedCITE-seqLevel1 +Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Oligo-dT', 'Random', 'Poly-dT']",,MultiplexedCITE-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'ERCC', 'No Spike In', 'PhiX']",,MultiplexedCITE-seqLevel1 Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 +Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Dounce', 'gentleMACS', 'Not Applicable', 'Enzymatic Digestion']",,MultiplexedCITE-seqLevel1 +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,MultiplexedCITE-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['Nextera XT', 'Drop-seq', 'CEL-seq2', '10xV2', '10xV1.1', 'inDropsV2', 'sci-ATAC-seq', '10x Multiome', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', ""10x GEM 3'"", '10xV3.1', 'Smart-SeqV4', ""10x GEM 5'"", '10x FLEX']",,MultiplexedCITE-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Enzymatic Digestion', 'Not Applicable', 'Dounce']",,MultiplexedCITE-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'ERCC', 'PhiX', 'Other Spike In']",,MultiplexedCITE-seqLevel1 -Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,MultiplexedCITE-seqLevel1 -Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 -Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 -Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 +Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,MultiplexedCITE-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,MultiplexedCITE-seqLevel1 +Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 +Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 +Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 -Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",MultiplexedCITE-seqLevel1 +Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read1 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",MultiplexedCITE-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read1 is ""cDNA""']",MultiplexedCITE-seqLevel1 Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,MultiplexedCITE-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,MultiplexedCITE-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2 -Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,MultiplexedCITE-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MultiplexedCITE-seqLevel2 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,MultiplexedCITE-seqLevel2 -Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,MultiplexedCITE-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,MultiplexedCITE-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,MultiplexedCITE-seqLevel2 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel2 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,MultiplexedCITE-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,MultiplexedCITE-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,MultiplexedCITE-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MultiplexedCITE-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel2 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,MultiplexedCITE-seqLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,MultiplexedCITE-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,MultiplexedCITE-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel2 +Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,MultiplexedCITE-seqLevel2 +Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel2 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STARsolo', 'dropEST', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'Differentiation trajectory analysis', 'Cell annotation', 'HTSeq - FPKM', 'SEQC', 'DEXSeq', 'Other']",,MultiplexedCITE-seqLevel2 Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,MultiplexedCITE-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",MultiplexedCITE-seqLevel2 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Other', 'Gene Expression Quantification', 'Exon Expression Quantification', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification']",,MultiplexedCITE-seqLevel3 -Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,MultiplexedCITE-seqLevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,MultiplexedCITE-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,MultiplexedCITE-seqLevel3 -scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel3 -Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel3 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,MultiplexedCITE-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MultiplexedCITE-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STARsolo', 'dropEST', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'Differentiation trajectory analysis', 'Cell annotation', 'HTSeq - FPKM', 'SEQC', 'DEXSeq', 'Other']",,MultiplexedCITE-seqLevel3 Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,MultiplexedCITE-seqLevel3 +scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MultiplexedCITE-seqLevel3 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel3 +Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Transcript Expression', 'Gene Expression', 'Isoform Expression Quantification', 'Gene Expression Quantification', 'Splice Junction Quantification', 'Exon Expression Quantification', 'Other']",,MultiplexedCITE-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel3 +Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,MultiplexedCITE-seqLevel3 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel3 Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,MultiplexedCITE-seqLevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel4 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel3 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Batch Corrected Counts', 'Scaled Counts', 'Normalized Counts']",,MultiplexedCITE-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STARsolo', 'dropEST', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'Differentiation trajectory analysis', 'Cell annotation', 'HTSeq - FPKM', 'SEQC', 'DEXSeq', 'Other']",,MultiplexedCITE-seqLevel4 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel4 -Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel4 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['HCA Optimus', 'dropEST', 'Other', 'Differentiation trajectory analysis', 'Cell annotation', 'DEXSeq', 'STARsolo', 'Cufflinks', 'CellRanger', 'HTSeq - FPKM', 'SEQC']",,MultiplexedCITE-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MultiplexedCITE-seqLevel4 Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MultiplexedCITE-seqLevel4 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel4 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Single Read', 'Long Read', 'Mid-length', 'Paired End']",,BulkMethylation-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkMethylation-seqLevel2 +Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel4 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel4 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel4 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkMethylation-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 +Trimmer,Trimmer,Trimmer,Software used for trimming,True,,"['Trim Galore!', 'Kraken', 'Cutadapt', 'PRINSEQ', 'Adapter removal', 'ConDeTri', 'FASTX toolkit', 'SolexaQA', 'ERNE-FILTER', 'Trimmo-matic', 'Btrim']",,BulkMethylation-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel2 -Duplicate Removal Software,Duplicate Removal Software,DuplicateRemovalSoftware,Software used for remove duplicate reads,True,,"['Samtools sort', 'picard MarkDuplicates']",,BulkMethylation-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkMethylation-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkMethylation-seqLevel2 Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkMethylation-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkMethylation-seqLevel2 +Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Proportion of Minimum CpG Coverage 10X,Proportion of Minimum CpG Coverage 10X,ProportionofMinimumCpGCoverage10X,"Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.",False,,,,BulkMethylation-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel2 -Bulk Methylation Genomic Reference,Bulk Methylation Genomic Reference,BulkMethylationGenomicReference,The human genome reference used in the alignment of reads,True,,"['HG19', 'T2T CHM13', 'HG38']",,BulkMethylation-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkMethylation-seqLevel2 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkMethylation-seqLevel2 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkMethylation-seqLevel2 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkMethylation-seqLevel2 -Proportion of Minimum CpG Coverage 10X,Proportion of Minimum CpG Coverage 10X,ProportionofMinimumCpGCoverage10X,"Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.",False,,,,BulkMethylation-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BSMAP', 'BS-Seeker2', 'STAR 2-Pass Genome', 'BSmooth', 'Pash', 'RMAP', 'BS-Seeker', 'GSNAP', 'BWA', 'BWA-aln', 'BWA with Mark Duplicates and BQSR', 'STAR 2-Pass Transcriptome', 'None', 'BWA with BQSR', 'Other Alignment Workflow', 'BWA-meth', 'Bisulfighter', 'Bowtie', 'BatMeth', 'ERNE-BS5', 'BWA-mem', 'SOCS-B', 'STAR 2-Pass Chimeric', 'B-SOLANA', 'Bismark', 'BRAT-BW', 'MethylCoder', 'Segemehl', 'STAR 2-Pass', 'LAST']",,BulkMethylation-seqLevel2 +Bulk Methylation Genomic Reference,Bulk Methylation Genomic Reference,BulkMethylationGenomicReference,The human genome reference used in the alignment of reads,True,,"['HG19', 'HG38', 'T2T CHM13']",,BulkMethylation-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkMethylation-seqLevel2 Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 -Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['STAR 2-Pass Transcriptome', 'BSmooth', 'Bismark', 'BWA-aln', 'SOCS-B', 'Bowtie', 'BRAT-BW', 'BatMeth', 'BWA', 'BWA-meth', 'GSNAP', 'STAR 2-Pass Chimeric', 'Bisulfighter', 'BWA with BQSR', 'LAST', 'STAR 2-Pass', 'STAR 2-Pass Genome', 'BWA with Mark Duplicates and BQSR', 'ERNE-BS5', 'BS-Seeker2', 'MethylCoder', 'Other Alignment Workflow', 'Segemehl', 'BSMAP', 'Pash', 'None', 'B-SOLANA', 'RMAP', 'BWA-mem', 'BS-Seeker']",,BulkMethylation-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Paired End', 'Long Read', 'Mid-length', 'Single Read']",,BulkMethylation-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkMethylation-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkMethylation-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkMethylation-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkMethylation-seqLevel2 +Duplicate Removal Software,Duplicate Removal Software,DuplicateRemovalSoftware,Software used for remove duplicate reads,True,,"['picard MarkDuplicates', 'Samtools sort']",,BulkMethylation-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkMethylation-seqLevel2 Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkMethylation-seqLevel2 -Trimmer,Trimmer,Trimmer,Software used for trimming,True,,"['Trim Galore!', 'FASTX toolkit', 'ConDeTri', 'ERNE-FILTER', 'Adapter removal', 'Kraken', 'Cutadapt', 'PRINSEQ', 'SolexaQA', 'Trimmo-matic', 'Btrim']",,BulkMethylation-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkMethylation-seqLevel2 -Lambda methylation ratio,Lambda methylation ratio,Lambdamethylationratio,"Methylation ratio of mostly unmethylated lambda control, as a percentage",True,,,,BulkMethylation-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel3 -DMR Calling Tool,DMR Calling Tool,DMRCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['metilene', 'DSS', 'MethylSig', 'DSS-single', 'BiSeq', 'MACAU', 'BSmooth', 'MethylKit', 'MOABS']",,BulkMethylation-seqLevel3 -DMR Calling Workflow URL,DMR Calling Workflow URL,DMRCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3 -DMR data file Format,DMR data file Format,DMRdatafileFormat,Format of the data files.,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3 -DMC Calling Tool,DMC Calling Tool,DMCCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['metilene', 'DSS', 'MethylSig', 'DSS-single', 'BiSeq', 'MACAU', 'MethylDackel', 'BSmooth', 'MethylKit', 'MOABS']",,BulkMethylation-seqLevel3 +DMC data file format,DMC data file format,DMCdatafileformat,Format of the data files,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3 +DMC Calling Tool,DMC Calling Tool,DMCCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['MethylSig', 'BSmooth', 'DSS', 'BiSeq', 'metilene', 'MOABS', 'MACAU', 'MethylKit', 'DSS-single', 'MethylDackel']",,BulkMethylation-seqLevel3 DMC Calling Workflow URL,DMC Calling Workflow URL,DMCCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,BulkMethylation-seqLevel3 -pUC19 methylation ratio,pUC19 methylation ratio,PUC19methylationratio,"Methylation ratio of mostly methylated pUC19 control, as a percentage",True,,,,BulkMethylation-seqLevel3 +DMR Calling Tool,DMR Calling Tool,DMRCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['MethylSig', 'BSmooth', 'DSS', 'BiSeq', 'metilene', 'MOABS', 'MACAU', 'MethylKit', 'DSS-single']",,BulkMethylation-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel3 -DMC data file format,DMC data file format,DMCdatafileformat,Format of the data files,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3 -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel1 -Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel1 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,ImagingLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,BulkMethylation-seqLevel3 +pUC19 methylation ratio,pUC19 methylation ratio,PUC19methylationratio,"Methylation ratio of mostly methylated pUC19 control, as a percentage",True,,,,BulkMethylation-seqLevel3 +DMR data file Format,DMR data file Format,DMRdatafileFormat,Format of the data files.,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel3 +Lambda methylation ratio,Lambda methylation ratio,Lambdamethylationratio,"Methylation ratio of mostly unmethylated lambda control, as a percentage",True,,,,BulkMethylation-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel3 +DMR Calling Workflow URL,DMR Calling Workflow URL,DMRCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel1 +Pre-processing Required,Pre-processing Required,Pre-processingRequired,Pre-processing steps required to convert level 1 raw data to a single level 2 image,True,,"['Channel/Cycle Registration', 'Tile Stitching', 'Other', 'Illumination correction', 'None', 'TMA de-arraying']",,ImagingLevel1 +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel1 +Pre-processing Completed,Pre-processing Completed,Pre-processingCompleted,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,True,,"['Channel/Cycle Registration', 'Tile Stitching', 'Other', 'Illumination correction', 'None', 'TMA de-arraying']",,ImagingLevel1 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel1 -Pre-processing Completed,Pre-processing Completed,Pre-processingCompleted,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,True,,"['Other', 'Channel/Cycle Registration', 'TMA de-arraying', 'None', 'Illumination correction', 'Tile Stitching']",,ImagingLevel1 Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel1 -Pre-processing Required,Pre-processing Required,Pre-processingRequired,Pre-processing steps required to convert level 1 raw data to a single level 2 image,True,,"['Other', 'Channel/Cycle Registration', 'TMA de-arraying', 'None', 'Illumination correction', 'Tile Stitching']",,ImagingLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ImagingLevel1 +Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel1 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CODEX', 'MxIF', 'ExSeq', 'mIHC', 'RareCyte Orion', 'IMC', 'CyCIF', 'GeoMX-DSP', 'MERFISH', 'H&E', 'MIBI', 'IHC', 't-CyCIF', 'Not Applicable', 'SABER']",,ImagingLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel1 Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel1 -WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel2 -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel2 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel2 -Objective,Objective,Objective,Objective,False,,,,ImagingLevel2 -Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,ImagingLevel2 -FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2 -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,ImagingLevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel2 -Immersion,Immersion,Immersion,Immersion medium,False,,"['Oil', 'Water', 'Other', 'Air', '']",,ImagingLevel2 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['nm', 'mm', 'cm', 'Å', 'µm']",,ImagingLevel2 SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['nm', 'mm', 'cm', 'Å', 'µm']",,ImagingLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel2 -PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['uint32', 'int32', 'bit', 'uint16', 'double', 'uint8', 'float', 'int8', 'int16']",,ImagingLevel2 -PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ImagingLevel2 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2 -SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel2 -Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2 FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel2 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel2 +SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2 +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel2 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'µm', 'Å', 'nm', 'cm']",,ImagingLevel2 +Objective,Objective,Objective,Objective,False,,,,ImagingLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel2 PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ImagingLevel2 -SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,ImagingLevel2 -MERFISH Codebook File,MERFISH Codebook File,MERFISHCodebookFile,The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.,False,,,,ImagingLevel2 +PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'µm', 'Å', 'nm', 'cm']",,ImagingLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel2 +LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ImagingLevel2 SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ImagingLevel2 -WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2 -SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,ImagingLevel2 -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel2 -FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel2 +MERFISH Codebook File,MERFISH Codebook File,MERFISHCodebookFile,The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.,False,,,,ImagingLevel2 +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel2 +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2 FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel2 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CODEX', 'MxIF', 'ExSeq', 'mIHC', 'RareCyte Orion', 'IMC', 'CyCIF', 'GeoMX-DSP', 'MERFISH', 'H&E', 'MIBI', 'IHC', 't-CyCIF', 'Not Applicable', 'SABER']",,ImagingLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel2 +FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ImagingLevel2 +SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,ImagingLevel2 +Immersion,Immersion,Immersion,Immersion medium,False,,"['Water', 'Other', 'Oil', 'Air', '']",,ImagingLevel2 +Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,ImagingLevel2 MERFISH Positions File,MERFISH Positions File,MERFISHPositionsFile,The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.,False,,,,ImagingLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel2 -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2 -PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2 +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,ImagingLevel2 Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel2 -DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCTZ', 'XYZTC', 'XYCZT', 'XYZCT', 'XYTZC']",,ImagingLevel2 -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel2 -FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel2 -PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2 -Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['true', 'false']",,ImagingLevel2 -LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2 Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel2 -Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel3Segmentation -Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Probability Map', 'Mask', 'Point', 'Polygon', 'Outline']",,ImagingLevel3Segmentation -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Segmentation -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Segmentation -Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation +DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['XYZTC', 'ZYX', 'XYCZT', 'XYTZC', 'XYZCT', 'XYCTZ']",,ImagingLevel2 +WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel2 +SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['bit', 'int32', 'uint32', 'int8', 'double', 'uint16', 'float', 'int16', 'uint8']",,ImagingLevel2 +WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ImagingLevel2 +PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ImagingLevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel2 +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['yes', 'No - Channels QC']",,ImagingLevel2 +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ImagingLevel2 +Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['false', 'true']",,ImagingLevel2 +PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2 +Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2 +FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ImagingLevel2 +FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel2 Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel3Segmentation +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Segmentation Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel3Segmentation -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Segmentation +Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation +Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Mask', 'Outline', 'Probability Map', 'Polygon', 'Point']",,ImagingLevel3Segmentation Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Segmentation -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel3Segmentation Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Segmentation +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ImagingLevel3Segmentation +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Segmentation +Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel3Segmentation +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Segmentation Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ImagingLevel3Segmentation -WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel3Image -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Image -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel3Image +FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Image -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel3Image +HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel3Image +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel3Image Objective,Objective,Objective,Objective,False,,,,ImagingLevel3Image -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,ImagingLevel3Image -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel3Image -Immersion,Immersion,Immersion,Immersion medium,False,,"['Oil', 'Water', 'Other', 'Air', '']",,ImagingLevel3Image -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel3Image -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Image -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel3Image -FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,ImagingLevel3Image -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel3Image -FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel3Image -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Image +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Image Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Image +LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ImagingLevel3Image +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel3Image +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Image Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel3Image +FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel3Image +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CODEX', 'MxIF', 'ExSeq', 'mIHC', 'RareCyte Orion', 'IMC', 'CyCIF', 'GeoMX-DSP', 'MERFISH', 'H&E', 'MIBI', 'IHC', 't-CyCIF', 'Not Applicable', 'SABER']",,ImagingLevel3Image +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel3Image +Immersion,Immersion,Immersion,Immersion medium,False,,"['Water', 'Other', 'Oil', 'Air', '']",,ImagingLevel3Image +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,ImagingLevel3Image Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel3Image -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel3Image -HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel3Image -FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel3Image -LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel3Image -WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel3Image -FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel3Image -FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ImagingLevel3Image +WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel3Image +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel3Image +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['yes', 'No - Channels QC']",,ImagingLevel3Image +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel3Image +FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel3Image +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Image +FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ImagingLevel3Image +FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ImagingLevel3Image +WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ImagingLevel3Image +Antibody Role,Antibody Role,AntibodyRole,"""Is this antibody acting as a primary or secondary antibody""",True,,"['Primary', 'Secondary', 'Neither-Dye/Stain']",,ImagingLevel3Channels +Target Name,Target Name,TargetName,Short descriptive name (abbreviation) for this target (antigen),True,,,,ImagingLevel3Channels Vendor,Vendor,Vendor,Vendor,False,,,,ImagingLevel3Channels -Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission spectrum (nm),False,,,,ImagingLevel3Channels -Channel Passed QC,Channel Passed QC,ChannelPassedQC,Identify stains that did not pass QC but are included in the dataset.,True,,"['No - Channel Failed QC', 'yes']",,ImagingLevel3Channels -Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels +Cycle Number,Cycle Number,CycleNumber,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),False,,,,ImagingLevel3Channels Antibody Name,Antibody Name,AntibodyName,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",True,,,,ImagingLevel3Channels -Oligo Barcode Lower Strand,Oligo Barcode Lower Strand,OligoBarcodeLowerStrand,Oligo Barcode - Lower Strand,False,,,,ImagingLevel3Channels -Fluorophore,Fluorophore,Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),False,,,,ImagingLevel3Channels -Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels Excitation Bandwidth,Excitation Bandwidth,ExcitationBandwidth,Nominal width of excitation spectrum (nm),False,,,,ImagingLevel3Channels Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,ImagingLevel3Channels -HTAN Channel Metadata ID,HTAN Channel Metadata ID,HTANChannelMetadataID,HTAN ID for this channel metadata table (same for all rows),True,,,,ImagingLevel3Channels -Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels -Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels -Dilution,Dilution,Dilution,Dilution (eg 1:1000),False,,,,ImagingLevel3Channels -Channel Name,Channel Name,ChannelName,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin'),True,,,,ImagingLevel3Channels -Antibody Role,Antibody Role,AntibodyRole,"""Is this antibody acting as a primary or secondary antibody""",True,,"['Primary', 'Neither-Dye/Stain', 'Secondary']",,ImagingLevel3Channels -Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels Concentration,Concentration,Concentration,Concentration (eg 10ug/mL),False,,,,ImagingLevel3Channels -Metal Isotope Mass,Metal Isotope Mass,MetalIsotopeMass,Element mass number,False,,,,ImagingLevel3Channels -Sub Cycle Number,Sub Cycle Number,SubCycleNumber,Sub cycle number,False,,,,ImagingLevel3Channels +Channel Name,Channel Name,ChannelName,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin'),True,,,,ImagingLevel3Channels +Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels +Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels RRID identifier,RRID identifier,RRIDidentifier,Research Resource Identifier (eg “RRID: AB_394606”),True,,,,ImagingLevel3Channels -Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Sr', 'Lr', 'Sm', 'Rh', 'Fr', 'Zr', 'Ac', 'Te', 'Ta', 'H', 'Ge', 'Be', 'Gd', 'Ag', 'Hg', 'I', 'Li', 'Ti', 'Er', 'Rb', 'Np', 'no', 'Rg', 'Lu', 'Y', 'Lv', 'B', 'Ni', 'Sn', 'C', 'Ne', 'Fm', 'Pd', 'Hf', 'Pm', 'Tb', 'Md', 'Dy', 'Cs', 'V', 'Nb', 'Kr', 'Cd', 'W', 'Zn', 'Bh', 'Ba', 'Nd', 'Ga', 'Pt', 'Re', 'U', 'Cn', 'Cr', 'Ts', 'Mo', 'Br', 'He', 'Cu', 'Sg', 'Am', 'Mt', 'Eu', 'Al', 'Rf', 'Sb', 'Db', 'Ra', 'Co', 'Os', 'Th', 'Ir', 'Ar', 'Tl', 'Au', 'Hs', 'Bk', 'Si', 'Rn', 'K', 'Yb', 'Og', 'Pa', 'Fe', 'Ds', 'Se', 'Po', 'Na', 'Es', 'Bi', 'La', 'In', 'Pr', 'Mn', 'Pb', 'Tm', 'Ru', 'P', 'As', 'Ca', 'F', 'Mc', 'Pu', 'Mg', 'Ho', 'Cl', 'S', 'Fl', 'N', 'Tc', 'O', 'Sc', 'Xe', 'Cf', 'Nh', 'Ce', 'At', '']",,ImagingLevel3Channels -Cycle Number,Cycle Number,CycleNumber,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),False,,,,ImagingLevel3Channels -Target Name,Target Name,TargetName,Short descriptive name (abbreviation) for this target (antigen),True,,,,ImagingLevel3Channels +Sub Cycle Number,Sub Cycle Number,SubCycleNumber,Sub cycle number,False,,,,ImagingLevel3Channels +Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission spectrum (nm),False,,,,ImagingLevel3Channels +Metal Isotope Mass,Metal Isotope Mass,MetalIsotopeMass,Element mass number,False,,,,ImagingLevel3Channels +Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Ce', 'Tl', 'no', 'Tb', 'F', 'Sc', 'Th', 'Cr', 'Ge', 'Ho', 'Ts', 'Pa', 'Ra', 'Hf', 'C', 'At', 'Si', 'K', 'Zn', 'Es', 'Os', 'P', 'Lu', 'Zr', 'B', 'I', 'Rg', 'Kr', 'Ga', 'Er', 'As', 'W', 'Ti', 'He', 'Pm', 'Xe', 'Bh', 'Ds', 'Br', 'Sm', 'Ni', 'Pt', 'Pu', 'Au', 'V', 'Ag', 'Mc', 'Gd', 'S', 'Lr', 'Mn', 'Ar', 'Mg', 'Rh', 'Db', 'Eu', 'Bk', 'Cf', 'U', 'Ir', 'In', 'Hg', 'Ac', 'Rb', 'Co', 'Am', 'Dy', 'Ne', 'Na', 'Pb', 'Fr', 'Sb', 'Nd', 'Tm', 'Re', 'Md', 'Ta', 'Tc', 'Mt', 'Fl', 'Be', 'Cn', 'Rf', 'Np', 'Lv', 'Rn', 'Cs', 'Fe', 'Sn', 'Li', 'Y', 'Sg', 'La', 'Og', 'Ba', 'Cu', 'N', 'Nb', 'Fm', 'Sr', 'Ca', 'O', 'Se', 'Ru', 'Cl', 'Yb', 'Bi', 'Pr', 'Mo', 'Cd', 'H', 'Nh', 'Al', 'Pd', 'Hs', 'Po', 'Te', '']",,ImagingLevel3Channels Lot,Lot,Lot,Lot number from vendor,False,,,,ImagingLevel3Channels -Channel QC Failure Type,Channel QC Failure Type,ChannelQCFailureType,Reason the channel failed QC,False,True,"['Auto-fluoresence', 'Staining artefacet', 'Other/multiple channel QC faliure types', 'Off-target staining', 'Imaging artefact', '']","['Channel Passed QC is ""No - Channel Failed QC""']",ImagingLevel3Channels +Fluorophore,Fluorophore,Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),False,,,,ImagingLevel3Channels +Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels +HTAN Channel Metadata ID,HTAN Channel Metadata ID,HTANChannelMetadataID,HTAN ID for this channel metadata table (same for all rows),True,,,,ImagingLevel3Channels +Dilution,Dilution,Dilution,Dilution (eg 1:1000),False,,,,ImagingLevel3Channels +Channel Passed QC,Channel Passed QC,ChannelPassedQC,Identify stains that did not pass QC but are included in the dataset.,True,,"['No - Channel Failed QC', 'yes']",,ImagingLevel3Channels +Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels +Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels +Oligo Barcode Lower Strand,Oligo Barcode Lower Strand,OligoBarcodeLowerStrand,Oligo Barcode - Lower Strand,False,,,,ImagingLevel3Channels +Channel QC Failure Type,Channel QC Failure Type,ChannelQCFailureType,Reason the channel failed QC,False,True,"['Off-target staining', 'Other/multiple channel QC faliure types', 'Auto-fluoresence', 'Staining artefacet', 'Imaging artefact', '']","['Channel Passed QC is ""No - Channel Failed QC""']",ImagingLevel3Channels Channel QC Failure Comment,Channel QC Failure Comment,ChannelQCFailureComment,Custom comment on channel QC faliure,False,True,,"['Channel is ""Other/multiple channel QC faliure types""']",ImagingLevel3Channels -Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel4 -Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic,Function used to summarize object/feature intensity,False,,"['Not Specified', 'Median', 'Mean', '']",,ImagingLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel4 -Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel4 Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel4 -HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel4 +Number of Features,Number of Features,NumberofFeatures,The number of features (eg channels) described,True,,,,ImagingLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel4 Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel4 +Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel4 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel4 -Number of Features,Number of Features,NumberofFeatures,The number of features (eg channels) described,True,,,,ImagingLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ImagingLevel4 Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ImagingLevel4 +HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel4 +Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel4 +Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic,Function used to summarize object/feature intensity,False,,"['Median', 'Not Specified', 'Mean', '']",,ImagingLevel4 Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ImagingLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Image Re-orientation,Image Re-orientation,ImageRe-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.",False,,"['FALSE', 'TRUE', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['3 Prime', '5 Prime', 'Full Length Transcript']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Slide Version,Slide Version,SlideVersion,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,False,,"['V4', 'V1', 'V2', 'V3', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['Nextera XT', 'Drop-seq', '10xV2', '10xV1.1', 'inDropsV2', '10xV3', 'Smart-seq2', '10xV1.0', 'TruDrop', 'inDropsV3', '10xV3.1', 'Smart-SeqV4']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Poly-dT', 'Feature barcoding', 'Oligo-dT', 'Random']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'D', 'B1', 'D1', 'C1', 'A', 'C', 'B', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Permeabilization Time,Permeabilization Time,PermeabilizationTime,Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Image Re-orientation,Image Re-orientation,ImageRe-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.",False,,"['TRUE', 'FALSE', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['R1&R2', 'I1', 'R1', 'R2', 'Other']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['5 Prime', 'Full Length Transcript', '3 Prime']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Slide Version,Slide Version,SlideVersion,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,False,,"['V1', 'V2', 'V3', 'V4', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV1.0', '10xV3', '10xV1.1', '10xV2', 'Nextera XT', 'Drop-seq', 'inDropsV3', 'TruDrop', 'inDropsV2', '10xV3.1', 'Smart-seq2', 'Smart-SeqV4']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Oligo-dT', 'Random', 'Poly-dT']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Spatial Barcode Length,Spatial Barcode Length,SpatialBarcodeLength,Length of spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Whitelist Spatial Barcode File Link,Whitelist Spatial Barcode File Link,WhitelistSpatialBarcodeFileLink,Link to file listing all possible spatial barcodes. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'D', 'B1', 'D1', 'C1', 'A', 'C', 'B', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Whitelist Spatial Barcode File Link,Whitelist Spatial Barcode File Link,WhitelistSpatialBarcodeFileLink,Link to file listing all possible spatial barcodes. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'D', 'B1', 'D1', 'C1', 'A', 'C', 'B', '']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['low res image', 'qc result html', 'unfiltered mex', 'detected jpg', 'tissue_positions', 'high res image', 'filtered mex', 'json scale factors', 'fiducial image jpg', 'features', 'detected image png', 'fiducial image png', 'reference png', 'probe dataset csv', 'barcodes', 'reference jpg']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'B', 'A', 'D1', 'B1', 'C', 'C1', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['low res image', 'qc result html', 'unfiltered mex', 'detected jpg', 'tissue_positions', 'high res image', 'filtered mex', 'json scale factors', 'fiducial image jpg', 'features', 'detected image png', 'fiducial image png', 'reference png', 'probe dataset csv', 'barcodes', 'reference jpg']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['qc result html', 'probe dataset csv', 'features', 'detected image png', 'filtered mex', 'high res image', 'fiducial image jpg', 'unfiltered mex', 'fiducial image png', 'low res image', 'json scale factors', 'barcodes', 'tissue_positions', 'reference jpg', 'reference png', 'detected jpg']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles Mean Reads per Spatial Spot,Mean Reads per Spatial Spot,MeanReadsperSpatialSpot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Proportion Reads Mapped to Transcriptome,Proportion Reads Mapped to Transcriptome,ProportionReadsMappedtoTranscriptome,Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['A1', 'D', 'B1', 'D1', 'C1', 'A', 'C', 'B', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['qc result html', 'probe dataset csv', 'features', 'detected image png', 'filtered mex', 'high res image', 'fiducial image jpg', 'unfiltered mex', 'fiducial image png', 'low res image', 'json scale factors', 'barcodes', 'tissue_positions', 'reference jpg', 'reference png', 'detected jpg']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Visium Workflow Parameters Description,Visium Workflow Parameters Description,VisiumWorkflowParametersDescription,Parameters used to run the workflow..,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 Visium Workflow Type,Visium Workflow Type,VisiumWorkflowType,Generic name for the workflow used to analyze the visium data set.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Visium Workflow Parameters Description,Visium Workflow Parameters Description,VisiumWorkflowParametersDescription,Parameters used to run the workflow..,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP Library Preparation Kit Version,GeoMx DSP Library Preparation Kit Version,GeoMxDSPLibraryPreparationKitVersion,Version of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP NGS Sequencing Platform,GeoMx DSP NGS Sequencing Platform,GeoMxDSPNGSSequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP NGS Library Selection Method,GeoMx DSP NGS Library Selection Method,GeoMxDSPNGSLibrarySelectionMethod,How RNA molecules are isolated.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 GeoMx DSP NGS Library Preparation Kit Name,GeoMx DSP NGS Library Preparation Kit Name,GeoMxDSPNGSLibraryPreparationKitName,Name of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +GeoMx DSP Library Preparation Kit Vendor,GeoMx DSP Library Preparation Kit Vendor,GeoMxDSPLibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +GeoMx DSP Library Preparation Kit Version,GeoMx DSP Library Preparation Kit Version,GeoMxDSPLibraryPreparationKitVersion,Version of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -Synapse ID of GeoMx Lab Worksheet File,Synapse ID of GeoMx Lab Worksheet File,SynapseIDofGeoMxLabWorksheetFile,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 Filename,Filename,Filename,Name of a file,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 Synapse ID of GeoMx DSP PKC File,Synapse ID of GeoMx DSP PKC File,SynapseIDofGeoMxDSPPKCFile,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP Library Preparation Kit Vendor,GeoMx DSP Library Preparation Kit Vendor,GeoMxDSPLibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Biological probe median,Biological probe median,Biologicalprobemedian,Is the median count from all probes except the negative control probes. A measure of signal to background for each segment,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Deduplicated reads,Deduplicated reads,Deduplicatedreads,Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +GeoMx DSP NGS Library Selection Method,GeoMx DSP NGS Library Selection Method,GeoMxDSPNGSLibrarySelectionMethod,How RNA molecules are isolated.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +GeoMx DSP NGS Sequencing Platform,GeoMx DSP NGS Sequencing Platform,GeoMxDSPNGSSequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +Synapse ID of GeoMx Lab Worksheet File,Synapse ID of GeoMx Lab Worksheet File,SynapseIDofGeoMxLabWorksheetFile,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -In Situ Negative median,In Situ Negative median,InSituNegativemedian,Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Aligned reads,Aligned reads,Alignedreads,Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Raw reads,Raw reads,Rawreads,Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Stitched reads,Stitched reads,Stitchedreads,"Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Aligned reads,Aligned reads,Alignedreads,Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Biological probe median,Biological probe median,Biologicalprobemedian,Is the median count from all probes except the negative control probes. A measure of signal to background for each segment,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +In Situ Negative median,In Situ Negative median,InSituNegativemedian,Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Stitched reads,Stitched reads,Stitchedreads,"Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Deduplicated reads,Deduplicated reads,Deduplicatedreads,Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Slide name,Slide name,Slidename,"Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Binding Density,Binding Density,BindingDensity,The binding density as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Positive norm factor,Positive norm factor,Positivenormfactor,The Positive Control Normalization factor calculated using pos-hyb controls,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +QC status,QC status,QCstatus,ROI quality control flag as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Tissue Stain,Tissue Stain,TissueStain,e.g. CD45 or PanCK (if masking was performed),False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Positive norm factor,Positive norm factor,Positivenormfactor,The Positive Control Normalization factor calculated using pos-hyb controls,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Binding Density,Binding Density,BindingDensity,The binding density as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Tissue Stain,Tissue Stain,TissueStain,e.g. CD45 or PanCK (if masking was performed),False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -QC status,QC status,QCstatus,ROI quality control flag as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -GeoMx DSP Assay Type,GeoMx DSP Assay Type,GeoMxDSPAssayType,The assay type which was used for the GeoMx DSP pipeline.,True,,"['Protein NGS', 'RNA NGS', 'Protein nCounter', 'RNA nCounter']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Batch Corrected Counts', 'Normalized Counts']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Workflow Parameter Description,GeoMx DSP Workflow Parameter Description,GeoMxDSPWorkflowParameterDescription,Parameters used to run the GeoMx DSP workflow.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID of GeoMx DSP ROI Segment Annotation File,SynapseIDofGeoMxDSPROISegmentAnnotationFile,Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Assay Type,GeoMx DSP Assay Type,GeoMxDSPAssayType,The assay type which was used for the GeoMx DSP pipeline.,True,,"['Protein NGS', 'RNA NGS', 'RNA nCounter', 'Protein nCounter']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Workflow Parameter Description,GeoMx DSP Workflow Parameter Description,GeoMxDSPWorkflowParameterDescription,Parameters used to run the GeoMx DSP workflow.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +Filename,Filename,Filename,Name of a file,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Unique Target Count,GeoMx DSP Unique Target Count,GeoMxDSPUniqueTargetCount,Total number of unique genes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Workflow Link,GeoMx DSP Workflow Link,GeoMxDSPWorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 GeoMx DSP Genomic Reference,GeoMx DSP Genomic Reference,GeoMxDSPGenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID of GeoMx DSP ROI Segment Annotation File,SynapseIDofGeoMxDSPROISegmentAnnotationFile,Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Workflow Type,GeoMx DSP Workflow Type,GeoMxDSPWorkflowType,Generic name for the workflow used to analyze the GeoMx DSP data set.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Unique Target Count,GeoMx DSP Unique Target Count,GeoMxDSPUniqueTargetCount,Total number of unique genes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 GeoMx DSP Unique Probe Count,GeoMx DSP Unique Probe Count,GeoMxDSPUniqueProbeCount,Total number of unique probes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -Filename,Filename,Filename,Name of a file,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Workflow Type,GeoMx DSP Workflow Type,GeoMxDSPWorkflowType,Generic name for the workflow used to analyze the GeoMx DSP data set.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Workflow Link,GeoMx DSP Workflow Link,GeoMxDSPWorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,HI-C-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Not Reported', 'Ultima Genomics UG100', 'Illumina Genome Analyzer IIx', 'Illumina MiSeq', 'Illumina Next Seq 550', 'Illumina NextSeq 2000', 'Illumina NovaSeq 6000', 'unknown', 'Oxford Nanopore minION', 'Illumina HiSeq 2000', 'Illumina Genome Analyzer II', 'Ion Torrent Proton', 'Illumina Next Seq 2500', 'AB SOLiD 2', 'Illumina HiSeq 4000', 'Illumina NextSeq', 'AB SOLiD 3', 'Illumina HiSeq X Ten', 'GridION', 'Other', 'PacBio RS', 'Ion Torrent PGM', 'Ion Torrent S5', 'NovaSeqS4', 'AB SOLiD 4', 'Revio', 'Illumina NextSeq 1000', 'NovaSeq 6000', 'Illumina HiSeq X Five', 'Complete Genomics', 'Illumina Next Seq 500', '454 GS FLX Titanium', 'PacBio Sequel2', 'Illumina HiSeq 2500', 'PromethION']",,HI-C-seqLevel1 -Ligation Condition,Ligation Condition,LigationCondition,Name of ligase and condition for proximity ligation,True,,,,HI-C-seqLevel1 -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,HI-C-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Batch Corrected Counts', 'Scaled Counts', 'Normalized Counts']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Single Cell', 'Bulk Nuclei', 'Micro-region', 'Bulk Whole Cell']",,HI-C-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,HI-C-seqLevel1 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel1 +Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Tn5-059', 'Nextera Tn5', 'EZ-Tn5', 'Diagenode-unloaded Apex-Bio', 'In-House', 'Diagenode-loaded Apex-Bio', 'Tn5']",,HI-C-seqLevel1 +Ligation Condition,Ligation Condition,LigationCondition,Name of ligase and condition for proximity ligation,True,,,,HI-C-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,HI-C-seqLevel1 +Crosslinking Condtion,Crosslinking Condtion,CrosslinkingCondtion,Detailed condition for DNA crosslinking,True,,,,HI-C-seqLevel1 +Nuclei Permeabilization Method,Nuclei Permeabilization Method,NucleiPermeabilizationMethod,Detergent and treatment condition for nuclei permeabilization and crosslinking softening,True,,,,HI-C-seqLevel1 Biotin Enrichment,Biotin Enrichment,BiotinEnrichment,Whether biotin is used for enriching ligation product,True,,"['no', 'yes']",,HI-C-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,HI-C-seqLevel1 +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,HI-C-seqLevel1 +DNA Digestion Condition,DNA Digestion Condition,DNADigestionCondition,Enzymes and treatment length/temperature for genome digestion,True,,,,HI-C-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Single Nucleus', 'Bulk Nuclei', 'Bulk Whole Cell', 'Micro-region', 'Single Cell']",,HI-C-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,HI-C-seqLevel1 -Crosslinking Condtion,Crosslinking Condtion,CrosslinkingCondtion,Detailed condition for DNA crosslinking,True,,,,HI-C-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer II', 'Ion Torrent Proton', 'PromethION', 'Not Reported', 'Illumina HiSeq 4000', 'Ion Torrent S5', 'Illumina HiSeq 2500', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Ion Torrent PGM', 'Illumina HiSeq 2000', 'Illumina NextSeq 2000', 'Complete Genomics', 'Illumina Next Seq 500', 'AB SOLiD 3', 'Illumina Genome Analyzer IIx', 'unknown', 'NovaSeqS4', 'Other', 'Ultima Genomics UG100', 'Revio', 'Illumina NovaSeq 6000', 'Oxford Nanopore minION', 'Illumina HiSeq X Ten', '454 GS FLX Titanium', 'Illumina MiSeq', 'PacBio RS', 'AB SOLiD 2', 'GridION', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Illumina NextSeq', 'Illumina NextSeq 1000', 'AB SOLiD 4', 'Illumina HiSeq X Five']",,HI-C-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,HI-C-seqLevel1 DNA Input Amount,DNA Input Amount,DNAInputAmount,"Amount of DNA for library construction, in nanograms.",True,,,,HI-C-seqLevel1 -DNA Digestion Condition,DNA Digestion Condition,DNADigestionCondition,Enzymes and treatment length/temperature for genome digestion,True,,,,HI-C-seqLevel1 -Nuclei Permeabilization Method,Nuclei Permeabilization Method,NucleiPermeabilizationMethod,Detergent and treatment condition for nuclei permeabilization and crosslinking softening,True,,,,HI-C-seqLevel1 Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,HI-C-seqLevel1 -Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Nextera Tn5', 'Tn5-059', 'In-House', 'Diagenode-unloaded Apex-Bio', 'Tn5', 'EZ-Tn5', 'Diagenode-loaded Apex-Bio']",,HI-C-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel2 +Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,HI-C-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel2 Resolution,Resolution,Resolution,"Binning size used for generating contact matrix, in basepair.",True,,,,HI-C-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,True,,,,HI-C-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,HI-C-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,HI-C-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel2 Tool,Tool,Tool,Were any software or computational tools generated for this content,True,,"['no', 'yes']",,HI-C-seqLevel2 -Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,HI-C-seqLevel2 -Stripe Window,Stripe Window,StripeWindow,Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.,True,,,,HI-C-seqLevel3 Loop Window,Loop Window,LoopWindow,Binning size used for calling significant dot interactions (loops),True,,,,HI-C-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel3 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel3 -Loop Calling,Loop Calling,LoopCalling,Tool used for identifying loop interactions,True,,"['HiCCUPS', 'Other', 'Cooltools']",,HI-C-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,HI-C-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel3 Stripe Calling,Stripe Calling,StripeCalling,"Tool used for identifying architectural stripe-forming, interaction hotspots.",True,,"['MACS2', 'Other']",,HI-C-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSImagingLevel2 -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,SRRSImagingLevel2 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,SRRSImagingLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,SRRSImagingLevel2 -Objective,Objective,Objective,Objective,False,,,,SRRSImagingLevel2 -Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,SRRSImagingLevel2 -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,SRRSImagingLevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSImagingLevel2 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['nm', 'mm', 'cm', 'Å', 'µm']",,SRRSImagingLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,HI-C-seqLevel3 +Loop Calling,Loop Calling,LoopCalling,Tool used for identifying loop interactions,True,,"['Cooltools', 'Other', 'HiCCUPS']",,HI-C-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel3 +Stripe Window,Stripe Window,StripeWindow,Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.,True,,,,HI-C-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel3 SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,SRRSImagingLevel2 -PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['uint32', 'int32', 'bit', 'uint16', 'double', 'uint8', 'float', 'int8', 'int16']",,SRRSImagingLevel2 -PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,SRRSImagingLevel2 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,SRRSImagingLevel2 SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,SRRSImagingLevel2 -Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2 +PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2 +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,SRRSImagingLevel2 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'µm', 'Å', 'nm', 'cm']",,SRRSImagingLevel2 +Objective,Objective,Objective,Objective,False,,,,SRRSImagingLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSImagingLevel2 PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 -SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2 +Filename,Filename,Filename,Name of a file,True,,,,SRRSImagingLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,SRRSImagingLevel2 SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,SRRSImagingLevel2 +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,SRRSImagingLevel2 +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CODEX', 'MxIF', 'ExSeq', 'mIHC', 'RareCyte Orion', 'IMC', 'CyCIF', 'GeoMX-DSP', 'MERFISH', 'H&E', 'MIBI', 'IHC', 't-CyCIF', 'Not Applicable', 'SABER']",,SRRSImagingLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,SRRSImagingLevel2 +SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2 +Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,SRRSImagingLevel2 +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,SRRSImagingLevel2 +Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,SRRSImagingLevel2 +DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['XYZTC', 'ZYX', 'XYCZT', 'XYTZC', 'XYZCT', 'XYCTZ']",,SRRSImagingLevel2 SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['CyCIF', 'MxIF', 'IMC', 'Not Applicable', 'ExSeq', 'H&E', 'SABER', 'mIHC', 't-CyCIF', 'CODEX', 'MIBI', 'GeoMX-DSP', 'MERFISH', 'RareCyte Orion', 'IHC']",,SRRSImagingLevel2 +PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['bit', 'int32', 'uint32', 'int8', 'double', 'uint16', 'float', 'int16', 'uint8']",,SRRSImagingLevel2 +PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSImagingLevel2 +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['yes', 'No - Channels QC']",,SRRSImagingLevel2 NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,SRRSImagingLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSImagingLevel2 -Filename,Filename,Filename,Name of a file,True,,,,SRRSImagingLevel2 -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2 -PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2 -DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYCTZ', 'XYZTC', 'XYCZT', 'XYZCT', 'XYTZC']",,SRRSImagingLevel2 -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,SRRSImagingLevel2 -Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['true', 'false']",,SRRSImagingLevel2 HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSImagingLevel2 -Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,SRRSImagingLevel2 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,SRRSImagingLevel2 +Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['false', 'true']",,SRRSImagingLevel2 +Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSImagingLevel2 Comment,Comment,Comment,Free text field (generally for QC comment),False,True,,"['Passed QC is ""No - Channels QC""']",SRRSImagingLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10XGenomicsXeniumISSExperiment +Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,10XGenomicsXeniumISSExperiment +Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10XGenomicsXeniumISSExperiment Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,10XGenomicsXeniumISSExperiment -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,10XGenomicsXeniumISSExperiment +Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,10XGenomicsXeniumISSExperiment +Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,10XGenomicsXeniumISSExperiment Xenium IF image HTAN File ID,Xenium IF image HTAN File ID,XeniumIFimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment -Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,10XGenomicsXeniumISSExperiment -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10XGenomicsXeniumISSExperiment +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10XGenomicsXeniumISSExperiment +Filename,Filename,Filename,Name of a file,True,,,,10XGenomicsXeniumISSExperiment +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,10XGenomicsXeniumISSExperiment +Xenium HE image HTAN File ID,Xenium HE image HTAN File ID,XeniumHEimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10XGenomicsXeniumISSExperiment +Decoded Transcripts,Decoded Transcripts,DecodedTranscripts,"In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).",True,,,,10XGenomicsXeniumISSExperiment +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10XGenomicsXeniumISSExperiment +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10XGenomicsXeniumISSExperiment +ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,10XGenomicsXeniumISSExperiment Xenium Bundle Contents,Xenium Bundle Contents,XeniumBundleContents,A comma separated list of filenames within the Xenium bundle zip file,True,,,,10XGenomicsXeniumISSExperiment -Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,10XGenomicsXeniumISSExperiment -Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,10XGenomicsXeniumISSExperiment +Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,10XGenomicsXeniumISSExperiment Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,10XGenomicsXeniumISSExperiment +Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,10XGenomicsXeniumISSExperiment Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,10XGenomicsXeniumISSExperiment -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10XGenomicsXeniumISSExperiment -Filename,Filename,Filename,Name of a file,True,,,,10XGenomicsXeniumISSExperiment -Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10XGenomicsXeniumISSExperiment -Decoded Transcripts,Decoded Transcripts,DecodedTranscripts,"In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).",True,,,,10XGenomicsXeniumISSExperiment -ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,10XGenomicsXeniumISSExperiment -Xenium HE image HTAN File ID,Xenium HE image HTAN File ID,XeniumHEimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment -Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,10XGenomicsXeniumISSExperiment -Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,10XGenomicsXeniumISSExperiment -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel3 +Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,RPPALevel3 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,RPPALevel3 Filename,Filename,Filename,Name of a file,True,,,,RPPALevel3 -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,RPPALevel3 HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel3 -Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,RPPALevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel4 +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel3 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,RPPALevel4 Filename,Filename,Filename,Name of a file,True,,,,RPPALevel4 -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel4 -Batch Correction Method,Batch Correction Method,BatchCorrectionMethod,Method that was used to batch correct Level 3 data,False,,,,RPPALevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,RPPALevel4 HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel4 -Unique Genes,Unique Genes,UniqueGenes,The total unique genes detected above background,False,,,,NanostringCosMxSMIExperiment -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanostringCosMxSMIExperiment -CosMx Bundle Contents,CosMx Bundle Contents,CosMxBundleContents,A comma separated list of filenames within the CosMx bundle zip file,True,,,,NanostringCosMxSMIExperiment +Batch Correction Method,Batch Correction Method,BatchCorrectionMethod,Method that was used to batch correct Level 3 data,False,,,,RPPALevel4 +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel4 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel4 +Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanostringCosMxSMIExperiment +Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,NanostringCosMxSMIExperiment Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanostringCosMxSMIExperiment -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,NanostringCosMxSMIExperiment -Mean Total Transcripts per Area,Mean Total Transcripts per Area,MeanTotalTranscriptsperArea,The mean total transcripts per um3,True,,,,NanostringCosMxSMIExperiment -CosMx Assay Type,CosMx Assay Type,CosMxAssayType,The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay,True,,"['protein', 'RNA']",,NanostringCosMxSMIExperiment -Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,NanostringCosMxSMIExperiment -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,NanostringCosMxSMIExperiment -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanostringCosMxSMIExperiment -Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,NanostringCosMxSMIExperiment Total Negative Probe Counts,Total Negative Probe Counts,TotalNegativeProbeCounts,Mean Total Negative probe counts/cell,True,,,,NanostringCosMxSMIExperiment +Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,NanostringCosMxSMIExperiment Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,NanostringCosMxSMIExperiment -Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,NanostringCosMxSMIExperiment -Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,NanostringCosMxSMIExperiment +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanostringCosMxSMIExperiment +Filename,Filename,Filename,Name of a file,True,,,,NanostringCosMxSMIExperiment +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,NanostringCosMxSMIExperiment Number of FOVs,Number of FOVs,NumberofFOVs,The total number of FOVs recorded for the sample on a single flow cell,True,,,,NanostringCosMxSMIExperiment +Mean Total Transcripts per Area,Mean Total Transcripts per Area,MeanTotalTranscriptsperArea,The mean total transcripts per um3,True,,,,NanostringCosMxSMIExperiment +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanostringCosMxSMIExperiment Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanostringCosMxSMIExperiment -Filename,Filename,Filename,Name of a file,True,,,,NanostringCosMxSMIExperiment -Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,NanostringCosMxSMIExperiment -Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanostringCosMxSMIExperiment -Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,NanostringCosMxSMIExperiment -Polarity,Polarity,Polarity,The polarity of the mass analysis (positive or negative ion modes),True,,"['negative', 'positive']",,MassSpectrometryLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel1 +CosMx Bundle Contents,CosMx Bundle Contents,CosMxBundleContents,A comma separated list of filenames within the CosMx bundle zip file,True,,,,NanostringCosMxSMIExperiment +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,NanostringCosMxSMIExperiment +CosMx Assay Type,CosMx Assay Type,CosMxAssayType,The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay,True,,"['RNA', 'protein']",,NanostringCosMxSMIExperiment +Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,NanostringCosMxSMIExperiment +Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,NanostringCosMxSMIExperiment +Unique Genes,Unique Genes,UniqueGenes,The total unique genes detected above background,False,,,,NanostringCosMxSMIExperiment +Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,NanostringCosMxSMIExperiment +Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,NanostringCosMxSMIExperiment Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MassSpectrometryLevel1 -Mass Range High Value,Mass Range High Value,MassRangeHighValue,The high value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MassSpectrometryLevel1 -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,True,,"['cDNA Libraries Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'cfDNA Analyte', 'Plasma', 'DNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'Serum Analyte', 'protein', 'PBMCs', 'lipid', 'metabolite', 'RNA Analyte', 'Tissue Section Analyte']",,MassSpectrometryLevel1 -MS-based Assay Type,MS-based Assay Type,MS-basedAssayType,Analytes are the target molecules being measured with the assay.,True,,"['LC-MS', 'LC-MS/MS', 'TMT', 'MS']",,MassSpectrometryLevel1 +MS Batch ID,MS Batch ID,MSBatchID,Batch ID indicating a set of samples that were run together.,True,,,,MassSpectrometryLevel1 +LC Gradient,LC Gradient,LCGradient,The program dictates the mobile phase solvent composition over the course of the chromatographic run.,True,,,,MassSpectrometryLevel1 +LC ID Value,LC ID Value,LCIDValue,LC column inner diameter in microns.,True,,,,MassSpectrometryLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel1 +Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel1 +MS-based Targeted,MS-based Targeted,MS-basedTargeted,Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.,True,,"['Targeted', 'Untargeted']",,MassSpectrometryLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MassSpectrometryLevel1 LC Column Vendor and Model,LC Column Vendor and Model,LCColumnVendorandModel,"The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'",True,,,,MassSpectrometryLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel1 -LC Mobile Phase A,LC Mobile Phase A,LCMobilePhaseA,Composition of mobile phase A,True,,,,MassSpectrometryLevel1 -MS Scan Mode,MS Scan Mode,MSScanMode,"Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)",True,,"['MS', 'Other', 'MS3', 'MS/MS']",,MassSpectrometryLevel1 +MS-based Assay Type,MS-based Assay Type,MS-basedAssayType,Analytes are the target molecules being measured with the assay.,True,,"['MS', 'LC-MS', 'TMT', 'LC-MS/MS']",,MassSpectrometryLevel1 MS Labeling,MS Labeling,MSLabeling,"Indicates whether samples were labeled prior to MS analysis (e.g., TMT)",True,,,,MassSpectrometryLevel1 -LC Instrument Vendor and Model,LC Instrument Vendor and Model,LCInstrumentVendorandModel,The manufacturer of the instrument used for LC.,True,,,,MassSpectrometryLevel1 -Data Collection Mode,Data Collection Mode,DataCollectionMode,Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.,True,,"['DIA', 'DDA', 'Other']",,MassSpectrometryLevel1 -MS-based Targeted,MS-based Targeted,MS-basedTargeted,Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.,True,,"['Targeted', 'Untargeted']",,MassSpectrometryLevel1 -MS Instrument Vendor and Model,MS Instrument Vendor and Model,MSInstrumentVendorandModel,An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.,True,,,,MassSpectrometryLevel1 -MS Batch ID,MS Batch ID,MSBatchID,Batch ID indicating a set of samples that were run together.,True,,,,MassSpectrometryLevel1 LC Flow Rate,LC Flow Rate,LCFlowRate,LC flow rate in nL/min.,True,,,,MassSpectrometryLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel1 +LC Instrument Vendor and Model,LC Instrument Vendor and Model,LCInstrumentVendorandModel,The manufacturer of the instrument used for LC.,True,,,,MassSpectrometryLevel1 +LC Temp Value,LC Temp Value,LCTempValue,LC temperature in C.,True,,,,MassSpectrometryLevel1 LC Length Value,LC Length Value,LCLengthValue,LC column length in cm.,True,,,,MassSpectrometryLevel1 +MS Instrument Vendor and Model,MS Instrument Vendor and Model,MSInstrumentVendorandModel,An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.,True,,,,MassSpectrometryLevel1 +MS Source,MS Source,MSSource,"The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)",True,,"['MALDI', 'SIMS', 'DESI', 'nESI', 'Other', 'MALDI-2']",,MassSpectrometryLevel1 +MS Scan Mode,MS Scan Mode,MSScanMode,"Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)",True,,"['MS/MS', 'MS3', 'MS', 'Other']",,MassSpectrometryLevel1 +LC Resin,LC Resin,LCResin,"Details of the resin used for lc, including vendor, particle size, pore size",True,,,,MassSpectrometryLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MassSpectrometryLevel1 Mass Range Low Value,Mass Range Low Value,MassRangeLowValue,The low value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1 -LC Temp Value,LC Temp Value,LCTempValue,LC temperature in C.,True,,,,MassSpectrometryLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel1 -LC ID Value,LC ID Value,LCIDValue,LC column inner diameter in microns.,True,,,,MassSpectrometryLevel1 -Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel1 +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,True,,"['Tissue Block Analyte', 'metabolite', 'lipid', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'PBMCs or Plasma or Serum Analyte', 'cDNA Libraries Analyte', 'Serum Analyte', 'PBMCs', 'protein', 'DNA Analyte', 'Tissue Section Analyte', 'Plasma']",,MassSpectrometryLevel1 MS Instrument Metadata File,MS Instrument Metadata File,MSInstrumentMetadataFile,Additional file containing instrument metadata details. Use either synapse_path or entity_Id,False,,,,MassSpectrometryLevel1 -LC Resin,LC Resin,LCResin,"Details of the resin used for lc, including vendor, particle size, pore size",True,,,,MassSpectrometryLevel1 +Mass Range High Value,Mass Range High Value,MassRangeHighValue,The high value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1 +Data Collection Mode,Data Collection Mode,DataCollectionMode,Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.,True,,"['DIA', 'DDA', 'Other']",,MassSpectrometryLevel1 +LC Mobile Phase A,LC Mobile Phase A,LCMobilePhaseA,Composition of mobile phase A,True,,,,MassSpectrometryLevel1 +Polarity,Polarity,Polarity,The polarity of the mass analysis (positive or negative ion modes),True,,"['negative', 'positive']",,MassSpectrometryLevel1 LC Mobile Phase B,LC Mobile Phase B,LCMobilePhaseB,Composition of mobile phase B,True,,,,MassSpectrometryLevel1 -LC Gradient,LC Gradient,LCGradient,The program dictates the mobile phase solvent composition over the course of the chromatographic run.,True,,,,MassSpectrometryLevel1 -MS Source,MS Source,MSSource,"The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)",True,,"['Other', 'MALDI', 'DESI', 'SIMS', 'MALDI-2', 'nESI']",,MassSpectrometryLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel1 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel2 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MassSpectrometryLevel2 -MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel2 Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MassSpectrometryLevel2 +MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel2 Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel2 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,False,,,,MassSpectrometryLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",False,,,,MassSpectrometryLevel2 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel3 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MassSpectrometryLevel3 -MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel3 Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MassSpectrometryLevel3 +MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel3 Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel3 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,False,,,,MassSpectrometryLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",False,,,,MassSpectrometryLevel3 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel4 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,MassSpectrometryLevel4 -MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel4 Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,MassSpectrometryLevel4 +MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel4 Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel1 -EM dwell or exposure time,EM dwell or exposure time,EMdwellorexposuretime,Duration in microseconds (µs) of electron beam data collection per pixel or frame,False,,,,ElectronMicroscopyLevel1 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ElectronMicroscopyLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ElectronMicroscopyLevel1 -EM spot size,EM spot size,EMspotsize,Beam spot size in micrometers (µm),False,,,,ElectronMicroscopyLevel1 -EM voltage,EM voltage,EMvoltage,Accelerating voltage in kiloelectronvolts (keV),False,,,,ElectronMicroscopyLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ElectronMicroscopyLevel1 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,False,,,,MassSpectrometryLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",False,,,,MassSpectrometryLevel4 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel4 SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ElectronMicroscopyLevel1 -PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 +EM signal processing,EM signal processing,EMsignalprocessing,SNR improvement strategies used,False,,"['line integration', 'frame averaging', 'None', 'frame integration', '']",,ElectronMicroscopyLevel1 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ElectronMicroscopyLevel1 SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1 -EM stage tilt,EM stage tilt,EMstagetilt,Physical stage tilt in degrees with respect to the electron beam,False,,,,ElectronMicroscopyLevel1 +EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel1 +EM voltage,EM voltage,EMvoltage,Accelerating voltage in kiloelectronvolts (keV),False,,,,ElectronMicroscopyLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel1 PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 -EM signal or contrast mech,EM signal or contrast mech,EMsignalorcontrastmech,How the electron microscopy signal is generated from the sample,True,,"['phase', 'SE', 'BSE', 'dark-field', 'bright-field']",,ElectronMicroscopyLevel1 +EM spot size,EM spot size,EMspotsize,Beam spot size in micrometers (µm),False,,,,ElectronMicroscopyLevel1 +Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel1 +EM signal or contrast mech,EM signal or contrast mech,EMsignalorcontrastmech,How the electron microscopy signal is generated from the sample,True,,"['bright-field', 'SE', 'BSE', 'dark-field', 'phase']",,ElectronMicroscopyLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ElectronMicroscopyLevel1 SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ElectronMicroscopyLevel1 -EM signal processing,EM signal processing,EMsignalprocessing,SNR improvement strategies used,False,,"['line integration', 'None', 'frame integration', 'frame averaging', '']",,ElectronMicroscopyLevel1 -EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel1 -EM method,EM method,EMmethod,Electron microscopy method used,True,,"['FIB-SEM', 'TEM', 'SBF-SEM', 'AT', 'SEM', 'ET', 'cryo ET', 'ssTEM']",,ElectronMicroscopyLevel1 -EM instrument,EM instrument,EMinstrument,Make and model of the EM instrument used,True,,,,ElectronMicroscopyLevel1 +EM dwell or exposure time,EM dwell or exposure time,EMdwellorexposuretime,Duration in microseconds (µs) of electron beam data collection per pixel or frame,False,,,,ElectronMicroscopyLevel1 +EM method,EM method,EMmethod,Electron microscopy method used,True,,"['SBF-SEM', 'FIB-SEM', 'ET', 'cryo ET', 'ssTEM', 'AT', 'SEM', 'TEM']",,ElectronMicroscopyLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ElectronMicroscopyLevel1 SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1 -EM beam current,EM beam current,EMbeamcurrent,Beam current in nanoamps (nA),False,,,,ElectronMicroscopyLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel1 -Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel1 +PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 +EM instrument,EM instrument,EMinstrument,Make and model of the EM instrument used,True,,,,ElectronMicroscopyLevel1 +EM stage tilt,EM stage tilt,EMstagetilt,Physical stage tilt in degrees with respect to the electron beam,False,,,,ElectronMicroscopyLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ElectronMicroscopyLevel1 PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ElectronMicroscopyLevel1 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ElectronMicroscopyLevel1 -PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'cm', 'Å', 'µm', '']",,ElectronMicroscopyLevel1 -EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel1 +EM beam current,EM beam current,EMbeamcurrent,Beam current in nanoamps (nA),False,,,,ElectronMicroscopyLevel1 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ElectronMicroscopyLevel1 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ElectronMicroscopyLevel1 +PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'µm', 'Å', 'nm', 'cm', '']",,ElectronMicroscopyLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ElectronMicroscopyLevel2 Tile overlap X,Tile overlap X,TileoverlapX,Percentage of image overlap to allow tile stitching in x direction,True,,,,ElectronMicroscopyLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel2 +EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel2 Tile overlap Y,Tile overlap Y,TileoverlapY,Percentage of image overlap to allow tile stitching in x direction,True,,,,ElectronMicroscopyLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ElectronMicroscopyLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel3 Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ElectronMicroscopyLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ElectronMicroscopyLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel3 Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ElectronMicroscopyLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel3 Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ElectronMicroscopyLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel4 Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ElectronMicroscopyLevel4 +Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['tar', 'gtf', 'OME-TIFF', 'sqlite', 'dcc', 'RData', 'scn', 'idat', 'bedpe', 'plink', 'recal', 'gff3', 'bpm', 'cell am', 'sf', 'tiff', 'mex', 'bed gappedPeak', 'bcf', 'Sentrix descriptor file', 'chp', 'abf', '7z', 'mpg', 'bed broadPeak', 'bigwig', 'rcc', 'sra', 'dup', 'rmd', 'ab1', 'jpg', 'raw', 'cel', 'sif', 'hic', 'excel', 'tagAlign', 'mzML', 'dat', 'doc', 'hyperlink', 'zip', 'powerpoint', 'pkc', 'R script', 'sdf', 'bed narrowPeak', 'Python script', 'fasta', 'gzip', 'locs', 'fig', 'csv', 'sam', 'Am', 'maf', 'sav', 'czi', 'cloupe', 'Md', 'json', 'bgzip', 'xml', 'pzfx', 'svg', 'idx', 'bai', 'txt', 'msf', 'fastq', 'pdf', 'vcf', 'bedgraph', 'seg', 'mtx', 'mov', 'gct', 'bam', 'hdf5', 'html', 'flagstat', 'M', 'tif', 'wiggle', 'tsv', 'tranches', 'bed', 'DICOM', 'svs', 'png', 'avi']",,ElectronMicroscopyLevel4 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['sif', 'avi', 'gff3', 'tagAlign', 'rmd', 'json', 'M', 'cloupe', 'bam', 'hdf5', '7z', 'bpm', 'bedpe', 'bedgraph', 'tar', 'idx', 'abf', 'fasta', 'plink', 'bed gappedPeak', 'mzML', 'doc', 'recal', 'scn', 'ab1', 'bed narrowPeak', 'Python script', 'gzip', 'gtf', 'bcf', 'sav', 'rcc', 'wiggle', 'dup', 'mov', 'dat', 'jpg', 'flagstat', 'RData', 'sam', 'fig', 'Md', 'sqlite', 'locs', 'maf', 'cel', 'txt', 'bai', 'mex', 'xml', 'svs', 'sf', 'bed broadPeak', 'sra', 'OME-TIFF', 'pkc', 'fastq', 'Am', 'gct', 'czi', 'chp', 'bed', 'pdf', 'dcc', 'tif', 'vcf', 'bigwig', 'hyperlink', 'mtx', 'tsv', 'zip', 'Sentrix descriptor file', 'sdf', 'tranches', 'raw', 'hic', 'pzfx', 'mpg', 'excel', 'R script', 'png', 'seg', 'DICOM', 'powerpoint', 'bgzip', 'tiff', 'msf', 'svg', 'idat', 'html', 'csv', 'cell am']",,ElectronMicroscopyLevel4 -Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel4 diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index f880905a..c856036f 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -4910,9 +4910,6 @@ { "@id": "bts:OvarianCancerSurgicalOutcome" }, - { - "@id": "bts:ReadIndicator" - }, { "@id": "bts:ExpressionUnits" }, @@ -4940,6 +4937,9 @@ { "@id": "bts:Race" }, + { + "@id": "bts:ReadIndicator" + }, { "@id": "bts:SlicingMethod" }, @@ -33919,7 +33919,7 @@ { "@id": "bts:ReadIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", + "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads 1 (I1), Index Reads 2 (I2), or Other", "rdfs:label": "ReadIndicator", "rdfs:subClassOf": [ { @@ -33942,6 +33942,9 @@ { "@id": "bts:I1" }, + { + "@id": "bts:I2" + }, { "@id": "bts:Other" } @@ -53883,6 +53886,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:I2", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "I2", + "rdfs:subClassOf": [ + { + "@id": "bts:ReadIndicator" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "I2", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:CDNAOffset", "@type": "rdfs:Class",