HTAN.model.csv

Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
Assay,"A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]",,,,FALSE,,,http://purl.obolibrary.org/obo/OBI_0000070,
Device,"A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment",,,,FALSE,Assay,,https://w3id.org/biolink/vocab/Device,
Sequencing,Module for next generation sequencing assays,,,,FALSE,Assay,,,
Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",,,,TRUE,,,https://w3id.org/biolink/vocab/category,
Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organism,"Demographics, Family History, Exposure, Follow Up, Diagnosis, Therapy, Molecular Test",,
File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile,
Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$
File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,,
CDS Sequencing Template,"CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS library_id, CDS library_strategy, CDS library_source, CDS library_selection, CDS library_layout, CDS platform, CDS instrument_model, CDS design_description, CDS reference_genome_assembly, CDS custom_assembly_fasta_file_for_alignment, CDS bases, CDS number_of_reads, CDS coverage, CDS avg_read_length, CDS sequence_alignment_software",,TRUE,,,,
CDS library_id,Short unique identifier for the sequencing library.,,,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS library_strategy,Library strategy,"AMPLICON, ATAC-seq, Bisulfite-Seq, ChIA-PET, ChIP-Seq, CLONE, CLONEEND, CTS, DNase-Hypersensitivity, EST, FAIRE-seq, FINISHING, FL-cDNA, Hi-C, MBD-Seq, MeDIP-Seq, miRNA-Seq, MNase-Seq, MRE-Seq, ncRNA-Seq, OTHER, POOLCLONE, RAD-Seq, RIP-Seq, RNA-Seq, SELEX, ssRNA-seq, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, Tn-Seq, WCS, WGA, WGS, WXS",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS library_source,The Library Source specifies the type of source material that is being sequenced,"GENOMIC, GENOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, OTHER, SYNTHETIC, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, VIRAL RNA",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS library_selection,Library Selection Method,"5-methylcytidine antibody, CAGE, cDNA, cDNA_oligo_dT, cDNA_randomPriming, CF-H, CF-M, CF-S, CF-T, ChIP, DNAse, HMPR, Hybrid Selection, Inverse rRNA, MBD2 protein methyl-CpG binding domain, MDA, MF, MNase, MSLL, Oligo-dT, other, Padlock probes capture method, PCR, PolyA, RACE, RANDOM, RANDOM PCR, Reduced Representation, repeat fractionation, Restriction Digest, RT-PCR, size fractionation, unspecified",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS library_layout,Paired-end or Single,"Paired-end, Single-end",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS platform,Sequencing Platform used for Sequencing,"LS454, ABI_SOLID, BGISEQ, CAPILLARY, COMPLETE_GENOMICS, HELICOS, ILLUMINA, ION_TORRENT, OXFORD_NANOPORE, PACBIO_SMRT",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS instrument_model,Instrument model used for sequencing,"454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX+, 454 GS FLX Titanium, 454 GS Junior, HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina iSeq 100, Illumina NovaSeq 6000, Illumina MiniSeq, Illumina MiSeq, NextSeq 500, NextSeq 550, Helicos HeliScope, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500x-Wl Genetic Analyzer, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, Complete Genomics, PacBio RS, PacBio RS II, PacBio Sequel, PacBio Sequel II, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5 XL, Ion Torrent S5, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, GridION, MinION, PromethION, BGISEQ-500, DNBSEQ-G400, DNBSEQ-T7, DNBSEQ-G50, MGISEQ-2000RS",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS design_description,Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS reference_genome_assembly,This is only if you are submitting a bam file aligned against a NCBI assembly.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS custom_assembly_fasta_file_for_alignment,Please provide the name of the custom assembly fasta file used during alignment,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
CDS bases,Count of unique basecalls present in the data. Please count each base only once if using secondary alignments.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int
CDS number_of_reads,Count of the number of reads in the data. Please count each read only once if using secondary alignments.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int
CDS coverage,Depth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length),,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int
CDS avg_read_length,Found by (Bases)/(Reads),,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int
CDS sequence_alignment_software,The name of the software program used to align nucleotide sequencing data.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str
Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,,
HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning
HTAN Biospecimen ID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
HTAN Parent ID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,
HTAN Parent Biospecimen ID,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,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,
HTAN Parent Data File ID,HTAN Data File Identifier indicating the file(s) from which these files were derived,,,,TRUE,File,,,
Clinical Data Tier 2,Tier 2 Cancer Data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Sentinel Lymph Node Count, Sentinel Node Positive Assessment Count, Tumor Extranodal Extension Indicator, Satellite Metastasis Present Indicator, Other Biopsy Resection Site, Extent of Tumor Resection, Prior Sites of Radiation, Immunosuppression, Concomitant Medication Received Type, Family Member Vital Status Indicator, COVID19 Occurrence Indicator, COVID19 Current Status, COVID19 Positive Lab Test Indicator, COVID19 Antibody Testing, COVID19 Complications Severity, COVID19 Cancer Treatment Followup, Ecig vape use, Ecig vape 30 day use num, Ecig vape times per day, Type of smoke exposure cumulative years, Chewing tobacco daily use count, Second hand smoke exposure years, Known Genetic Predisposition Mutation, Hereditary Cancer Predisposition Syndrome, Cancer Associated Gene Mutations, Mutational Signatures, Mismatch Repair System Status, Lab Tests for MMR Status, Mode of Cancer Detection, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location",,FALSE,Patient,,,
SRRS Clinical Data Tier 2,Cancer related clinical data specific to SRRS,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location, Ethnicity, Gender, Race, Vital Status, Age at Diagnosis, Days to Last Follow up, Days to Last Known Disease Status, Days to Recurrence, Last Known Disease Status, Morphology, Primary Diagnosis, Progression or Recurrence, Site of Resection or Biopsy, Tissue or Organ of Origin, NCI Atlas Cancer Site, Tumor Grade, Pack Years Smoked, Years Smoked, Days to Follow Up, Gene Symbol, Molecular Analysis Method, Test Result, Treatment Type, Tumor Largest Dimension Diameter",,FALSE,Patient,,,
Lung Cancer Tier 3,Lung cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Lung Cancer Detection Method Type, Lung Cancer Participant Procedure History, Lung Adjacent Histology Type, Lung Tumor Location Anatomic Site, Lung Tumor Lobe Bronchial Location, Current Lung Cancer Symptoms, Lung Topography, Lung Cancer Harboring Genomic Aberrations",,FALSE,Patient,,,
Colorectal Cancer Tier 3,Colorectal cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Colorectal Cancer Detection Method Type, History of Prior Colon Polyps, Family Colon Cancer History Indicator, Family Medical History Colorectal Polyp Diagnosis, Immediate Family History Endometrial Cancer, Immediate Family History Ovarian Cancer, Patient Inflammatory Bowel Disease Personal Medica History, Patient Colonoscopy Performed Indicator, Colorectal Cancer Tumor Border Configuration, MLH1 Promoter Methylation Status, Colorectal Cancer KRAS Indicator, Colon Polyp Occurence Indicator, Family History Colorectal Polyp, Colorectal Polyp New Indicator, Colorectal Polyp Shape, Size of Polyp Removed, Colorectal Polyp Count, Colorectal Polyp Type, Colorectal Polyp Adenoma Type",,FALSE,Patient,,,
Breast Cancer Tier 3,Breast cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Breast Carcinoma Detection Method Type, Breast Carcinoma Histology Category, Invasive Lobular Breast Carcinoma Histologic Category, Invasive Ductal Breast Carcinoma Histologic Category, Breast Biopsy Procedure Finding Type, Breast Quadrant Site, Breast Cancer Assessment Tests, Breast Cancer Genomic Test Performed, Mammaprint Risk Group, Oncotype Risk Group, Breast Carcinoma Estrogen Receptor Status, Breast Carcinoma Progesteroner Receptor Status, Breast Cancer Allred Estrogen Receptor Score, Prior Invasive Breast Disease, Breast Carcinoma ER Status Percentage Value, Breast Carcinoma PR Status Percentage Value, HER2 Breast Carcinoma Copy Number Total, Breast Carcinoma Centromere 17 Copy Number, Breast Carcinoma HER2 Centromere17 Copynumber Total, Breast Carcinoma HER2 Chromosome17 Ratio, Breast Carcinoma Surgical Procedure Name, Breast Carcinoma HER2 Ratio Diagnosis, Breast Carcinoma HER2 Status, Hormone Therapy Breast Cancer Prevention Indicator, Breast Carcinoma ER Staining Intensity, Breast Carcinoma PR Staining Intensity, Oncotype Score, Breast Imaging Performed Type, Multifocal Breast Carcinoma Present Indicator, Multicentric Breast Carcinoma Present Indicator, BIRADS Mammography Breast Density Category",,FALSE,Patient,,,
Neuroblastoma and Glioma Tier 3,Brain cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,CNS Tumor Primary Anatomic Site, Glioma Specific Metastasis Sites, Glioma Specific Radiation Field, Supra Tentorial Ependymoma Molecular Subgroup, Infra Tentorial Ependymoma Molecular Subgroup, Neuroblastoma MYCN Gene Amplification Status",,FALSE,Patient,,,
Acute Lymphoblastic Leukemia Tier 3,Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Specimen Blast Count Percentage Value, NCI ALL Risk Group, MRD ALL Diagnostic Sensitivity, CNS Leukemia Status",,FALSE,Patient,,,
Ovarian Cancer Tier 3,Ovarian cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Ovarian Cancer Histologic Subtype, Ovarian Cancer Surgical Outcome, Ovarian Cancer Platinum Status",,FALSE,Patient,,,
Prostate Cancer Tier 3,Prostate cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Location Extent Extraprostatic Extension, Location Nature Positive Margins, Seminal Vesicle Invasion, Prostate Carcinoma Histologic Type, Prostate Cancer Local Extent, Additonal Findings Uninvolved Prostate, Prostate Cancer Cytologic Morphologic Subtypes",,FALSE,Patient,,,
Sarcoma Tier 3,Sarcoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Sarcoma Subtype, Sarcoma Diagnosis Classification Category, Sarcoma Tumor Extension Type",,FALSE,Patient,,,
Pancreatic Cancer Tier 3,Pancreatic cancer specific attributes in Clinical Tier Data 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Pancreas Precancer Histopathologic Grade, Pancreatic IPMN Pathology Epithelial Subtype, Pancreatic Duct Final Pathology Type",,FALSE,Patient,,,
Melanoma Tier 3,Melanoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Cutaneous Melanoma Tumor Infiltrating Lymphocytes, Cutaneous Melanoma Tumor Regression Range, Melanoma Specimen Clark Level Value, Cutaneous Melanoma Surgical Margins, Melanoma Lesion Size, History of Atypical Nevi, Fitzpatrick Skin Tone, History of Chronic UV Exposure, History of Blistering Sunburn, History of Tanning Bed Use, Immediate Family History Melanoma, Melanoma Biopsy Resection Sites, Cutaneous Melanoma Ulceration, Cutaneous Melanoma Additional Findings",,FALSE,Patient,,,
Demographics,Demographic attributes,,"Component, HTAN Participant ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Country of Residence, Age Is Obfuscated, Year Of Birth, Occupation Duration Years, Premature At Birth, Weeks Gestation at Birth",,FALSE,Patient,,,
Family History,Family cancer history,,"Component, HTAN Participant ID, Relative with Cancer History",,FALSE,Patient,,,
Exposure,Exposure to carcinogens,,"Component, HTAN Participant ID, Start Days from Index, Smoking Exposure, Alcohol Exposure, Asbestos Exposure, Coal Dust Exposure, Environmental Tobacco Smoke Exposure, Radon Exposure, Respirable Crystalline Silica Exposure",,FALSE,Patient,,,
Follow Up,Follow up clinical visits,,"Component, HTAN Participant ID, Days to Follow Up, Adverse Event, Progression or Recurrence, Barretts Esophagus Goblet Cells Present, BMI, Cause of Response, Comorbidity, Comorbidity Method of Diagnosis, Days to Adverse Event, Days to Comorbidity, Diabetes Treatment Type, Disease Response, DLCO Ref Predictive Percent, ECOG Performance Status, FEV1 FVC Post Bronch Percent, FEV 1 FVC Pre Bronch Percent, FEV1 Ref Post Bronch Percent, FEV1 Ref Pre Bronch Percent, Height, Hepatitis Sustained Virological Response, HPV Positive Type, Karnofsky Performance Status, Menopause Status, Pancreatitis Onset Year,  Reflux Treatment Type, Risk Factor, Risk Factor Treatment, Viral Hepatitis Serologies, Weight, Adverse Event Grade, AIDS Risk Factors, Body Surface Area, CD4 Count, CDC HIV Risk Factors, Days to Imaging, Evidence of Recurrence Type, HAART Treatment Indicator, HIV Viral Load, Hormonal Contraceptive Use, Hysterectomy Margins Involved, Hysterectomy Type, Imaging Result, Imaging Type, Immunosuppressive Treatment Type, Nadir CD4 Count, Pregnancy Outcome, Recist Targeted Regions Number, Recist Targeted Regions Sum, Scan Tracer Used",,FALSE,Patient,,,
Therapy,Clinical therapy or treatment,,"Component, HTAN Participant ID, Treatment or Therapy, Treatment Type, Treatment Effect, Treatment Outcome, Days to Treatment End, Treatment Anatomic Site, Days to Treatment Start, Initial Disease Status, Regimen or Line of Therapy, Therapeutic Agents, Treatment Intent Type, Chemo Concurrent to Radiation, Number of Cycles, Reason Treatment Ended, Treatment Arm, Treatment Dose, Treatment Dose Units, Treatment Effect Indicator, Treatment Frequency",,FALSE,Patient,,,
Diagnosis,Disease diagnosis,,"Component, HTAN Participant ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Precancerous Condition Type, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status,  Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition, Cog Neuroblastoma Risk Group, Cog Rhabdomyosarcoma Risk Group, Gleason Grade Group, Gleason Grade Tertiary, Gleason Patterns Percent, Greatest Tumor Dimension, IGCCCG Stage, INPC Grade, INPC Histologic Group, INRG Stage, INSS Stage, International Prognostic Index, IRS Group, IRS Stage, ISS Stage, Lymph Node Involved Site, Margin Distance, Margins Involved Site, Medulloblastoma Molecular Classification, Micropapillary Features, Mitosis Karyorrhexis Index, Non Nodal Regional Disease, Non Nodal Tumor Deposits, Ovarian Specimen Status, Ovarian Surface Involvement, Pregnant at Diagnosis, Primary Gleason Grade, Secondary Gleason Grade, Supratentorial Localization, Tumor Depth, WHO CNS Grade, WHO NTE Grade",,FALSE,Patient,,,
Molecular Test,Clinical molecular test data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Gene Symbol, Molecular Analysis Method, Test Result, AA Change, Antigen, Clinical Biospecimen Type, Blood Test Normal Range Upper, Blood Test Normal Range Lower, Cell Count, Chromosome, Clonality, Copy Number, Cytoband, Exon, Histone Family, Histone Variant, Intron, Laboratory Test, Loci Abnormal Count, Loci Count, Locus, Mismatch Repair Mutation, Molecular Consequence, Pathogenicity, Ploidy, Second Exon, Second Gene Symbol, Specialized Molecular Test, Test Analyte Type, Test Units, Test Value, Transcript, Variant Origin, Variant Type, Zygosity",,FALSE,Patient,,,
Biospecimen,"HTAN biological entity; this can be tissue, blood, analyte and subsamples of those",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Timepoint Label, Collection Days from Index, Adjacent Biospecimen IDs, Biospecimen Type, Acquisition Method Type, Fixative Type, Storage Method, Processing Days from Index, Protocol Link,  Site Data Source, Collection Media, Mounting Medium, Processing Location, Histology Assessment By, Histology Assessment Medium, Preinvasive Morphology, Tumor Infiltrating Lymphocytes, Degree of Dysplasia, Dysplasia Fraction, Number Proliferating Cells, Percent Eosinophil Infiltration, Percent Granulocyte Infiltration, Percent Inflam Infiltration, Percent Lymphocyte Infiltration, Percent Monocyte Infiltration, Percent Necrosis, Percent Neutrophil Infiltration, Percent Normal Cells, Percent Stromal Cells, Percent Tumor Cells, Percent Tumor Nuclei, Fiducial Marker, Slicing Method,  Lysis Buffer, Method of Nucleic Acid Isolation",,FALSE,Biosample,Patient,,
SRRS Biospecimen,"SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Adjacent Biospecimen IDs, Biospecimen Type, Timepoint Label, Collection Days from Index, Acquisition Method Type, Ischemic Time, Ischemic Temperature, Collection Media, Topography Code, Additional Topography, Fixative Type, Storage Method, Preinvasive Morphology, Histologic Morphology Code, Preservation Method, Processing Days from Index, Protocol Link",,FALSE,Biosample,Patient,,
Source HTAN Biospecimen ID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,,,,FALSE,Biosample,,,
Other Assay,Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay Type",,FALSE,Assay,Biospecimen,,
ExSeq Minimal,Minimal metadata for the ExSeq assay,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay Type",,FALSE,Assay,Biospecimen,,
Assay Type,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",,,,TRUE,Assay,,,
scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate Group",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913,
scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Sequencing,scRNA-seq Level 1,,
scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Sequencing,scRNA-seq Level 2,,
scRNA-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,scRNA-seq Level 3,,
Slide-seq Level 1,Raw sequencing files for the Slide-seq assay.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Read Indicator, Spatial Read1, Spatial Read2, End Bias, Reverse Transcription Primer, Spatial Barcode Offset, Spatial Barcode and UMI, Spike In, Sequencing Platform, Technical Replicate Group, Protocol Link, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index",,FALSE,Spatial Transcriptomics,Biospecimen,,
Slide-seq Level 2,Aligned sequencing files and QC for the Slide-seq assay.,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Spatial Barcode Tag, Matched Spatial Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Spatial Transcriptomics,Slide-seq Level 1,,
Slide-seq Level 3,Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Sequencing Batch ID, Data Category, Matrix Type, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Beads Total, Median UMI Counts per Spot, Median Number Genes per Spatial Spot, Slide-seq Bead File Type, Slide-seq Fragment Size",,FALSE,Spatial Transcriptomics,Slide-seq Level 2,,
Slide-seq Fragment Size,Average cDNA length associated with the experiemtn. Integer,,,,FALSE,Spatial Transcriptomics,,,
Matched Spatial Barcode Tag,SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific),,,,TRUE,Spatial Transcriptomics,,,
Beads Total,Number of sequenced beads. Applies to raw counts matrix only. Integer,,,,FALSE,Spatial Transcriptomics,,,
Slide-seq Workflow Type,Generic name for the workflow used to analyze the Slide-seq data set. String,,,,TRUE,Spatial Transcriptomics,,,
Slide-seq Workflow Parameter Description,Parameters used to run the Slide-seq workflow. String,,,,TRUE,Spatial Transcriptomics,,,
Slide-seq Bead File Type,The type of Level 3 file submitted as part of the Slide-seq workflow.,"Matrix Features, Matrix Barcodes, All Bead Locations, All Bead Barcodes, Matched Bead Barcodes, Matched Bead Locations, Not Applicable",,,TRUE,Spatial Transcriptomics,,,
Bulk RNA-seq Level 1,Bulk RNA-seq [EFO_0003738],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Library Layout, Read Indicator, Nucleic Acid Source, Micro-region Seq Platform, ROI Tag, Sequencing Platform, Sequencing Batch ID, Read Length, Library Selection Method, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Library Preparation Days from Index, Spike In, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Transcript Integrity Number, RIN, DV200, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0003738,
Bulk RNA-seq Level 2,Bulk RNA-seq alignment protocol description,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Is lowest level",,FALSE,Sequencing,Bulk RNA-seq Level 1,,
Bulk RNA-seq Level 3,Bulk RNA-seq gene expression matrices,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Pseudo Alignment Used, Data Category, Expression Units, Matrix Type, Fusion Gene Detected, Fusion Gene Identity",,FALSE,Sequencing,Bulk RNA-seq Level 2,,
Bulk WES Level 1,Bulk Whole Exome Sequencing raw files,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Read Indicator, Library Selection Method, Read Length, Target Capture Kit, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Sequencing Platform, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Multiplex Barcode, Library Preparation Days from Index, Size Selection Range, Target Depth, To Trim Adapter Sequence",,FALSE,Sequencing,Biospecimen,,
Bulk WES Level 2,Bulk Whole Exome Sequencing aligned files and QC,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Adapter Content, Basic Statistics, Encoding, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, QC Workflow Type, QC Workflow Version, QC Workflow Link, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X,Is lowest level",,FALSE,Sequencing,Bulk WES Level 1,,
Bulk WES Level 3,Bulk Whole Exome Sequencing called variants,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Genomic Reference, Genomic Reference URL, Germline Variants Workflow URL, Germline Variants Workflow Type, Somatic Variants Workflow URL, Somatic Variants Workflow Type, Somatic Variants Sample Type, Structural Variant Workflow URL, Structural Variant Workflow Type",,FALSE,Sequencing,Bulk WES Level 2,,
Microarray Level 1,Microarray Level 1 refers to the raw text table of probe level intensities,,"Component, Filename, File Format, HTAN Data File ID, HTAN Participant ID, HTAN Parent Biospecimen ID, Nucleic Acid Source, Microarray Platform ID, Microarray Molecule, Microarray Label, Microarray Value Definition, Microarray Protocol Auxiliary File",,FALSE,Assay,Biospecimen,,
Microarray Level 2,Microarray Level 2 provides a normalized matrix of values.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Parent Data File ID, HTAN Data File ID, Microarray Platform ID, Normalization Method",,FALSE,Assay,Microarray Level 1,,
scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, scATACseq Read3, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Sequencing,Biospecimen,,
scATAC-seq Level 2,"scATAC-seq files containing aligned sequence data, as a BAM file",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Median Percentage of Mitochondrial Reads per Nucleus, Contamination,Contamination Error",,FALSE,Sequencing,scATAC-seq Level 1,,
scATAC-seq Level 3,Processed data files containing peak information for cells,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATAC-seq Object ID, nCount Peaks, nFeature Peaks, Total Read-Pairs, Duplicate Read-Pairs, Chimeric Read-Pairs, Unmapped Read-Pairs, LowMapQ, Mitochondrial Read-Pairs, Passed Filters, TSS Fragments, DNase Sensitive Region Fragments, Enhancer Region Fragments, Promoter Region Fragments, On Target Fragments, Blacklist Region Fragments, Peak Region Fragments, Peak Region Cutsites, Nucleosome Signal, Nucleosome Percentile, TSS Enrichment, TSS Percentile, Pct Reads in Peaks, Blacklist Ratio, Seurat Clusters, nCount RNA, nFeature RNA, MACS2 Seqnames, MACS2 Start, MACS2 End, MACS2 Width, MACS2 Strand, MACS2 Name, MACS2 Score, MACS2 Fold Change, MACS2 Neg Log10 pvalue Summit, MACS2 Neg Log10 qvalue Summit, MACS2 Relative Summit Position",,FALSE,Sequencing,scATAC-seq Level 2,,
scmC-seq Level 1,Files contain raw scmC-seq data.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, scmCseq Read1, scmCseq Read2, scmCseq Read3, Single Cell Isolation Method, Single Nucleus Buffer, Single Nucleus Capture, Bisulfite Conversion, Library Layout, Nucleus Identifier, Sequencing Platform, Technical Replicate Group, Median Fraction of Reads in Peaks, Median Passing Read Percentage, Peaks Calling Software, Median Percentage of Mitochondrial Reads per Nucleus, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Total Reads",,FALSE,Sequencing,Biospecimen,,
scmC-seq Level 2,"Files contain scmC-seq files containing aligned sequence data, as a BAM file.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads",,FALSE,Sequencing,scmC-seq Level 1,,
scATAC-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATACseq Workflow Type, scATACseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,scATAC-seq Level 3,,
scDNA-seq Level 1,Single-cell DNA-seq,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Nucleic Acid Source, Library Selection Method, Read Length, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link",,FALSE,Sequencing,Biospecimen,,
scDNA-seq Level 2,Alignment workflows downstream of scDNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads,Proportion Reads Duplicated, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Proportion Mitochondrial Reads, Contamination, Contamination Error",,FALSE,Sequencing,scDNA-seq Level 1,,
Multiplexed CITE-seq Level 1,Raw sequencing files for the multiplexed CITE-seq assay,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source,Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method,Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Spike In Concentration, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate Group, Empty Well Barcode,Well Index,Feature Reference Id, Associated mRNA Library Data File ID, Single Cell Barcode Method Applied, Feature Barcode Library Type, Barcode Folder Synapse ID, Barcode Folder File List",,FALSE,Sequencing,Biospecimen,,
Multiplexed CITE-seq Level 2,Alignment workflows downstream of Multiplexed CITE-seq Level 1,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Associated mRNA Library Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Sequencing,Multiplexed CITE-seq Level 1,,
Multiplexed CITE-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Associated mRNA Library Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Sequencing,scRNA-seq Level 2,,
Multiplexed CITE-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Associated mRNA Library Data File ID, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,Multiplexed CITE-seq Level 3,,
Bulk Methylation-seq Level 1,"Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Bisulfite Conversion, Sequencing Platform, Replicate Type, Bulk Methylation Assay Type, Total DNA Input",,FALSE,Sequencing,Biospecimen,,
Bulk Methylation-seq Level 2,"Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Trimmer, Bulk Methylation Genomic Reference, Genomic Reference URL, Index File Name, Alignment Workflow Type, Duplicate Removal Software, Mean Coverage, Library Layout, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion of Minimum CpG Coverage 10X, Proportion Coverage 30X",,FALSE,Sequencing,"Bulk Methylation-seq Level 1, Biospecimen",,
Bulk Methylation-seq Level 3,"Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID,DMC Calling Tool, DMC Calling Workflow URL, DMR Calling Tool, DMR Calling Workflow URL, pUC19 methylation ratio, Lambda methylation ratio, DMC data file format, DMR data file Format",,FALSE,Sequencing,"Bulk Methylation-seq Level 2, Biospecimen",,
Imaging Level 1,Raw imaging data,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Imaging Assay Type, Protocol Link, Software and Version, Commit SHA, Pre-processing Completed, Pre-processing Required, Comment",,FALSE,Assay,Biospecimen,,
Imaging Level 2,Raw and pre-processed image data,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance,WorkingDistanceUnit, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVXUnit, FOVY, FOVYUnit, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType, MERFISH Positions File, MERFISH Codebook File",,FALSE,Assay,Imaging Level 1,,
MERFISH Positions File,The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.,,,,FALSE,Assay,,,
MERFISH Codebook File,The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.,,,,FALSE,Assay,,,
Imaging Level 3 Segmentation,Object segmentations,,"Component, Filename, File Format, HTAN Parent Data File ID,  HTAN Data File ID, Imaging Segmentation Data Type, Parameter file, Software and Version, Commit SHA, Imaging Object Class, Number of Objects",,FALSE,Assay,Imaging Level 2,,
Imaging Level 3 Image,Quality controlled imaging data,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Parent Channel Metadata ID, HTAN Data File ID, Imaging Assay Type, Protocol Link,Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVY, Frame Averaging",,FALSE,Assay,"Imaging Level 3 Channels, Imaging Level 2",,
10x Visium Spatial Transcriptomics - RNA-seq Level 1,Files contain raw RNA-seq data associated with spot/slide data.,,"Component, Filename, Run ID, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Read Indicator, Spatial Read1, Spatial Read2, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, End Bias, Reverse Transcription Primer, Sequencing Platform, Capture Area, Protocol Link, Slide Version, Slide ID, Image Re-orientation, Permeabilization Time, RIN, DV200",,FALSE,Spatial Transcriptomics,Biospecimen,,
10x Visium Spatial Transcriptomics - RNA-seq Level 2,Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.,,"Component, Filename, File Format, Checksum,HTAN Parent Data File ID, HTAN Data File ID, UMI Tag, Whitelist Spatial Barcode File Link, Spatial Barcode Tag, Applied Hard Trimming, Workflow Version, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, HTAN Parent Biospecimen ID, Run ID, Capture Area",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 1,,
10x Visium Spatial Transcriptomics - Auxiliary Files,"Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc)  from Spatial Transcriptomics.",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Visium File Type, Slide ID, Capture Area, Workflow Version, Workflow Link",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 1, 10x Visium Spatial Transcriptomics - RNA-seq Level 2",,
10x Visium Spatial Transcriptomics - RNA-seq Level 3,Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Visium File Type, Workflow Version, Workflow Link, Capture Area, Spots under tissue, Mean Reads per Spatial Spot, Median Number Genes per Spatial Spot, Sequencing Saturation, Proportion Reads Mapped, Proportion Reads Mapped to Transcriptome, Median UMI Counts per Spot",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 2, 10x Visium Spatial Transcriptomics - Auxiliary Files",,
10x Visium Spatial Transcriptomics - RNA-seq Level 4,Processed data files based on Spatial Transcriptomics RNA-seq Level 3.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Workflow Version, Workflow Link, Visium Workflow Type, Visium Workflow Parameters Description",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 3,,
Visium File Type,The file type generated for the visium experiment.,"reference png, reference jpg, json scale factors, probe dataset csv, qc result html, filtered mex, unfiltered mex, tissue_positions, barcodes, features, fiducial image png, fiducial image jpg, detected image png, detected jpg, high res image, low res image, json scale factors, probe dataset csv",,,TRUE,Spatial Transcriptomics,,,
Run ID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,,,,TRUE,Spatial Transcriptomics,,,
Capture Area,"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.","A, B, C, D, A1, B1, C1, D1",,,FALSE,Spatial Transcriptomics,,,
Slide Version,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,"V1, V2, V3, V4",,,FALSE,Spatial Transcriptomics,,,
Slide ID,"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,Spatial Transcriptomics,,,
Image Re-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.","TRUE, FALSE",,,FALSE,Spatial Transcriptomics,,,
Permeabilization Time,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,Spatial Transcriptomics,,,
Whitelist Spatial Barcode File Link,Link to file listing all possible spatial barcodes. URL,,,,TRUE,Spatial Transcriptomics,,,
Spatial Barcode Tag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),,,,TRUE,Spatial Transcriptomics,,,
Spatial Barcode Offset,Offset in sequence for spot barcode read (in bp): number,,,,TRUE,Spatial Transcriptomics,,,
Spatial Barcode Length,Length of spot barcode read (in bp): number,,,,TRUE,Spatial Transcriptomics,,,
Spatial Read1,Read 1 content description,"cDNA, Spatial Barcode and UMI",,,TRUE,Spatial Transcriptomics,,,
Spatial Read2,Read 2 content description,"cDNA, Spatial Barcode and UMI",,,TRUE,Spatial Transcriptomics,,,
Spatial Library Construction Method,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],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, Drop-seq, inDropsV2, inDropsV3, TruDrop, Nextera XT",,,TRUE,Spatial Transcriptomics,,,
Spatial Barcode and UMI,Spot and transcript identifiers,,"Spatial Barcode Offset, Spatial Barcode Length, UMI Barcode Offset, UMI Barcode Length",,TRUE,Spatial Transcriptomics,,,num
Mean Reads per Spatial Spot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",,,,TRUE,Spatial Transcriptomics,,,num
Visium Workflow Type,Generic name for the workflow used to analyze the visium data set.,,,,TRUE,Spatial Transcriptomics,,,
Visium Workflow Parameters Description,Parameters used to run the workflow..,,,,TRUE,Spatial Transcriptomics,,,
Spots under tissue,The number of barcodes associated with a spot under tissue.,,,,TRUE,Spatial Transcriptomics,,,num
Median UMI Counts per Spot,The median number of UMI counts per tissue covered spot.,,,,TRUE,Spatial Transcriptomics,,,num
Sequencing Saturation,"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,Spatial Transcriptomics,,,
Proportion Reads Mapped to Transcriptome,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,Spatial Transcriptomics,,,
Median Number Genes per Spatial Spot,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,Spatial Transcriptomics,,,num
NanoString GeoMx DSP Spatial Transcriptomics Level 1,Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Synapse ID of GeoMx DSP PKC File, GeoMx DSP NGS Sequencing Platform, GeoMx DSP NGS Library Selection Method, GeoMx DSP NGS Library Preparation Kit Name, GeoMx DSP Library Preparation Kit Vendor, GeoMx DSP Library Preparation Kit Version, Synapse ID of GeoMx Lab Worksheet File, Software and Version",,FALSE,Spatial Transcriptomics,"Biospecimen, NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,
GeoMx DSP Assay Type,The assay type which was used for the GeoMx DSP pipeline.,"RNA nCounter, Protein nCounter, Protein NGS, RNA NGS",,,TRUE,Spatial Transcriptomics,,,
Synapse ID of GeoMx DSP PKC File,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,,,,TRUE,Spatial Transcriptomics,,,list::regex match syn\d+
GeoMx DSP NGS Sequencing Platform,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,Spatial Transcriptomics,,,
GeoMx DSP NGS Library Selection Method,How RNA molecules are isolated.,,,,FALSE,Spatial Transcriptomics,,,
GeoMx DSP NGS Library Preparation Kit Name,Name of Library Preparation Kit. String,,,,FALSE,Spatial Transcriptomics,,,
GeoMx DSP Library Preparation Kit Vendor,Vendor of Library Preparation Kit. String,,,,FALSE,Spatial Transcriptomics,,,
GeoMx DSP Library Preparation Kit Version,Version of Library Preparation Kit. String,,,,FALSE,Spatial Transcriptomics,,,
Synapse ID of GeoMx Lab Worksheet File,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,,,,FALSE,Spatial Transcriptomics,,,list::regex match syn\d+
NanoString GeoMx DSP Spatial Transcriptomics Level 3,Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, GeoMx DSP Assay Type, Synapse ID of GeoMx DSP ROI Segment Annotation File, GeoMx DSP Unique Probe Count, GeoMx DSP Unique Target Count, GeoMx DSP Genomic Reference, Matrix Type, GeoMx DSP Workflow Type, GeoMx DSP Workflow Parameter Description, GeoMx DSP Workflow Link",,FALSE,Spatial Transcriptomics,"NanoString GeoMx DSP Spatial Transcriptomics Level 1, Imaging Level 2, NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,
Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.,,,,TRUE,Spatial Transcriptomics,,,list::regex match syn\d+
GeoMx DSP Genomic Reference,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,Spatial Transcriptomics,,,num
GeoMx DSP Unique Probe Count,Total number of unique probes reported.,,,,FALSE,Spatial Transcriptomics,,,num
GeoMx DSP Unique Target Count,Total number of unique genes reported.,,,,FALSE,Spatial Transcriptomics,,,num
GeoMx DSP Workflow Type,Generic name for the workflow used to analyze the GeoMx DSP data set.,,,,FALSE,Spatial Transcriptomics,,,
GeoMx DSP Workflow Parameter Description,Parameters used to run the GeoMx DSP workflow.,,,,FALSE,Spatial Transcriptomics,,,
GeoMx DSP Workflow Link,Link to workflow or command. DockStore.org recommended. URL,,,,FALSE,Spatial Transcriptomics,,,
NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. ,,"HTAN Parent Biospecimen ID, Scan name, ROI name, Segment name, ROI X Coordinate,ROI Y Coordinate, Tags, QC status, Scan Height, Scan Width, Scan Offset X, Scan Offset Y, Binding Density, Positive norm factor, Surface area, Nuclei count, Tissue Stain",,FALSE,Assay,,,
Scan name,GeoMx Scan name (as appears in Segment Summary),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
ROI name,ROI name (application generated). For Xenium this is referred to as the “region name”,,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
Segment name,Name given to segment at time of generation,,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
Tags,Unique descriptor of a variable group (ie. MAPK+),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
ROI X Coordinate,X location within the image,,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
ROI Y Coordinate,Y location within the image,,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
QC status,ROI quality control flag as reported by the application,,,,FALSE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
Scan Height,Height of the scan for GeoMx Analysis,,,,TRUE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
Scan Width,Width of the scan for GeoMx Analysis,,,,TRUE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
Scan Offset X,Offset X of the scan for GeoMx Analysis,,,,TRUE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
Scan Offset Y,Offset Y of the scan for GeoMx Analysis,,,,TRUE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
Binding Density,The binding density as reported by the application,,,,FALSE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
Positive norm factor,The Positive Control Normalization factor calculated using pos-hyb controls,,,,FALSE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
Surface area,"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,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
Nuclei count,Number of nuclei detected in the segment (if applicable),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
Tissue Stain,e.g. CD45 or PanCK (if masking was performed),,,,FALSE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. ,,"HTAN Parent Biospecimen ID, Scan name, Slide name, ROI name, Segment name, ROI X Coordinate,ROI Y Coordinate, Tags, Scan Height, Scan Width, Scan Offset X, Scan Offset Y, Surface area, Nuclei count, Sequencing Saturation, MapQ30, Raw reads, Stitched reads, Aligned reads, Deduplicated reads, In Situ Negative median, Biological probe median",,FALSE,Assay,,,
Slide name,"Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).",,,,FALSE,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
Raw reads,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,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
Stitched reads,"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,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
Aligned reads,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,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
Deduplicated reads,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,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
In Situ Negative median,Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.,,,,FALSE,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
Biological probe median,Is the median count from all probes except the negative control probes. A measure of signal to background for each segment,,,,FALSE,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
HI-C-seq Level 1,Unaligned sequence data,,"Component, HTAN Parent Biospecimen ID, HTAN Data File ID, Filename, File Format, Genomic Reference, Sequencing Platform, Nucleic Acid Source, Technical Replicate Group, Transposition Reaction, Crosslinking Condtion, DNA Digestion Condition, Nuclei Permeabilization Method, Ligation Condition, Biotin Enrichment, DNA Input Amount, Total Reads, Protocol Link",,FALSE,Sequencing,Biospecimen,,
HI-C-seq Level 2,"Aligned read pairs, contact matrix",,"Component, HTAN Data File ID, HTAN Parent Data File ID, Filename, File Format, Genomic Reference, Aligned Read Length, Tool, Resolution, Normalization Method",,FALSE,Sequencing,HI-C-seq Level 1,,
HI-C-seq Level 3,Summary data for the HI-C-seq assay.,,"Component, HTAN Parent Data File ID, HTAN Data File ID, Filename, File Format, Genomic Reference, Stripe Calling, Loop Window, Stripe Window, Loop Calling",,FALSE,Sequencing,HI-C-seq Level 2,,
Crosslinking Condtion,Detailed condition for DNA crosslinking,,,,TRUE,Sequencing,,,
DNA Digestion Condition,Enzymes and treatment length/temperature for genome digestion,,,,TRUE,Sequencing,,,
Nuclei Permeabilization Method,Detergent and treatment condition for nuclei permeabilization and crosslinking softening,,,,TRUE,Sequencing,,,
Ligation Condition,Name of ligase and condition for proximity ligation,,,,TRUE,Sequencing,,,
Biotin Enrichment,Whether biotin is used for enriching ligation product,"Yes, No",,,TRUE,Sequencing,,,
DNA Input Amount,"Amount of DNA for library construction, in nanograms.",,,,TRUE,Sequencing,,,int
Resolution,"Binning size used for generating contact matrix, in basepair.",,,,TRUE,Sequencing,,,
Stripe Calling,"Tool used for identifying architectural stripe-forming, interaction hotspots.","MACS2, Other",,,TRUE,Sequencing,,,
Loop Window,Binning size used for calling significant dot interactions (loops),,,,TRUE,Sequencing,,,list like :: regex search -?\d+
Stripe Window,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,Sequencing,,,list like :: regex search -?\d+
Loop Calling,Tool used for identifying loop interactions,"HiCCUPS, Cooltools, Other",,,TRUE,Sequencing,,,
Imaging Level 4,Derived imaging data: Object-by-feature array,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Channel Metadata ID, HTAN Data File ID, Parameter file, Software and Version, Commit SHA,Number of Objects, Number of Features,Imaging Object Class, Imaging Summary Statistic",,FALSE,Assay,Imaging Level 3 Channels,,
SRRS Imaging Level 2,SRRS-specific HTAN raw and pre-processed image data,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, Pyramid, Zstack, Tseries, Passed QC, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType",,FALSE,Assay,Biospecimen,,
10X Genomics Xenium ISS Experiment,All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Xenium Bundle Contents, Slide ID, ROI name, Panel Name, Protocol Link, Software and Version,Total Number of Cells, Total Number of Targets, Surface area, Experiment IF Channels, Transcripts per Cell, Percent of Transcripts within Cells, Decoded Transcripts, Xenium IF image HTAN File ID, Xenium HE image HTAN File ID",,FALSE,Spatial Transcriptomics,Biospecimen,,
Xenium Bundle Contents,A comma separated list of filenames within the Xenium bundle zip file,,,,TRUE,Spatial Transcriptomics,,,
Panel Name,"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,Spatial Transcriptomics,,,
Total Number of Cells,The total number of cells analyzed on the flow cell,,,,TRUE,Spatial Transcriptomics,,,
Total Number of Targets,Refers to the target of an assay. Can be genes/transcripts or probes,,,,TRUE,Spatial Transcriptomics,,,
Experiment IF Channels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",,,,TRUE,Spatial Transcriptomics,,,
Transcripts per Cell,Mean or Median transcript count per cell analyzed on the flow cell or slide,,,,TRUE,Spatial Transcriptomics,,,
Percent of Transcripts within Cells,The percentage of transcripts assigned to assayed cells,,,,TRUE,Spatial Transcriptomics,,,
Decoded Transcripts,"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,Spatial Transcriptomics,,,
Xenium IF image HTAN File ID,The HTAN Data File ID of a Imaging Level 2 file,,,,FALSE,Spatial Transcriptomics,,,
Xenium HE image HTAN File ID,The HTAN Data File ID of a Imaging Level 2 file,,,,FALSE,Spatial Transcriptomics,,,
RPPA Level 2,Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Parent Data File ID, HTAN Data File ID, HTAN RPPA Antibody Table, Assay Type, Protocol Link, Software and Version",,FALSE,Assay,Biospecimen,,
HTAN RPPA Antibody Table,A table containing antibody level metadata for RPPA,,"HTAN RPPA Antibody Table ID, Filename, File Format, Ab Name Reported on Dataset, GENCODE Gene Symbol Target, UNIPROT Protein ID Target, Phosphoprotein Flag, Vendor, Catalog Number, Internal Ab ID, Species, RPPA Dilution, Phospho Site, RPPA Validation Status, Clone, Clonality, Antibody Notes",,TRUE,RPPA Level 2,,,
RPPA Level 3,Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Software and Version, Normalization Method",,FALSE,Assay,Biospecimen,,
RPPA Level 4,Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Batch Correction Method",,FALSE,Assay,RPPA Level 2,,
Nanostring CosMx SMI Experiment,RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI),,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, CosMx Bundle Contents, Slide ID, CosMx Assay Type, Panel Name, Protocol Link, Software and Version, Total Number of Cells, Total Number of Targets, Number of FOVs, Surface area, Experiment IF Channels, Transcripts per Cell, Percent of Transcripts within Cells, Mean Total Transcripts per Area, Unique Genes, Total Negative Probe Counts",,FALSE,Spatial Transcriptomics,Biospecimen,,
CosMx Bundle Contents,A comma separated list of filenames within the CosMx bundle zip file,,,,TRUE,Spatial Transcriptomics,,,
CosMx Assay Type,The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay,"RNA, Protein",,,TRUE,Spatial Transcriptomics,,,
Number of FOVs,The total number of FOVs recorded for the sample on a single flow cell,,,,TRUE,Spatial Transcriptomics,,,
Mean Total Transcripts per Area,The mean total transcripts per um3,,,,TRUE,Spatial Transcriptomics,,,
Unique Genes,The total unique genes detected above background,,,,FALSE,Spatial Transcriptomics,,,
Total Negative Probe Counts,Mean Total Negative probe counts/cell,,,,TRUE,Spatial Transcriptomics,,,
Mass Spectrometry Level 1,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, MS Batch ID, MS-based Assay Type, Analyte Type, MS-based Targeted, MS Instrument Vendor and Model, MS Source, Polarity, Mass Range Low Value, Mass Range High Value, Data Collection Mode, MS Scan Mode, MS Labeling, Protocol Link, LC Instrument Vendor and Model, LC Column Vendor and Model, LC Resin, LC Length Value, LC Temp Value, LC ID Value, LC Flow Rate, LC Gradient, LC Mobile Phase A, LC Mobile Phase B, Software and Version, MS Instrument Metadata File",,FALSE,Assay,Biospecimen,,
Mass Spectrometry Level 2,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 1,,
Mass Spectrometry Level 3,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 2,,
Mass Spectrometry Level 4,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 3,,
Mass Spectrometry Auxiliary File,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID",,FALSE,Assay,,,
Imaging Level 3 Channels,Channel-level Metadata Attributes,,"HTAN Channel Metadata ID, Channel ID, Channel Name, Channel Passed QC, Cycle Number, Sub Cycle Number, Antibody Role, Target Name, Antibody Name, RRID identifier, Fluorophore, Clone, Lot, Vendor, Catalog Number, Excitation Wavelength, Emission Wavelength, Excitation Bandwidth, Emission Bandwidth, Metal Isotope Element, Metal Isotope Mass, Oligo Barcode Upper Strand, Oligo Barcode Lower Strand, Dilution, Concentration",,FALSE,Assay,,,
HTAN Channel Metadata ID,HTAN ID for this channel metadata table (same for all rows),,,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Channel ID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),,,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Channel Name,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin'),,,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Channel Passed QC,Identify stains that did not pass QC but are included in the dataset.,"Yes, No - Channel Failed QC",,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
No - Channel Failed QC,Channel failed QC,,Channel QC Failure Type,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Channel QC Failure Type,Reason the channel failed QC,"Off-target staining, Auto-fluoresence, Staining artefacet, Imaging artefact, Other/multiple channel QC faliure types",,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Other/multiple channel QC faliure types,QC failure type not speficied,,Channel QC Failure Comment,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Channel QC Failure Comment,Custom comment on channel QC faliure,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Cycle Number,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,int
Sub Cycle Number,Sub cycle number,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,int
Target Name,Short descriptive name (abbreviation) for this target (antigen),,,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Antibody Role," ""Is this antibody acting as a primary or secondary antibody""","Primary,Secondary,Neither-Dye/Stain",,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Antibody Name,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",,,,TRUE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
RRID identifier,Research Resource Identifier (eg “RRID: AB_394606”),,,,TRUE,Imaging Level 3 Channels,,https://scicrunch.org/resources,regex match AB_\d+|Not\sApplicable$
Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),,,,FALSE,Imaging Level 3 Channels,,http://purl.obolibrary.org/obo/MI_0857,
Clone,Clone,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Lot,Lot number from vendor,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Vendor,Vendor,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Catalog Number,Catalog Number,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Excitation Wavelength,Center/peak of the excitation spectrum (nm),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,num
Emission Wavelength,Center/peak of the emission spectrum (nm),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,num
Excitation Bandwidth,Nominal width of excitation spectrum (nm),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,num
Emission Bandwidth,Nominal width of emission spectrum (nm),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,num
Metal Isotope Element,Element abbreviation. eg “La” or “Nd”,"H, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac, Th, Pa, U, Np, Pu, Am, Bk, Cf, Es, Fm, Md, No, Lr, Rf, Db, Sg, Bh, Hs, Mt, Ds, Rg, Cn, Nh, Fl, Mc, Lv, Ts, Og",,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,str
Metal Isotope Mass,Element mass number,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,int
Oligo Barcode Upper Strand,Oligo Barcode - Upper Strand,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Oligo Barcode Lower Strand,Oligo Barcode - Lower Strand,,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Dilution,Dilution (eg 1:1000),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Concentration,Concentration (eg 10ug/mL),,,,FALSE,Imaging Level 3 Channels,,https://www.miti-consortium.org/,
Imaging Assay Type,Type of imaging assay,"H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH, ExSeq, RareCyte Orion, Not Applicable",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Channel Metadata Filename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,,,,TRUE,Imaging Level 2,,,
Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",,,,TRUE,Imaging,,http://purl.obolibrary.org/obo/OBI_0400169,
Objective,Objective,,,,FALSE,Imaging,,https://www.miti-consortium.org/,
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,Imaging,,https://www.miti-consortium.org/,num
LensNA,The numerical aperture of the lens. Floating point value > 0.,,,,FALSE,Imaging,,https://www.miti-consortium.org/,num
WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",,WorkingDistanceUnit,,FALSE,Imaging,,https://www.miti-consortium.org/,
WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,FALSE,Imaging,,https://www.miti-consortium.org/,
Immersion,Immersion medium,"Air, Oil, Water, Other",,,FALSE,Imaging,,https://www.miti-consortium.org/,
Pyramid,Does data file contain pyramid of images,"Yes, No",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Zstack,Does data file contain a Z-stack of images,"Yes, No",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Tseries,Does data file contain a time-series of images,"Yes, No",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Passed QC,Did all channels pass QC (if not add free text Comment),"Yes, No - Channels QC",,,TRUE,Imaging,,https://www.miti-consortium.org/,
No - Channels QC,Not all channels passed QC,,Comment,,FALSE,Imaging,,https://www.miti-consortium.org/,
Comment,Free text field (generally for QC comment),,,,FALSE,Imaging,,https://www.miti-consortium.org/,
FOV number,Index of FOV (as it pertains to its sequence order). Integer >= 1,,,,FALSE,Imaging,,https://www.miti-consortium.org/,num
FOVX,Field of view X dimension. Floating point,,FOVXUnit,,FALSE,Imaging,,https://www.miti-consortium.org/,num
FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,FALSE,Imaging,,https://www.miti-consortium.org/,
FOVY,Field  of view Y dimension. Floating point value,,FOVYUnit,,FALSE,Imaging,,https://www.miti-consortium.org/,num
FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,FALSE,Imaging,,https://www.miti-consortium.org/,
Frame Averaging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",,,,FALSE,Imaging,,https://www.miti-consortium.org/,
Image ID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",,,,TRUE,Imaging,,https://www.miti-consortium.org/,
DimensionOrder,The order in which the individual planes of data are interleaved.,"XYZCT, XYZTC, XYCTZ, XYCZT, XYTZC, ZYX",,,TRUE,Imaging,,https://www.miti-consortium.org/,
PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,,PhysicalSizeXUnit,,TRUE,Imaging,,,
PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging,,https://www.miti-consortium.org/,
PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,,PhysicalSizeYUnit,,TRUE,Imaging,,https://www.miti-consortium.org/,
PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging,,https://www.miti-consortium.org/,
PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,,PhysicalSizeZUnit,,TRUE,Imaging,,https://www.miti-consortium.org/,
PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Pixels BigEndian,Boolean (True/False),"True, False",,,TRUE,Imaging,,https://www.miti-consortium.org/,
PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",,,,TRUE,Imaging,,https://www.miti-consortium.org/,
SizeC,Number of channels. Integer >= 1,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
SizeT,Number of time points. Integer >= 1,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
SizeX,Size of image: X dimension (in pixels). Integer >= 1,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
SizeY,Size of image: Y dimension (in pixels). Integer >= 1,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
PixelType,"Data type for each pixel value. E.g. ""uint16""","int8, int16, int32, uint8, uint16, uint32, float, double, bit",,,TRUE,Imaging,,,
Imaging Segmentation Data Type,Specifies how the segmentation is stored,"Mask, Outline, Polygon, Probability Map, Point",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Parameter file,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,,,,FALSE,Imaging,,,
Commit SHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",,,,FALSE,Imaging,,,
Imaging Object Class,Defines the structure that the mask delineates,"nucleus, cytoplasm, plasma membrane, whole cell, spot, Imaging Object Class Other",,,TRUE,Imaging,,https://www.miti-consortium.org/,list like
Imaging Object Class Other,Imaging Object Class Other,,Imaging Object Class Description,,FALSE,Imaging,,https://www.miti-consortium.org/,
Imaging Object Class Description,Free text description of object class [string],,,,TRUE,Imaging,,https://www.miti-consortium.org/,
Number of Objects,The number of objects (eg cells) described,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
Number of Features,The number of features (eg channels) described,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
Imaging Summary Statistic,Function used to summarize object/feature intensity,"Mean,Median,Not Specified",,,FALSE,Imaging,,https://www.miti-consortium.org/,
Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei, Micro-region",,,TRUE,Sequencing,,,
Micro-region Seq Platform,The platform used for micro-regional RNA sequencing (if applicable),"Rarecyte Pick-Seq, Laser Capture Microdissection",,,FALSE,Sequencing,,,
ROI Tag,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,Sequencing,,,
Single Cell Isolation Method,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)","Microfluidics Chip, Droplets, FACS, Plates, 10x, Nuclei Isolation",,,TRUE,scRNA-seq Level 1,,,
Dissociation Method,The tissue dissociation method used for scRNASeq or scATAC-seq assays,"gentleMACS, Dounce, Enzymatic Digestion, Not Applicable",,,TRUE,scRNA-seq Level 1,,,
Library Layout,Sequencing read type,"Paired End, Single Read, Mid-length, Long Read",,,TRUE,Sequencing,,,
Nucleus Identifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,Nuclei Barcode,,,TRUE,scATAC-seq Level 1,,,
Nuclei Barcode,Nuclei Barcode,"Nuclei Barcode Read, Nuclei Barcode Length",,,FALSE,scATAC-seq Level 1,,,
scATACseq Library Layout,Sequencing read type,scATACseq Paired End,,,TRUE,scATAC-seq Level 1,,,
Nuclei Barcode Read,Nuclei Barcode Read,,,,TRUE,scATAC-seq Level 1,,,
Nuclei Barcode Length,Nuclei Barcode Length,,,,TRUE,scATAC-seq Level 1,,,
scATACseq Paired End,A library layout type,"scATACseq Read1, scATACseq Read2",,,FALSE,scATAC-seq Level 1,,,
scATACseq Read1,Read 1 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,TRUE,scATAC-seq Level 1,,,
scATACseq Read2,Read 2 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,TRUE,scATAC-seq Level 1,,,
scATACseq Read3,Read 3 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,FALSE,scATAC-seq Level 1,,,
scmCseq Read1,Read 1 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scmC-seq Level 1,,,
scmCseq Read2,Read 2 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scmC-seq Level 1,,,
scmCseq Read3,Read 3 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scmC-seq Level 1,,,
Threshold for Minimum Passing Reads,Threshold for calling cells,,,,TRUE,scATAC-seq Level 1,,,
Total Number of Passing Nuclei,Number of nuclei sequenced,,,,TRUE,scATAC-seq Level 1,,,
Median Fraction of Reads in Peaks,Median fraction of reads in peaks (FRIP),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,,
Median Fraction of Reads in Annotated cis DNA Elements,Median fraction of reads in annotated cis-DNA elements (FRIADE),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,,
Median Passing Read Percentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,,,,TRUE,scATAC-seq Level 1,,,
Median Percentage of Mitochondrial Reads per Nucleus,Contamination from mitochondrial sequences,,,,TRUE,scATAC-seq Level 1,,,
Peaks Calling Software,Generic name of peaks calling tool,,,,TRUE,scATAC-seq Level 1,,,
Read Indicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads 1 (I1), Index Reads 2 (I2),  or Other","R1, R2, R1&R2, I1, I2, Other",,,TRUE,Sequencing,,,
Read1,Read 1 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,,
Read2,Read 2 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,,
cDNA,"Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase",,"cDNA Offset, cDNA Length",,FALSE,Sequencing,,,
cDNA Offset,Offset in sequence for cDNA read (in bp): number,,,,TRUE,Sequencing,,,
cDNA Length,Length of cDNA read (in bp): number,,,,TRUE,Sequencing,,,
Cell Barcode and UMI,Cell and transcript identifiers,,"UMI Barcode Offset, UMI Barcode Length, Median UMIs per Cell Number, Cell Barcode Offset, Cell Barcode Length, Valid Barcodes Cell Number",,FALSE,scRNA-seq Level 1,,,
Cell Barcode Offset,Offset in sequence for cell barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,,
Cell Barcode Length,Length of cell barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,,
Valid Barcodes Cell Number,Number,,,,TRUE,scRNA-seq Level 1,,,
UMI Barcode Offset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",,,,TRUE,scRNA-seq Level 1,,https://www.ebi.ac.uk/arrayexpress/help/single-cell_submission_guide.html,
UMI Barcode Length,Length of UMI barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,,
Median UMIs per Cell Number,Number,,,,TRUE,scRNA-seq Level 1,,,
Cell Median Number Reads,Median number of reads per cell. Number,,,,TRUE,scRNA-seq Level 3,,,
Cell Median Number Genes,Median number of genes detected per cell. Number,,,,TRUE,scRNA-seq Level 3,,,
Cell Total,Number of sequenced  cells. Applies to raw counts matrix only.,,,,TRUE,scRNA-seq Level 3,,,
Library Construction Method,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],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop, sci-ATAC-seq, Nextera XT, 10x Multiome, 10x FLEX, 10x GEM 3', 10x GEM 5'",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711,
Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number",,,,TRUE,scRNA-seq Level 1,,,
CEL-seq2,Highly-multiplexed plate-based single-cell RNA-Seq assay,,"Empty Well Barcode, Well Index",,FALSE,scRNA-seq Level 1,,,
Empty Well Barcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,,,,TRUE,scRNA-seq Level 1,,,
Well Index,Indicate if protein expression (EPCAM/CD45) positive/negative data  is available for each cell in CEL-seq2 assays,"Yes, No",,,FALSE,scRNA-seq Level 1,,,
Library Preparation Days from Index,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,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,regex match \d+$|Not\sApplicable$|unknown$
Single Cell Dissociation Days from Index,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-seq Level 1,,,regex match \d+$|Not\sApplicable$|unknown$
Sequencing Library Construction Days from Index,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,Sequencing,,,regex match \d+$|Not\sApplicable$|unknown$
Nucleic Acid Capture Days from Index,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,Sequencing,,,regex match \d+$|Not\sApplicable$|unknown$
Cryopreserved Cells in Sample,Indicate if library preparation was based on revived frozen cells.,"Yes, No",,,TRUE,scRNA-seq Level 1,,,
End Bias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript","3 Prime, 5 Prime, Full Length Transcript",,,TRUE,scRNA-seq Level 1,,,
Reverse Transcription Primer,"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","Oligo-dT, Poly-dT, Feature barcoding, Random",,,TRUE,scRNA-seq Level 1,,http://www.sequenceontology.org/so_wiki/index.php/Category:SO:0000112_!_primer,
Feature barcoding,A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc],,Feature Reference Id,,FALSE,scRNA-seq Level 1,,https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc,
Feature Reference Id,"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,scRNA-seq Level 1,,,
Spike In,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,"ERCC, Other Spike In, No Spike In, PhiX",,,TRUE,scRNA-seq Level 1,,,
ERCC,The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization,,Spike In Concentration,,FALSE,Spike In,,,
Spike In Concentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],,,,TRUE,ERCC,,https://www.ncbi.nlm.nih.gov/pubmed/21816910,
Sequencing Platform,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.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000,  Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000,  Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Technical Replicate Group,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,Sequencing,,,
Total Number of Input Cells,Number of cells loaded/placed on plates,,,,TRUE,Sequencing,,,
Sequencing Batch ID,Links samples to a specific local sequencer run. Can be string or 'null',,,,TRUE,Sequencing,,,
Single Nucleus Buffer,Nuclei isolation buffer,"NIB, 10x, Omni,TST",,,TRUE,scATAC-seq Level 1,,,
Transposition Reaction,"Name of the transposase, transposon sequences","Tn5, EZ-Tn5, Tn5-059, Nextera Tn5, Diagenode-unloaded Apex-Bio, Diagenode-loaded Apex-Bio, In-House",,,TRUE,scATAC-seq Level 1,,,
Read Length,"The length of the sequencing reads. Can be integer, null",,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Target Capture Kit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.","Not Applicable, Custom Targets File Provided, Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes, Custom GENIE-DFCI OncoPanel - 275 Genes, Custom GENIE-DFCI Oncopanel - 300 Genes, Custom GENIE-DFCI Oncopanel - 447 Genes, Custom HaloPlex DLBCL Panel - 370 Genes, Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes, Custom Large Construct Capture TARGET-OS Panel - 8 Genes, Custom MSK IMPACT Panel - 341 Genes, Custom MSK IMPACT Panel - 410 Genes, Custom MSK IMPACT Panel - 468 Genes, Custom Myeloid GENIE-VICC Panel - 37 Genes, Custom Personalis ACEcp VAREPOP-APOLLO Panel v2, Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes, Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes, Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1, Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2, Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb, Custom Solid Tumor GENIE-VICC Panel - 34 Genes, Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb, Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb, Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb, Custom SureSelect GENIE-UHN Panel - 555 Genes, Custom SureSelect Human All Exon v1.1 Plus 3 Boosters, Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb, Custom Twist Broad Exome v1.0 - 35.0 Mb, Custom Twist Broad PanCancer Panel - 396 Genes, Foundation Medicine T5a Panel - 322 Genes, Foundation Medicine T7 Panel - 429 Genes, Ion AmpliSeq Cancer Hotspot Panel v2, Ion AmpliSeq Comprehensive Cancer Panel, Nextera DNA Exome, Nextera Rapid Capture Exome v1.2, SeqCap EZ HGSC VCRome v2.1, SeqCap EZ Human Exome v2.0, SeqCap EZ Human Exome v3.0, SureSelect Human All Exon v3, SureSelect Human All Exon v4, SureSelect Human All Exon v5, SureSelect Human All Exon v5 + UTR, TruSeq Amplicon Cancer Panel, TruSeq Exome Enrichment - 62 Mb, TruSeq RNA Exome, TruSight Myeloid Sequencing Panel, xGen Exome Research Panel v1.0, xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn, 25 rxn xGen Universal Blocking Oligo – TS HT-i7, SureSelect Human All Exon v6, unknown",,,TRUE,Sequencing,,,
Library Selection Method,How RNA molecules are isolated.,"Hybrid Selection, PCR, Affinity Enrichment, Poly-T Enrichment, Random, rRNA Depletion, miRNA Size Fractionation, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Library Preparation Kit Name,Name of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Library Preparation Kit Vendor,Vendor of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Library Preparation Kit Version,Version of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Adapter Name,Name of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Adapter Sequence,Base sequence of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Base Caller Name,Name of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Base Caller Version,Version of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Flow Cell Barcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Fragment Maximum Length,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Fragment Mean Length,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Fragment Minimum Length,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Fragment Standard Deviation Length,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Lane Number,"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,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Library Strand,Library stranded-ness.,"Unstranded, First Stranded, Second Stranded, Not Applicable",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Multiplex Barcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Size Selection Range,Range of size selection. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Target Depth,The targeted read depth prior to sequencing. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
To Trim Adapter Sequence,Does the user suggest adapter trimming?,"Yes - Trim Adapter Sequence, No",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
Yes - Trim Adapter Sequence,Trim adapter sequence,"Adapter Trimmer Name, Adapter Trimmer Version, Adapter Trimmer Options",,,FALSE,Sequencing,,,
Adapter Trimmer Name,Name of adapter trimmer,,,,FALSE,Sequencing,,,
Adapter Trimmer Version,Version of the adapter trimmer,,,,FALSE,Sequencing,,,
Adapter Trimmer Options,Options used by adapter trimmer,,,,FALSE,Sequencing,,,
Transcript Integrity Number,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
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,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Adapter Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Basic Statistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Encoding,Version of ASCII encoding of quality values found in the file. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Kmer Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Overrepresented Sequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Per Base N Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Per Base Sequence Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Per Base Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Per Sequence GC Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Per Sequence Quality Score,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Per Tile Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Percent GC Content,The overall %GC of all bases in all sequences. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Sequence Duplication Levels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Sequence Length Distribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Total Reads,Total number of reads per sample. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Whitelist Cell Barcode File Link,Link to file listing all possible cell barcodes. URL,,,,TRUE,Sequencing,,,
Cell Barcode Tag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),,,,TRUE,Sequencing,,,
UMI Tag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",,,,TRUE,Sequencing,,,
Applied Hard Trimming,Was Hard Trimming applied,"Yes - Applied Hard Trimming, No",,,TRUE,Sequencing,,,
Yes - Applied Hard Trimming,Hard Trimming was applied,,Aligned Read Length,,FALSE,Sequencing,,,
Aligned Read Length,Read length used for alignment if hard trimming was applied,,,,TRUE,Sequencing,,,
scRNAseq Workflow Type,Generic name for the workflow used to analyze a data set.,"CellRanger, STARsolo, HCA Optimus, dropEST, SEQC, Cufflinks, DEXSeq, HTSeq - FPKM, Cell annotation, Differentiation trajectory analysis, Other",,,TRUE,Sequencing,,,
Workflow Version,Major version of the workflow (e.g. Cell Ranger v3.1),,,,TRUE,Sequencing,,,
scRNAseq Workflow Parameters Description,"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,Sequencing,,,
scATACseq Workflow Type,Generic name for the workflow used to analyze a data set.,,,,TRUE,Sequencing,,,
scATACseq Workflow Parameters Description,Parameters used to run the scATAC-seq workflow.,,,,TRUE,Sequencing,,,
Workflow Link,Link to workflow or command. DockStore.org recommended. URL,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow,
QC Workflow Type,Generic name for the workflow used to analyze a data set. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
QC Workflow Version,Major version for a workflow. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
QC Workflow Link,Link to workflow used. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc,
Germline Variants Workflow URL,"Link to workflow document, e.g. Github, DockStore.org recommended",,,,TRUE,Sequencing,,,
Germline Variants Workflow Type,Generic name for the workflow used to analyze a data set,"GATK4, Other Germline Variants Workflow Type, None",,,FALSE,Sequencing,,,
Other Germline Variants Workflow Type,Other Germline Variants Workflow Type,,Custom Germline Variants Workflow Type,,FALSE,Sequencing,,,
Custom Germline Variants Workflow Type,Specify the name of a custom alignment workflow,,,,TRUE,Sequencing,,,
Somatic Variants Workflow URL,Generic name for the workflow used to analyze a data set.,,,,TRUE,Sequencing,,,
Somatic Variants Workflow Type,Generic name for the workflow used to analyze a data set.,"CaVEMan, GATK4, MuTect2, MuSE, MuTect2, Pindel, SomaticSniper, VarScan2, Other Somatic Variants Workflow Type, None",,,FALSE,Sequencing,,,
Other Somatic Variants Workflow Type,Other Somatic Variants Workflow Type,,Custom Somatic Variants Workflow Type,,FALSE,Sequencing,,,
Custom Somatic Variants Workflow Type,Specify the name of a custom workflow name,,,,TRUE,Sequencing,,,
Somatic Variants Sample Type,Is the sample case or control in somatic variant analysis,"Case Sample, Control Sample, Not Applicable",,,TRUE,Sequencing,,,
Structural Variant Workflow URL,Link to workflow document. DockStore.org recommended. URL,,,,TRUE,Sequencing,,,
Structural Variant Workflow Type,Generic name for the workflow used to analyze a data set.,"BRASS, GATK4, CNV, CNVkit, Other Structural Variant Workflow Type, None",,,FALSE,Sequencing,,,
Other Structural Variant Workflow Type,Other Structural Variant Workflow Type,,Custom Structural Variant Workflow Type,,FALSE,Sequencing,,,
Custom Structural Variant Workflow Type,Specify the name of a custom workflow name,,,,TRUE,Sequencing,,,
Alignment Workflow Url,Link to workflow used for read alignment. DockStore.org recommended. String,,,,TRUE,Sequencing,,,
Alignment Workflow Type,Generic name for the workflow used to analyze a data set.,"BWA, BWA with BQSR, BWA-aln, BWA-mem, BWA with Mark Duplicates and BQSR, STAR 2-Pass, STAR 2-Pass Chimeric, STAR 2-Pass Genome, STAR 2-Pass Transcriptome, Bowtie, Bismark, GSNAP, BSMAP, BSmooth, BS-Seeker2, BS-Seeker, RMAP, MethylCoder, BRAT-BW, Pash, Segemehl, Bisulfighter, BatMeth, LAST, ERNE-BS5, B-SOLANA, SOCS-B, BWA-meth, Other Alignment Workflow, None",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow,
Other Alignment Workflow,Other Alignment Workflow,,Custom Alignment Workflow,,FALSE,Sequencing,,,
Custom Alignment Workflow,Specify the name of a custom alignment workflow,,,,TRUE,Sequencing,,,
MSI Workflow Link,Link to method workflow (or command) used in estimating the MSI. URL,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
MSI Score,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,,,,FALSE,Sequencing,,,
MSI Status,MSIsensor determination of either microsatellite stability or instability.,"MSI, MSI-low, MSI-high, MSS",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Genomic Reference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow,
Genomic Reference URL,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,Sequencing,,,
Genome Annotation URL,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,Sequencing,,,
Index File Name,The name (or part of a name) of a file (of any type). String,,,,TRUE,Sequencing,,,
Average Base Quality,Average base quality collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads_index,
Average Insert Size,Average insert size collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Average Read Length,Average read length collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Contamination Error,Estimation error of cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Mean Coverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Pairs On Diff CHR,Pairs on different chromosomes collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Total Uniquely Mapped,Number of reads that map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Total Unmapped reads,Number of reads that did not map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Proportion Reads Duplicated,Proportion of duplicated reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Proportion Reads Mapped,Proportion of mapped reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Proportion Targets No Coverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Proportion Base Mismatch,Proportion of mismatched bases collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Proportion Coverage 10x,"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,Sequencing,,,
Proportion Mitochondrial Reads,Proportion of reads mapping to mitochondria.,,,,FALSE,Sequencing,,,
Proportion Coverage 30X,"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,Sequencing,,,
Short Reads,Number of reads that were too short. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,
Pseudo Alignment Used,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,"Yes - Pseudo Alignment Used, No",,,TRUE,Sequencing,,,
Software and Version,Name of software used to generate expression values. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow,
Yes - Pseudo Alignment Used,Pseudo aligner was used,,"Workflow Link, Software and Version, Genomic Reference, Genomic Reference URL",,FALSE,Sequencing,,,
Data Category,Specific content type of the data file.,"Gene Expression, Transcript Expression, Exon Expression Quantification, Gene Expression Quantification, Isoform Expression Quantification, Splice Junction Quantification, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=gene_expression,
Expression Units,How quantities are corrected for gene length,"TPM, RPKM, FPKM, Counts, Other, NA",,,TRUE,Sequencing,,,
Fusion Gene Detected,Was a fusion gene identified?,"Yes - Fusion Gene Detected, No, unknown",,,FALSE,Sequencing,,,
Yes - Fusion Gene Detected,A fusion gene was detected,,Fusion Gene Identity,,FALSE,Sequencing,,,
Fusion Gene Identity,The gene symbols of fused genes.,"EWS-FLI, EWS-ERG, SYT-SSX1, SYT-SSX2, EWS-WT1, Other Fusion Gene",,,FALSE,Sequencing,,,list like
Other Fusion Gene,Other fusion gene detected.,,Specify Other Fusion Gene,,FALSE,Sequencing,,,
Specify Other Fusion Gene,"Specify fusion gene detected, if not in list",,,,FALSE,Sequencing,,,
Matrix Type,Type of data stored in matrix.,"Raw Counts, Normalized Counts, Scaled Counts, Batch Corrected Counts",,,TRUE,Sequencing,,,
Linked Matrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,,,,FALSE,Sequencing,,,
Biospecimen Type,Biospecimen Type,"Tissue Biospecimen Type, Blood Biospecimen Type, Analyte Biospecimen Type, Mouth Rinse Biospecimen Type, Stool Biospecimen Type, Urine Biospecimen Type, Ascites Biospecimen Type, Sputum Biospecimen Type, Fluids Biospecimen Type, Bone Marrow Biospecimen Type, Cells Biospecimen Type",,,TRUE,Biospecimen,,,
Analyte Biospecimen Type,A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,,"Analyte Type, Fixation Duration, Slide Charge Type, Section Thickness Value, Sectioning Days from Index, Shipping Condition Type, Ischemic Time, Ischemic Temperature",,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2513915&version=2.0,
Tissue Biospecimen Type,Tissue biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method, Biospecimen Dimension 1, Biospecimen Dimension 2, Biospecimen Dimension 3, Section Number in Sequence",,FALSE,Biospecimen,,,
Bone Marrow Biospecimen Type,Bone Marrow biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method, Biospecimen Dimension 1, Biospecimen Dimension 2, Biospecimen Dimension 3, Section Number in Sequence",,FALSE,Biospecimen,,,
Urine Biospecimen Type,Urine biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method",,FALSE,Biospecimen,,,
Blood Biospecimen Type,Blood biospecimen,,Shipping Condition Type,,FALSE,Biospecimen,,,
Timepoint Label,"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,,,
Collection Days from Index,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',,,,TRUE,Biospecimen,,,regex match \d+$|Not\sApplicable$|unknown$
Protocol Link,"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,Information Content Entity,,,
Adjacent Biospecimen IDs,"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,,,
Mounting Medium,"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","Aqueous water based, Non-Aqueous Solvent based, Xylene,Toluene,Antifade with DAPI,Antifade without DAPI,PBS,unknown,Not Reported",,,FALSE,Biospecimen,,,
Analyte Type,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,"cfDNA Analyte, DNA Analyte, RNA Analyte, Total RNA Analyte, Tissue Block Analyte, Tissue Section Analyte, PBMCs or Plasma or Serum Analyte, cDNA Libraries Analyte, PBMCs, Plasma, Serum Analyte, lipid, protein, metabolite",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2513915&version=2.0,
Acquisition Method Type,Records the method of acquisition or source for the specimen under consideration.,"Autopsy, Biopsy, Fine Needle Aspirate, Surgical Resection, Punch Biopsy, Shave Biopsy, Excision, Re-excision, Sentinel Node Biopsy, Lymphadenectomy - Regional Nodes, Other Acquisition Method, Non induced sputum, Induced sputum, BAL (bronchial alveolar lavage), Cytobrush, Blood draw, Fluid collection, Forceps biopsy, Core needle biopsy, Endoscopic biopsy, Not specified",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6626651&version=1.0,
Other Acquisition Method,A custom acquisition method,,Acquisition Method Other Specify,,FALSE,Biospecimen,,,
Acquisition Method Other Specify,A custom acquisition method [Text - max length 100 characters],,,,TRUE,Biospecimen,,,
Preservation Method,Text term that represents the method used to preserve the sample.,"Cryopreserved, Cryopreservation in liquid nitrogen - dead tissue, Cryopreservation in dry ice - dead tissue, Cryopreservation in liquid nitrogen - live cells, Formalin fixed paraffin embedded - FFPE, Formalin fixed-unbuffered, Formalin fixed-buffered, Fresh, Fresh dissociated and single cell sorted into plates in NP40 buffer, OCT, Snap Frozen, Frozen, Negative 80 Deg C, Liquid Nitrogen, Fresh dissociated, Fresh dissociated and single cell sorted, Fresh dissociated and single cell sorted into plates, Methacarn fixed paraffin embedded - MFPE, unknown, Not Reported",,,TRUE,Biospecimen,,,
Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Carnoy's Fixative, Polaxamer, Other, None, unknown, Unfixed",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=65078&version=3.0,
Fixation Duration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5230144&version=1.0,
Ischemic Time,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",,,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,
Ischemic Temperature,Specify whether specimen experienced warm or cold ischemia.,"Warm Ischemia, Cold Ischemia, Ambient air, 4C wet ice, Negative -20C, Dry Ice, Liquid Nitrogen, unknown",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,
Collection Media,Material Specimen is collected into post procedure,"DMEM, DMEM+Serum, RPMI, RPMI+Serum, PBS, PBS+Serum, None",,,FALSE,Biospecimen,,,
Specimen Laterality,"For tumors in paired organs, designates the side on which the specimen was obtained.","Bilateral, Left, Right, unknown, Not Reported, Not Applicable",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2007875&version=1.0,
Portion Weight,"Numeric value that represents the sample portion weight, measured in milligrams.",,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432593&version=1.0,
Total Volume,Numeric value for the total amount of sample or specimen,,Total Volume Unit,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3005019&version=1.0,
Total Volume Unit,Unit of measurement used for the total amount of sample or specimen,"mL,cubic millimeter,square centimeter",,,FALSE,Biospecimen,,,
Tumor Tissue Type,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),"Additional Primary, Local recurrence, Metastatic, Premalignant, Primary, Recurrent, Normal, Normal adjacent, Normal distant, Post therapy, Post therapy neoadjuvant, Post therapy adjuvant, Not Otherwise Specified, Premalignant - in situ, Atypia - hyperplasia, Not analyzed",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3288124&version=1.0,
Histologic Morphology Code,"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,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3226275&version=1.0,
Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN","Melanocytic hyperplasia, Atypical melanocytic proliferation, Melanoma in situ - superficial spreading, Melanoma in situ - lentigo maligna type, Melanoma in situ - acral-lentiginous, Melanoma in situ - arising in a giant congenital nevus, Persistent melanoma in situ, Melanoma in situ - not otherwise classified, Scar - no residual melanoma, Invasive melanoma - superficial spreading, Invasive melanoma - nodular type, Invasive melanoma - lentigo maligna, Invasive melanoma - acral lentiginous, Invasive melanoma - desmoplastic, Invasive melanoma - nevoid, Invasive melanoma - other, Normal WDA, Reserve cell hyperplasia, Squamous metaplasia - mature, Squamous metaplasia - immature, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Squamous Carcinoma in situ, Atypical adenomatous hyperplasia, Adenocarcinoma in situ - non mucinous, Adenocarcinoma in situ - mucinous, Benign tumor NOS, Hamartoma, Carcinoma NOS, No diagnosis possible",,,FALSE,Biospecimen,,,
Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5227611&version=1.0,
Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3024951&version=1.0,
Sectioning Days from Index,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',,,,TRUE,Biospecimen,,,regex match \d+$|Not\sApplicable$|unknown$
Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -20C, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, 4C in vacuum chamber, Desiccant at 4C, Not Applicable, unknown",,,TRUE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method,
Processing Days from Index,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',,,,TRUE,Biospecimen,,,regex match \d+$|Not\sApplicable$|unknown$
Shipping Condition Type,Text descriptor of the shipping environment of a biospecimen.,"Ambient Pack, Cold Pack, Dry Ice, Ice Pack, Liquid Nitrogen, Specimen at Room Temperature, Other Shipping Environment, Not Shipped",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5495533&version=1.0,
Site Data Source,"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,,,
Processing Location,"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,Text term describing who (in what role) made the histological assessments of the sample,"Pathologist, Research Scientist, Other, unknown",,,FALSE,Biospecimen,,,
Histology Assessment Medium,The method of assessment used to characterize histology,"Digital, Microscopy, Other, unknown",,,FALSE,Biospecimen,,,
Tumor Infiltrating Lymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],,,,FALSE,Biospecimen,,,
Degree of Dysplasia,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.,"Normal or basal cell hyperplasia or metaplasia, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Carcinoma in Situ, unknown",,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5543188&version=1.0,
Dysplasia Fraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2390593&version=1.0,
Number Proliferating Cells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432636&version=1.0,
Percent Eosinophil Infiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2897700&version=2.0,
Percent Granulocyte Infiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2897705&version=2.0,
Percent Inflam Infiltration,"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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2897695&version=1.0,
Percent Lymphocyte Infiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2897710&version=2.0,
Percent Monocyte Infiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5455535&version=1.0,
Percent Necrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2841237&version=1.0,
Percent Neutrophil Infiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2841233&version=1.0,
Percent Normal Cells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2841233&version=1.0,
Percent Stromal Cells,"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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2841241&version=1.0,
Percent Tumor Cells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5432686&version=1.0,
Percent Tumor Nuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,,,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2841225&version=1.0,
Fiducial Marker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,"Nuclear Stain - DAPI, Fluorescent Beads, Grid Slides - Hemocytometer, Adhesive Markers, Other, unknown, Not Reported",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi,
Slicing Method,Imaging specific: the method by which the tissue was sliced.,"Vibratome, Cryosectioning, Tissue molds, Sliding microtome, Sectioning, Other, unknown, Not Reported",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi,
Lysis Buffer,scRNA-seq specific: Type of lysis buffer used,,,,FALSE,Biospecimen,,,
Method of Nucleic Acid Isolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",,,,FALSE,Biospecimen,,,
Biospecimen Dimension 1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",,Dimensions Unit,,FALSE,Biospecimen,,,
Biospecimen Dimension 2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",,,,FALSE,Biospecimen,,,
Biospecimen Dimension 3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",,,,FALSE,Biospecimen,,,
Dimensions Unit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)","mm, cm",,,FALSE,Biospecimen,,,
Section Number in Sequence,"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,Biospecimen,,,
Start Days from Index,"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,Patient,,,regex match \d+$|Not\sApplicable$|unknown$
Stop Days from Index,"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,Patient,,,regex match \d+$|Not\sApplicable$|unknown$
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.","hispanic or latino, not hispanic or latino, unknown, Not Reported, not allowed to collect",,,TRUE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2192217&version=2.0,
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.]","female, male, unknown, unspecified, Not Reported",,,TRUE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2200604&version=3.0,
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.","white, american indian or alaska native, black or african american, asian, native hawaiian or other pacific islander, other, unknown, Not Reported, not allowed to collect",,,TRUE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2192199&version=1.0,
Vital Status,The survival state of the person registered on the protocol.,"Alive, Dead, unknown, Not Reported",,,TRUE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5&version=5.0,
Dead,This indicates the participant is dead and defines further required metadata,,"Year of Death, Cause of Death, Cause of Death Source, Days to Death",,FALSE,Demographics,,,
Days to Birth,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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154723&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Year of Death,Numeric value to represent the year of the death of an individual.,,,,TRUE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2897030&version=1.0,
Country of Residence,Country of Residence at enrollment,"Afghanistan,Albania,Algeria,Andorra,Angola,Anguilla,Antigua and Barbuda,Argentina,Armenia,Aruba,Australia,Austria,Azerbaijan,Bahamas,Bahrain,Bangladesh,Barbados,Belarus,Belgium,Belize,Benin,Bermuda,Bhutan,Bolivia,Bosnia and Herzegovina,Botswana,Brazil,Brunei,Bulgaria,Burkina Faso,Burundi,Cambodia,Cameroon,Canada,Cape Verde,Cayman Islands,Central African Republic,Chad,Chile,China,Colombia,Comoros,Congo,Cook Islands,Costa Rica,Cote d'Ivoire,Croatia,Cuba,Curacao,Cyprus,Czech Republic (Czechia),Democratic Republic of the Congo,Denmark,Djibouti,Dominica,Dominican Republic,Ecuador,Egypt,El Salvador,Equatorial Guinea,Eritrea,Estonia,Eswatini,Ethiopia,Falkland Islands (Malvinas),Faroe Islands,Federated States of Micronesia,Fiji,Finland,France,French Guiana,French Polynesia,Gabon,Gambia,Georgia,Germany,Ghana,Gibraltar,Greece,Greenland,Grenada,Guadeloupe,Guam,Guatemala,Guernsey,Guinea,Guinea-Bissau,Guyana,Haiti,Holy See,Honduras,Hong Kong,Hungary,Iceland,India,Indonesia,Iran,Iraq,Ireland,Isle of Man,Israel,Italy,Jamaica,Japan,Jersey,Jordan,Kazakhstan,Kenya,Kiribati,Kosovo,Kuwait,Kyrgyzstan,Laos,Latvia,Lebanon,Lesotho,Liberia,Libya,Liechtenstein,Lithuania,Luxembourg,Macau,Madagascar,Malawi,Malaysia,Maldives,Mali,Malta,Marshall Islands,Martinique,Mauritania,Mauritius,Mayotte,Mexico,Moldova,Monaco,Mongolia,Montenegro,Montserrat,Morocco,Mozambique,Myanmar,Namibia,Nauru,Nepal,Netherlands,New Caledonia,New Zealand,Nicaragua,Niger,Nigeria,Niue,North Korea,North Macedonia,Northern Mariana Islands,Norway,Oman,Pakistan,Palau,Panama,Papua New Guinea,Paraguay,Peru,Philippines,Poland,Portugal,Puerto Rico,Qatar,Reunion,Romania,Russia,Rwanda,Saint Helena Ascension and Tristan da Cunha,Saint Kitts and Nevis,Saint Lucia,Saint Pierre and Miquelon,Saint Vincent and the Grenadines,Samoa,San Marino,Sao Tome and Principe,Saudi Arabia,Senegal,Serbia,Seychelles,Sierra Leone,Singapore,Slovakia,Slovenia,Solomon Islands,Somalia,South Africa,South Korea,South Sudan,Spain,Sri Lanka,State of Palestine,Sudan,Suriname,Svalbard & Jan Mayen Islands,Sweden,Switzerland,Syria,Taiwan,Tajikistan,Tanzania,Thailand,Timor-Leste,Togo,Tokelau,Tonga,Trinidad and Tobago,Tunisia,Turkey,Turkmenistan,Tuvalu,Uganda,Ukraine,United Arab Emirates,United Kingdom,United States,Uruguay,Uzbekistan,Vanuatu,Venezuela,Vietnam,Virgin Islands British,Virgin Islands U.S.,Wallis and Futuna,Western Sahara,Yemen,Zambia,Zimbabwe",,,FALSE,Demographics,,,
Age Is Obfuscated,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.,"true, false",,,FALSE,Demographics,,,
Year Of Birth,Numeric value to represent the calendar year in which an individual was born.,,,,FALSE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2896954&version=1.0,
Cause of Death,The cause of death,"Cancer Related, Cardiovascular Disorder NOS, End-stage Renal Disease, Infection, Not Cancer Related, Renal Disorder NOS, Spinal Muscular Atrophy, Surgical Complications, Toxicity, Not Reported, unknown, Not Applicable",,,TRUE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2554674&version=3.0,
Cause of Death Source,The text term used to describe the source used to determine the patient's cause of death.,"Autopsy, Death Certificate, Medical Record, Social Security Death Index, Obituary, unknown, Not Reported",,,FALSE,Demographics,,,
Days to Death,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,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154724&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Occupation Duration Years,The number of years a patient worked in a specific occupation.,,,,FALSE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2435424&version=1.0,
Premature At Birth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,"Yes, No, unknown, Not Reported",,,FALSE,Demographics,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6010765&version=1.0,
Weeks Gestation at Birth,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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2737369&version=1.0,
Education Level,Highest level of education that the patient completed (direct patient-derived information),"Bachelor's degree, Doctoral degree or professional degree, Grade school, Graduate or professional degree, High school graduate (including equivalency), Master's degree, No formal education, Not high school graduate, Some college or associate degree, Data not available",,,FALSE,Clinical Tier 2,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2681552&version=1.0,
Country of Birth,Country where the patient was born.,"Afghanistan,Albania,Algeria,Andorra,Angola,Anguilla,Antigua and Barbuda,Argentina,Armenia,Aruba,Australia,Austria,Azerbaijan,Bahamas,Bahrain,Bangladesh,Barbados,Belarus,Belgium,Belize,Benin,Bermuda,Bhutan,Bolivia,Bosnia and Herzegovina,Botswana,Brazil,Brunei,Bulgaria,Burkina Faso,Burundi,Cambodia,Cameroon,Canada,Cape Verde,Cayman Islands,Central African Republic,Chad,Chile,China,Colombia,Comoros,Congo,Cook Islands,Costa Rica,Cote d'Ivoire,Croatia,Cuba,Curacao,Cyprus,Czech Republic (Czechia),Democratic Republic of the Congo,Denmark,Djibouti,Dominica,Dominican Republic,Ecuador,Egypt,El Salvador,Equatorial Guinea,Eritrea,Estonia,Eswatini,Ethiopia,Falkland Islands (Malvinas),Faroe Islands,Federated States of Micronesia,Fiji,Finland,France,French Guiana,French Polynesia,Gabon,Gambia,Georgia,Germany,Ghana,Gibraltar,Greece,Greenland,Grenada,Guadeloupe,Guam,Guatemala,Guernsey,Guinea,Guinea-Bissau,Guyana,Haiti,Holy See,Honduras,Hong Kong,Hungary,Iceland,India,Indonesia,Iran,Iraq,Ireland,Isle of Man,Israel,Italy,Jamaica,Japan,Jersey,Jordan,Kazakhstan,Kenya,Kiribati,Kosovo,Kuwait,Kyrgyzstan,Laos,Latvia,Lebanon,Lesotho,Liberia,Libya,Liechtenstein,Lithuania,Luxembourg,Macau,Madagascar,Malawi,Malaysia,Maldives,Mali,Malta,Marshall Islands,Martinique,Mauritania,Mauritius,Mayotte,Mexico,Moldova,Monaco,Mongolia,Montenegro,Montserrat,Morocco,Mozambique,Myanmar,Namibia,Nauru,Nepal,Netherlands,New Caledonia,New Zealand,Nicaragua,Niger,Nigeria,Niue,North Korea,North Macedonia,Northern Mariana Islands,Norway,Oman,Pakistan,Palau,Panama,Papua New Guinea,Paraguay,Peru,Philippines,Poland,Portugal,Puerto Rico,Qatar,Reunion,Romania,Russia,Rwanda,Saint Helena Ascension and Tristan da Cunha,Saint Kitts and Nevis,Saint Lucia,Saint Pierre and Miquelon,Saint Vincent and the Grenadines,Samoa,San Marino,Sao Tome and Principe,Saudi Arabia,Senegal,Serbia,Seychelles,Sierra Leone,Singapore,Slovakia,Slovenia,Solomon Islands,Somalia,South Africa,South Korea,South Sudan,Spain,Sri Lanka,State of Palestine,Sudan,Suriname,Svalbard & Jan Mayen Islands,Sweden,Switzerland,Syria,Taiwan,Tajikistan,Tanzania,Thailand,Timor-Leste,Togo,Tokelau,Tonga,Trinidad and Tobago,Tunisia,Turkey,Turkmenistan,Tuvalu,Uganda,Ukraine,United Arab Emirates,United Kingdom,United States,Uruguay,Uzbekistan,Vanuatu,Venezuela,Vietnam,Virgin Islands British,Virgin Islands U.S.,Wallis and Futuna,Western Sahara,Yemen,Zambia,Zimbabwe, unknown",,,FALSE,Clinical Tier 2,,,
Medically Underserved Area,"Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population:  Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select ""Query Data"". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select ""View Data"". Enter the name of the county (_______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data.  If the designation type in the third column is ""medically underserved area"" enter ""Yes"" as the value. If the county generates a ""No data available in table"" enter ""No"" as the value.  A value of ""Unknown"" indicates that sufficient data was not available to look up the value.  If value is yes, complete the Medically_underserved_score data element.","Medically Underserved Area - Yes, Medically Underserved Area - No, Medically Underserved Area - Unknown",,,FALSE,Clinical Tier 2,,,
Medically Underserved Area - Yes,Patient's zip code is in a medically underserved area,,Medically Underserved Score,,FALSE,Clinical Tier 2,,,
Medically Underserved Area - No,Patient's zip code is not in a medically underserved area,,,,FALSE,Clinical Tier 2,,,
Medically Underserved Area - Unknown,Insufficient data to look up the Medically Underserved Area value,,,,FALSE,Clinical Tier 2,,,
Medically Underserved Score,"Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first ""Service Area"" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.",,,,FALSE,Clinical Tier 2,,,
Rural vs Urban,"Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county.  If the total population is <2,500 enter a value of ""Rural Population""; if 2,500 - 50,000 enter a value of ""Urban Cluster""; or if >50,000 enter ""Urban Population""","Urban Population (population >50000), Urban Cluster (population 2500 - 50000), Rural Population (population <2500)",,,FALSE,Clinical Tier 2,,,
Cancer Incidence,"Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the ""primary_diagnosis"" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data.  Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose ""Incidence"" from the Topic dropdown menu, state of interest from the Area menu, ""All Races"" from the Race menu, and the cancer type (""Both Sexes"" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.",,,,FALSE,Clinical Tier 2,,,
Cancer Incidence Location,"The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as ""County, State"" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website",,,,FALSE,Clinical Tier 2,,,
Relationship Gender,The text term used to describe the gender of the patient's relative with a history of cancer.,"Female, Male, unknown, unspecified, Not Reported",,,FALSE,Family History,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161021&version=1.0,
Relationship Age at Diagnosis,The age (in years) when the patient's relative was first diagnosed.,,,,FALSE,Family History,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5300571&version=1.0,
Relationship Primary Diagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,"Adrenal Gland Cancer, Basal Cell Cancer, Bile Duct Cancer, Bladder Cancer, Blood Cancer, Bone Cancer, Brain Cancer, Breast Cancer, Cancer, Cervical Cancer, Chondrosarcoma, CNS Cancer, Colorectal Cancer, Esophageal Cancer, Ewing Sarcoma, Gallbladder Cancer, Gastric Cancer, Glioblastoma, Gynecologic Cancer, Head and Neck Cancer, Hematologic Cancer, Kaposi Sarcoma, Kidney Cancer, Laryngeal Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma, Melanoma, Mesothelioma, Multiple Myeloma, Neuroblastoma, Osteosarcoma, Ovarian Cancer, Pancreas Cancer, Prostate Cancer, Rectal Cancer, Rhabdomyosarcoma, Sarcoma, Skin Cancer, Spleen Cancer, Testicular Cancer, Throat Cancer, Thyroid Cancer, Tongue Cancer, Tonsillar Cancer, Uterine Cancer, Wilms Tumor, unknown, Not Reported",,,FALSE,Family History,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161022&version=1.0,
Relationship Type,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,"Adopted Daughter, Adopted Son, Adoptive Brother, Adoptive Father, Adoptive Mother, Adoptive Sister, Aunt, Brother, Brother-in-law, Child, Cousin, Daughter, Daughter-in-law, Domestic Partner, Father, Father-in-law, Female Cousin, First Cousin, First Cousin Once Removed, Foster Brother, Foster Daughter, Foster Father, Foster Mother, Foster Sister, Foster Son,  Fraternal Twin Brother, Fraternal Twin Sibling, Fraternal Twin Sister,      Full Brother, Full Sister, Grand Nephew, Grand Niece, Grandchild, Granddaughter, Grandfather, Grandmother, Grandparent, Grandson, Great Grandchild, Half Brother, Half Sibling, Half Sister, Husband, Identical Twin Brother, Identical Twin Sibling, Identical Twin Sister, Legal Guardian, Male Cousin, Maternal Aunt, Maternal First Cousin, Maternal First Cousin Once Removed, Maternal Grandfather, Maternal Grandmother, Maternal Grandparent, Maternal Great Aunt, Maternal Great Grandparent, Maternal Great Uncle, Maternal Half Brother, Maternal Half Sibling, Maternal Half Sister, Maternal Uncle, Mother, Mother-in-law, Natural Brother, Natural Child, Natural Daughter, Natural Father, Natural Grandchild, Natural Grandfather, Natural Grandmother, Natural Grandparent, Natural Mother, Natural Parent, Natural Sibling, Natural Sister, Natural Son, Nephew, Niece, Niece Second Degree Relative, Other, Parent, Paternal Aunt, Paternal First Cousin, Paternal First Cousin Once Removed, Paternal Grandfather, Paternal Grandmother, Paternal Grandparent, Paternal Great Aunt, Paternal Great Grandparent, Paternal Great Uncle, Paternal Half Brother, Paternal Half Sibling, Paternal Half Sister, Paternal Uncle, Refused, Sibling, Sister, Sister-in-law, Son, Son-in-law, Spouse, Step Child, Step Sibling, Stepbrother, Stepdaughter, Stepfather, Stepmother, Stepsister, Stepson, Twin Sibling, Uncle, Unrelated, Ward, Wife, unknown, Not Reported",,,FALSE,Family History,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2690165&version=2.0,
Relative with Cancer History,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,"Yes - Cancer History Relative, None, unknown, Not Reported",,,FALSE,Family History,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161023&version=1.0,
Relatives with Cancer History Count,The number of relatives the patient has with a known history of cancer.,,,,FALSE,Family History,,,
Yes - Cancer History Relative,Individual has a relative with cancer history,,"Relatives with Cancer History Count, Relationship Type, Relationship Primary Diagnosis, Relationship Gender,Relationship Age at Diagnosis",,FALSE,Family History,,,
Smoking Exposure,Indicate if individual has smoking exposure,"Yes - Smoking Exposure, No - Smoking Exposure, Not Reported",,,TRUE,Exposure,,,
Yes - Smoking Exposure,Individual has been exposed to smoke; requires additional metadata,,"Years Smoked, Pack Years Smoked, Cigarettes per Day, Smoking Frequency, Type of Smoke Exposure, Time between Waking and First Smoke, Tobacco Smoking Onset Year, Tobacco Smoking Quit Year, Tobacco Smoking Status, Type of Tobacco Used, Secondhand Smoke as Child, Smoke Exposure Duration, Tobacco Use per Day, Smokeless Tobacco Quit Age",,FALSE,Exposure,,,
Pack Years Smoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,,,,TRUE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2955385&version=1.0,
Years Smoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,,,,TRUE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3137957&version=1.0,
Alcohol Exposure,Indicate if individual has alcohol exposure,"Yes - Alcohol Exposure, No - Alcohol Exposure, Not Reported",,,TRUE,Exposure,,,
Yes - Alcohol Exposure,Individual has been exposed to alcohol,,"Alcohol Days Per Week, Alcohol Drinks Per Day, Alcohol History, Alcohol Intensity, Alcohol Type",,FALSE,Exposure,,,
Alcohol Days Per Week,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,,,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3114013&version=1.0,int
Alcohol Drinks Per Day,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,,,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3124961&version=1.0,
Alcohol History,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.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2201918&version=1.0,
Alcohol Intensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,"Drinker, Heavy Drinker, Lifelong Non-Drinker, Non-Drinker, Occasional Drinker, unknown, Not Reported",,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3457767&version=1.0,
Alcohol Type,Type of alcohol use,"Beer, Liquor, Other, Wine, unknown, Not Reported",,,FALSE,Exposure,,,
Asbestos Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=1253&version=3.0,
Cigarettes per Day,The average number of cigarettes smoked per day.,,,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2001716&version=4.0,
Coal Dust Exposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,"Yes, No, unknown",,,FALSE,Exposure,,,
Environmental Tobacco Smoke Exposure,"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.","Yes, No, unknown",,,FALSE,Exposure,,,
Radon Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2816352&version=1.0,
Respirable Crystalline Silica Exposure,"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.","Yes, No, unknown",,,FALSE,Exposure,,,
Smoking Frequency,The text term used to generally decribe how often the patient smokes.,"Every day, Some days, unknown",,,FALSE,Exposure,,,
Secondhand Smoke as Child,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6841888&version=1.0,
Smoke Exposure Duration,Text term used to describe the length of time the patient was exposed to an environmental factor.,"Six Weeks or More, unknown,Not Reported",,,FALSE,Exposure,,,
Type of Smoke Exposure,The text term used to describe the patient's specific type of smoke exposure.,"Accidental building fire smoke,Accidental grass fire smoke, Accidental fire smoke NOS,Accidental forest fire smoke,Accidental vehicle fire smoke,Aircraft smoke,Burning tree smoke,Coal smoke NOS, Cooking related smoke NOS,Electronic cigarette smoke NOS,Electrical fire smoke,Environmental tobacco smoke,Factory smokestack smoke,Field burning smoke,Fire smoke NOS,Furnace or boiler smoke,Gas burning smoke propane,Grease fire smoke,Grilling smoke,Hashish smoke,Indoor coal burning stove or fireplace smoke,Indoor stove or fireplace smoke NOS,Indoor wood burning stove or fireplace smoke,Machine smoke,Marijuana smoke,No Smoke Exposure,Oil burning smoke Kerosene,Oil burning smoke NOS,Recreational fire smoke,Smoke exposure NOS,Smokehouse smoke,Tobacco smoke cigar,Tobacco smoke cigarettes,Tobacco smoke pipe,unknown,Volcanic smoke,Waste burning smoke,Wood burning smoke factory,Wood burning smoke NOS, Workrelated smoke artificial smoke machines, Workrelated smoke fire fighting,Workrelated smoke foundry,Workrelated smoke generators,Workrelated smoke military,Workrelated smoke NOS,Workrelated smoke paint baking,Workrelated smoke plastics factory,Workrelated smoke plumbing,Workrelated smoke soldering/welding",,,FALSE,Exposure,,,
Marijuana smoke,Marijuana smoke exposure,,Marijuana Use Per Week,,FALSE,Exposure,,,
Marijuana Use Per Week,Numeric value that represents the number of times the patient uses marijuana each day.,,,,FALSE,Exposure,,,
Tobacco Use per Day,Numeric value that represents the number of times the patient uses tobacco each day.,,,,FALSE,Exposure,,,
Smokeless Tobacco Quit Age,Smokeless tobacco quit age,,,,FALSE,Exposure,,,
Time between Waking and First Smoke,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.,"Within 5 Minutes, 6-30 Minutes, 31-60 Minutes, After 60 Minutes, unknown",,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3279220&version=1.0,
Tobacco Smoking Onset Year,The year in which the participant began smoking.,,,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2228604&version=1.0,
Tobacco Smoking Quit Year,The year in which the participant quit smoking.,,,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2228610&version=1.0,
Tobacco Smoking Status,Category describing current smoking status and smoking history as self-reported by a patient,"Lifelong Non-Smoker, Current Smoker, Current Reformed Smoker for > 15 yrs, Current Reformed Smoker for < or = 15 yrs, Current Reformed Smoker, Duration Not Specified, Smoking history not documented, unknown, Not Reported",,,FALSE,Exposure,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2181650&version=1.0,
Type of Tobacco Used,The text term used to describe the specific type of tobacco used by the patient.,"Cigarettes, Cigar, Electronic Cigarette, Other, Pipe, Smokeless Tobacco, Marijuana, unknown, Not Reported",,,FALSE,Exposure,,,
Days to Follow Up,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,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154727&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Adverse Event,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,"Abdominal Distension, Abdominal Infection,Abdominal Pain,Abdominal Soft Tissue Necrosis,Abducens Nerve Disorder,Accessory Nerve Disorder,Acidosis,Acoustic Nerve Disorder NOS,Activated Partial Thromboplastin Time Prolonged,Acute Coronary Syndrome,Acute Kidney Injury,Adrenal Insufficiency,Adult Respiratory Distress Syndrome, Agitation, Akathisia, Alanine Aminotransferase Increased,Alcohol Intolerance,Alkaline Phosphatase Increased,Alkalosis,Allergic Reaction,Allergic Rhinitis, Alopecia, Amnesia,Anal Fistula,Anal Hemorrhage,Anal Mucositis, Anal Necrosis,Anal Pain,Anal Stenosis,Anal Ulcer,Anaphylaxis,Anemia,Ankle Fracture,Anorectal Infection,Anorexia,Anorgasmia,Anxiety,Aortic Injury,Aortic Valve Disease,Aphonia,Apnea,Appendicitis,Appendicitis Perforated,Arachnoiditis,Arterial Injury,Arteritis Infective,Arthralgia,Arthritis,Ascites,Aspartate Aminotransferase Increased,Aspiration,Asystole,Ataxia,Atelectasis,Atrial Fibrillation,Atrial Flutter,Atrioventricular Block Complete,Atrioventricular Block First Degree,Autoimmune Disorder,Avascular Necrosis,Azoospermia,Back Pain,Bile Duct Stenosis,Biliary Anastomotic Leak,Biliary Fistula,Biliary Tract Infection,Bladder Anastomotic Leak,Bladder Infection,Bladder Perforation,Bladder Spasm,Bloating,Blood and Lymphatic System Disorders Other,Blood Antidiuretic Hormone Abnormal,Blood Bilirubin Increased,Blood Corticotrophin Decreased,Blood Gonadotrophin Abnormal,Blood Prolactin Abnormal,Blurred Vision,Body Odor,Bone Infection,Bone Marrow Hypocellular,Bone Pain,Brachial Plexopathy,Breast Atrophy,Breast Infection,Breast Pain,Bronchial Fistula,Bronchial Infection,Bronchial Obstruction,Bronchial Stricture,Bronchopleural Fistula,Bronchopulmonary Hemorrhage,Bronchospasm,Bruising,Bullous Dermatitis,Burn,Buttock Pain,Capillary Leak Syndrome,Carbon Monoxide Diffusing Capacity Decreased,Cardiac Arrest,Cardiac Disorders Other,Cardiac Troponin I Increased,Cardiac Troponin T Increased,Cataract,Catheter Related Infection,CD4 Lymphocytes Decreased,Cecal Hemorrhage,Cecal Infection,Central Nervous System Necrosis,Cerebrospinal Fluid Leakage,Cervicitis Infection,Cheilitis,Chest Pain Cardiac,Chest Wall Pain,Chills,Cholecystitis,Cholesterol High,Chronic Kidney Disease,Chylothorax,Cognitive Disturbance,Colitis,Colonic Fistula,Colonic Hemorrhage,Colonic Obstruction,Colonic Perforation,Colonic Stenosis,Colonic Ulcer,Concentration Impairment,Conduction Disorder,Confusion,Congenital, Familial and Genetic Disorders Other,Conjunctivitis,Conjunctivitis Infective,Constipation,Constrictive Pericarditis,Corneal Infection,Corneal Ulcer,Cough,CPK Increased,Cranial Nerve Infection,Creatinine Increased,Cushingoid,Cystitis Noninfective,Cytokine Release Syndrome,Death Neonatal,Death NOS,Dehydration,Delayed Orgasm,Delayed Puberty,Delirium,Delusions,Dental Caries,Depressed Level of Consciousness,Depression,Dermatitis Radiation,Device Related Infection,Diarrhea,Disseminated Intravascular Coagulation,Dizziness,Dry Eye,Dry Mouth,Dry Skin,Duodenal Fistula,Duodenal Hemorrhage,Duodenal Infection,Duodenal Obstruction,Duodenal Perforation,Duodenal Stenosis,Duodenal Ulcer,Dysarthria,Dysesthesia,Dysgeusia,Dysmenorrhea,Dyspareunia,Dyspepsia,Dysphagia,Dysphasia,Dyspnea,Ear and Labyrinth Disorders Other,Ear Pain,Edema Cerebral,Edema Face,Edema Limbs,Edema Trunk,Ejaculation Disorder,Ejection Fraction Decreased,Electrocardiogram QT Corrected Interval Prolonged,Encephalitis Infection,Encephalomyelitis Infection,Encephalopathy,Endocarditis Infective,Endocrine Disorders Other,Endophthalmitis,Enterocolitis,Enterocolitis Infectious,Enterovesical Fistula,Epistaxis,Erectile Dysfunction,Erythema Multiforme,Erythroderma,Esophageal Anastomotic Leak,Esophageal Fistula,Esophageal Hemorrhage,Esophageal Infection,Esophageal Necrosis,Esophageal Obstruction,Esophageal Pain,Esophageal Perforation,Esophageal Stenosis,Esophageal Ulcer,Esophageal Varices Hemorrhage,Esophagitis,Euphoria,Exostosis,External Ear Inflammation,External Ear Pain,Extraocular Muscle Paresis,Extrapyramidal Disorder,Eye Disorders Other,Eye Infection,Eye Pain,Eyelid Function Disorder,Facial Muscle Weakness,Facial Nerve Disorder,Facial Pain,Fall,Fallopian Tube Anastomotic Leak,Fallopian Tube Obstruction,Fallopian Tube Perforation,Fallopian Tube Stenosis,Fat Atrophy,Fatigue,Febrile Neutropenia,Fecal Incontinence,Female Genital Tract Fistula,Feminization Acquired,Fetal Death,Fetal Growth Retardation,Fever,Fibrinogen Decreased,Fibrosis Deep Connective Tissue,Flank Pain,Flashing Lights,Flatulence,Floaters,Flu Like Symptoms,Flushing,Forced Expiratory Volume Decreased,Fracture,Gait Disturbance,Gallbladder Fistula,Gallbladder Infection,Gallbladder Necrosis,Gallbladder Obstruction,Gallbladder Pain,Gallbladder Perforation,Gastric Anastomotic Leak,Gastric Fistula,Gastric Hemorrhage,Gastric Necrosis,Gastric Perforation,Gastric Stenosis,Gastric Ulcer,Gastritis,Gastroesophageal Reflux Disease,Gastrointestinal Anastomotic Leak,Gastrointestinal Disorders Other,Gastrointestinal Fistula,Gastrointestinal Pain,Gastrointestinal Stoma Necrosis,Gastroparesis,General Disorders and Administration Site Conditions Other,Generalized Muscle Weakness,Genital Edema,GGT Increased,Gingival Pain,Glaucoma,Glossopharyngeal Nerve Disorder,Glucose Intolerance,Growth Accelerated,Growth Hormone Abnormal,Growth Suppression,Gum Infection,Gynecomastia,Hallucinations,Haptoglobin Decreased,Head Soft Tissue Necrosis,Headache,Hearing Impaired,Heart Failure,Hematoma,Hematosalpinx,Hematuria,Hemoglobin Increased,Hemoglobinuria,Hemolysis,Hemolytic Uremic Syndrome,Hemorrhoidal Hemorrhage,Hemorrhoids,Hepatic Failure,Hepatic Hemorrhage,Hepatic Infection,Hepatic Necrosis,Hepatic Pain,Hepatitis Viral,Hepatobiliary Disorders Other,Hiccups,Hip Fracture,Hirsutism,Hoarseness,Hot Flashes,Hydrocephalus,Hypercalcemia,Hyperglycemia,Hyperhidrosis,Hyperkalemia,Hypermagnesemia,Hypernatremia,Hyperparathyroidism,Hypersomnia,Hypertension,Hyperthyroidism,Hypertrichosis,Hypertriglyceridemia,Hyperuricemia,Hypoalbuminemia,Hypocalcemia,Hypoglossal Nerve Disorder,Hypoglycemia,Hypohidrosis,Hypokalemia,Hypomagnesemia,Hyponatremia,Hypoparathyroidism,Hypophosphatemia,Hypotension,Hypothermia,Hypothyroidism,Hypoxia,Ileal Fistula,Ileal Hemorrhage,Ileal Obstruction,Ileal Perforation,Ileal Stenosis,Ileal Ulcer,Ileus,Immune System Disorders Other,Infections and Infestations Other,Infective Myositis,Infusion Related Reaction,Infusion Site Extravasation,Injection Site Reaction,Injury to Carotid Artery,Injury to Inferior Vena Cava,Injury to Jugular Vein,Injury to Superior Vena Cava,Injury, Poisoning and Procedural Complications Other,INR Increased,Insomnia,Intestinal Stoma Leak,Intestinal Stoma Obstruction,Intestinal Stoma Site Bleeding,Intra-Abdominal Hemorrhage,Intracranial Hemorrhage,Intraoperative Arterial Injury,Intraoperative Breast Injury,Intraoperative Cardiac Injury,Intraoperative Ear Injury,Intraoperative Endocrine Injury,Intraoperative Gastrointestinal Injury,Intraoperative Head and Neck Injury,Intraoperative Hemorrhage,Intraoperative Hepatobiliary Injury,Intraoperative Musculoskeletal Injury,Intraoperative Neurological Injury,Intraoperative Ocular Injury,Intraoperative Renal Injury,Intraoperative Reproductive Tract Injury,Intraoperative Respiratory Injury,Intraoperative Skin Injury,Intraoperative Splenic Injury,Intraoperative Urinary Injury,Intraoperative Venous Injury,Investigations Other,Iron Overload,Irregular Menstruation,Irritability,Ischemia Cerebrovascular,IVth Nerve Disorder,Jejunal Fistula,Jejunal Hemorrhage,Jejunal Obstruction,Jejunal Perforation,Jejunal Stenosis,Jejunal Ulcer,Joint Effusion,Joint Infection,Joint Range of Motion Decreased,Joint Range of Motion Decreased Cervical Spine,Joint Range of Motion Decreased Lumbar Spine,Keratitis,Kidney Anastomotic Leak,Kidney Infection,Kyphosis,Lactation Disorder,Large Intestinal Anastomotic Leak,Laryngeal Edema,Laryngeal Fistula,Laryngeal Hemorrhage,Laryngeal Inflammation,Laryngeal Mucositis,Laryngeal Obstruction,Laryngeal Stenosis,Laryngitis,Laryngopharyngeal Dysesthesia,Laryngospasm,Left Ventricular Systolic Dysfunction,Lethargy,Leukemia Secondary to Oncology Chemotherapy,Leukocytosis,Leukoencephalopathy,Libido Decreased,Libido Increased,Lip Infection,Lip Pain,Lipase Increased,Lipohypertrophy,Localized Edema,Lordosis,Lower Gastrointestinal Hemorrhage,Lung Infection,Lymph Gland Infection,Lymph Leakage,Lymph Node Pain,Lymphedema,Lymphocele,Lymphocyte Count Decreased,Lymphocyte Count Increased,Malabsorption,Malaise,Mania,Mediastinal Hemorrhage,Mediastinal Infection,Memory Impairment,Meningismus,Meningitis,Menopause,Menorrhagia,Metabolism and Nutrition Disorders Other,Middle Ear Inflammation,Mitral Valve Disease,Mobitz (Type) II Atrioventricular Block,Mobitz Type I,Movements Involuntary,Mucosal Infection,Mucositis Oral,Multi-Organ Failure,Muscle Weakness Left-Sided,Muscle Weakness Lower Limb,Muscle Weakness Right-Sided,Muscle Weakness Trunk,Muscle Weakness Upper Limb,Musculoskeletal and Connective Tissue Disorders Other,Musculoskeletal Deformity,Myalgia,Myelitis,Myelodysplastic Syndrome,Myocardial Infarction,Myocarditis,Myositis,Nail Discoloration,Nail Infection,Nail Loss,Nail Ridging,Nasal Congestion,Nausea,Neck Edema,Neck Pain,Neck Soft Tissue Necrosis,Neoplasms Benign, Malignant and Unspecified (Incl Cysts and Polyps) Other,Nervous System Disorders Other,Neuralgia,Neutrophil Count Decreased,Night Blindness,Nipple Deformity,Non-Cardiac Chest Pain,Nystagmus,Obesity,Obstruction Gastric,Oculomotor Nerve Disorder,Olfactory Nerve Disorder,Oligospermia,Optic Nerve Disorder,Oral Cavity Fistula,Oral Dysesthesia,Oral Hemorrhage,Oral Pain,Osteonecrosis of Jaw,Osteoporosis,Otitis Externa,Otitis Media,Ovarian Hemorrhage,Ovarian Infection,Ovarian Rupture,Ovulation Pain,Pain,Pain in Extremity,Pain of Skin,Palmar-Plantar Erythrodysesthesia Syndrome,Palpitations,Pancreas Infection,Pancreatic Anastomotic Leak,Pancreatic Duct Stenosis,Pancreatic Enzymes Decreased,Pancreatic Fistula,Pancreatic Hemorrhage,Pancreatic Necrosis,Pancreatitis,Papilledema,Papulopustular Rash,Paresthesia,Paronychia,Paroxysmal Atrial Tachycardia,Pelvic Floor Muscle Weakness,Pelvic Infection,Pelvic Pain,Pelvic Soft Tissue Necrosis,Penile Infection,Penile Pain,Perforation Bile Duct,Pericardial Effusion,Pericardial Tamponade,Pericarditis,Perineal Pain,Periodontal Disease,Periorbital Edema,Periorbital Infection,Peripheral Ischemia,Peripheral Motor Neuropathy,Peripheral Nerve Infection,Peripheral Sensory Neuropathy,Peritoneal Infection,Peritoneal Necrosis,Personality Change,Phantom Pain,Pharyngeal Anastomotic Leak,Pharyngeal Fistula,Pharyngeal Hemorrhage,Pharyngeal Mucositis,Pharyngeal Necrosis,Pharyngeal Stenosis,Pharyngitis,Pharyngolaryngeal Pain,Phlebitis,Phlebitis Infective,Photophobia,Photosensitivity,Platelet Count Decreased,Pleural Effusion,Pleural Hemorrhage,Pleural Infection,Pleuritic Pain,Pneumonitis,Pneumothorax,Portal Hypertension,Portal Vein Thrombosis,Postnasal Drip,Postoperative Hemorrhage,Postoperative Thoracic Procedure Complication,Precocious Puberty,Pregnancy, Puerperium and Perinatal Conditions Other,Premature Delivery,Premature Menopause,Presyncope,Proctitis,Productive Cough,Prolapse of Intestinal Stoma,Prolapse of Urostomy,Prostate Infection,Prostatic Hemorrhage,Prostatic Obstruction,Prostatic Pain,Proteinuria,Pruritus,Psychiatric Disorders Other,Psychosis,Pulmonary Edema,Pulmonary Fibrosis,Pulmonary Fistula,Pulmonary Hypertension,Pulmonary Valve Disease,Purpura,Pyramidal Tract Syndrome,Radiation Recall Reaction (Dermatologic),Radiculitis,Rash Acneiform,Rash Maculo-Papular,Rash Pustular,Rectal Anastomotic Leak,Rectal Fistula,Rectal Hemorrhage,Rectal Mucositis,Rectal Necrosis,Rectal Obstruction,Rectal Pain,Rectal Perforation,Rectal Stenosis,Rectal Ulcer,Recurrent Laryngeal Nerve Palsy,Renal and Urinary Disorders Other,Renal Calculi,Renal Colic,Renal Hemorrhage,Reproductive System and Breast Disorders Other,Respiratory Failure,Respiratory, Thoracic and Mediastinal Disorders Other,Restlessness,Restrictive Cardiomyopathy,Retinal Detachment,Retinal Tear,Retinal Vascular Disorder,Retinoic Acid Syndrome,Retinopathy,Retroperitoneal Hemorrhage,Reversible Posterior Leukoencephalopathy Syndrome,Rhinitis Infective,Right Ventricular Dysfunction,Salivary Duct Inflammation,Salivary Gland Fistula,Salivary Gland Infection,Scalp Pain,Scleral Disorder,Scoliosis,Scrotal Infection,Scrotal Pain,Seizure,Sepsis,Seroma,Serum Amylase Increased,Serum Sickness,Sick Sinus Syndrome,Sinus Bradycardia,Sinus Disorder,Sinus Pain,Sinus Tachycardia,Sinusitis,Skin and Subcutaneous Tissue Disorders Other,Skin Atrophy,Skin Hyperpigmentation,Skin Hypopigmentation,Skin Induration,Skin Infection,Skin Ulceration,Sleep Apnea,Small Intestinal Anastomotic Leak,Small Intestinal Mucositis,Small Intestinal Obstruction,Small Intestinal Perforation,Small Intestinal Stenosis,Small Intestine Infection,Small Intestine Ulcer,Sneezing,Social Circumstances Other,Soft Tissue Infection,Soft Tissue Necrosis Lower Limb,Soft Tissue Necrosis Upper Limb,Somnolence,Sore Throat,Spasticity,Spermatic Cord Anastomotic Leak,Spermatic Cord Hemorrhage,Spermatic Cord Obstruction,Spinal Fracture,Spleen Disorder,Splenic Infection,Stenosis of Gastrointestinal Stoma,Stevens-Johnson Syndrome,Stoma Site Infection,Stomach Pain,Stomal Ulcer,Stridor,Stroke,Sudden Death NOS,Suicidal Ideation,Suicide Attempt,Superficial Soft Tissue Fibrosis,Superficial Thrombophlebitis,Superior Vena Cava Syndrome,Supraventricular Tachycardia,Surgical and Medical Procedures Other,Syncope,Telangiectasia,Testicular Disorder,Testicular Hemorrhage,Testicular Pain,Thromboembolic Event,Thrombotic Thrombocytopenic Purpura,Tinnitus,Tooth Development Disorder,Tooth Discoloration,Tooth Infection,Toothache,Toxic Epidermal Necrolysis,Tracheal Fistula,Tracheal Hemorrhage,Tracheal Mucositis,Tracheal Obstruction,Tracheal Stenosis,Tracheitis,Tracheostomy Site Bleeding,Transient Ischemic Attacks,Treatment Related Secondary Malignancy,Tremor,Tricuspid Valve Disease,Trigeminal Nerve Disorder,Trismus,Tumor Lysis Syndrome,Tumor Pain,Typhlitis,Unequal Limb Length,Unintended Pregnancy,Upper Gastrointestinal Hemorrhage,Upper Respiratory Infection,Ureteric Anastomotic Leak,Urethral Anastomotic Leak,Urethral Infection,Urinary Fistula,Urinary Frequency,Urinary Incontinence,Urinary Retention,Urinary Tract Infection,Urinary Tract Obstruction,Urinary Tract Pain,Urinary Urgency,Urine Discoloration,Urine Output Decreased,Urostomy Leak,Urostomy Obstruction,Urostomy Site Bleeding,Urostomy Stenosis,Urticaria,Uterine Anastomotic Leak,Uterine Fistula,Uterine Hemorrhage,Uterine Infection,Uterine Obstruction,Uterine Pain,Uterine Perforation,Uveitis,Vaginal Anastomotic Leak,Vaginal Discharge,Vaginal Dryness,Vaginal Fistula,Vaginal Hemorrhage,Vaginal Infection,Vaginal Inflammation,Vaginal Obstruction,Vaginal Pain,Vaginal Perforation,Vaginal Stricture,Vaginismus,Vagus Nerve Disorder,Vas Deferens Anastomotic Leak,Vascular Access Complication,Vascular Disorders Other,Vasculitis,Vasovagal Reaction,Venous Injury,Ventricular Arrhythmia,Ventricular Fibrillation,Ventricular Tachycardia,Vertigo,Vestibular Disorder,Virilization,Visceral Arterial Ischemia,Vital Capacity Abnormal,Vitreous Hemorrhage,Voice Alteration,Vomiting,Vulval Infection,Watering Eyes,Weight Gain,Weight Loss,Wheezing,White Blood Cell Decreased,Wolff-Parkinson-White Syndrome,Wound Complication,Wound Dehiscence,Wound Infection,Wrist Fracture",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3125302&version=1.1,
BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2006410&version=3.0,
Cause of Response,The text term used to describe the suspected cause or reason for the patient disease response.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161025&version=1.0,
Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.","Acute Renal Failure, Adenocarcinoma, Adrenocortical Insufficiency, Adenomatous Polyposis Coli, Allergies, Alpha-1 Antitrypsin, Anemia, Anxiety, Arrhythmia, Arthritis, Asthma, Atrial Fibrillation, Avascular Necrosis, Barrett's Esophagus,Basal Cell Carcinoma, Beckwith-Wiedemann, Behcet's Disease, Biliary Disorder, Blood Clots, Bone Fracture(s), Bronchitis, Calcium Channel Blockers, Cancer, Cataracts, Celiac Disease, Cirrhosis, unknown Etiology, Cerebrovascular Disease, Cholelithiasis, Chronic Renal Failure, Colon Polyps, Common Variable Immunodeficiency, Congestive Heart Failure (CHF), Connective Tissue Disorder, COPD, Coronary Artery Disease, Crohn's Disease, Cryptogenic Organizing Pneumonia, Deep Vein Thrombosis / Thromboembolism, Denys-Drash Syndrome, Depression, Diabetes, Diabetes, Type II, Diabetic Neuropathy, Diet Controlled Diabetes, Diverticulitis,DVT/PE, Dyslipidemia, Epilepsy, Eczema, Epstein-Barr Virus, Familial Adenomatous Polyposis, Fanconi Anemia, Fibrosis, Gastroesophageal Reflux Disease, GERD, Glaucoma, Glycogen Storage Disease, Gout, Gonadal Dysfunction, Gorlin Syndrome, H. pylori Infection, Hashimoto's Thyroiditis, Headache, Heart Disease, Hemihypertrophy, Hemorrhagic Cystitis, Hepatitis, Hepatitis A Infection, Hepatitis B Infection, Hepatitis C Infection, Chronic Hepatitis, Hereditary Non-polyposis Colon Cancer, Herpes, High Grade Liver Dysplastic Nodule, HIV / AIDS, Human Papillomavirus Infection, HUS/TTP, Hypercholesterolemia, Hypercalcemia, Hyperglycemia, Hyperlipidemia, Hypertension, Hypospadias, Hypothyroidism, Inflammatory Bowel Disease, Insulin Controlled Diabetes, Interstitial Pneumontis or ARDS, Intraductal Papillary Mucinous Neoplasm, Iron Overload, Ischemic Heart Disease, ITP, Joint Replacement, Kidney Disease, Liver Cirrhosis (Liver Disease), Liver Toxicity (Non-Infectious), Li-Fraumeni Syndrome, Low Grade Liver Dysplastic Nodule, Lupus, Lynch Syndrome, MAI, Myasthenia Gravis, Myocardial Infarction, Neuroendocrine Tumor, Nonalcoholic Steatohepatitis, Obesity, Organ transplant (site), Osteoarthritis, Osteoporosis or Osteopenia, Other, Other Cancer Within 5 Years, Other Nonmalignant Systemic Disease, Other Pulmonary Complications, Pancreatitis, Pain (Various), Peptic Ulcer (Ulcer), Peripheral Neuropathy, Peripheral Vascular Disease, Peutz-Jeghers Disease, Pregnancy in Patient or Partner, Primary Sclerosing Cholangitis, Psoriasis, Pulmonary Fibrosis, Pulmonary Hemorrhage, Renal Failure (Requiring Dialysis), Renal Dialysis, Renal Insufficiency, Rheumatologic Disease, Rheumatoid Arthritis, Rubinstein-Taybi Syndrome, Sarcoidosis, Seizure, Sleep apnea, Smoking, Steatosis, Stroke, Transient Ischemic Attack, Tuberculosis, Turcot Syndrome, Tyrosinemia, Ulcerative Colitis, Wagr Syndrome, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2970715&version=1.0,
Comorbidity Method of Diagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,"Histology, Pathology, Radiology, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6142386&version=1.0,
Days to Adverse Event,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,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154728&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Days to Comorbidity,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,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154729&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Days to Progression,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,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154730&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Days to Progression Free,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,Diagnosis,,,regex match \d+$|Not\sApplicable$|unknown$
Days to Recurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',,,,TRUE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154731&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Diabetes Treatment Type,Text term used to describe the types of treatment used to manage diabetes.,"Alpha-Glucosidase Inhibitor, Biguanide, Diet, Injected Insulin, Insulin, Oral Hypoglycemic, Sulfonylurea, Thiazolidinedione, Other, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3587247&version=1.0,
Disease Response,Code assigned to describe the patient's response or outcome to the disease.,"AJ-Adjuvant Therapy, BED-Biochemical Evidence of Disease, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PDM-Persistent Distant Metastasis, PLD-Persistent Locoregional Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, TF-Tumor Free, VGPR-Very Good Partial Response, WT-With Tumor, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5750671&version=1.0,
DLCO Ref Predictive Percent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2180255&version=1.0,
ECOG Performance Status,The ECOG functional performance status of the patient/participant.,"""0"", ""1"", ""2"", ""3"", ""4"", ""5"", ""0.0"", ""1.0"", ""2.0"", ""3.0"", ""4.0"", ""5.0"", unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=88&version=5.1,
FEV1 FVC Post Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3302956&version=1.0,
FEV 1 FVC Pre Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3302955&version=1.0,
FEV1 Ref Post Bronch Percent,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,Follow Up,,"https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3302948&version=1.0""",
FEV1 Ref Pre Bronch Percent,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,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3302947&version=1.0,
Height,The height of the patient in centimeters.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=649&version=4.1,
Hepatitis Sustained Virological Response,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.,"Yes, No, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6423783&version=1.0,
HPV Positive Type,Text classification to represent the strain or type of human papillomavirus identified in an individual.,"""16"", ""18"", ""26"", ""31"", ""33"", ""35"", ""39"", ""45"", ""51"", ""52"", ""53"", ""56"", ""58"", ""59"", ""63"", ""66"", ""68"", ""70"", ""73"", ""82"", Other, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2922649&version=1.0,
Karnofsky Performance Status,Text term used to describe the classification used of the functional capabilities of a person.,"""0"", ""10"", ""20"", ""30"", ""40"", ""50"", ""60"", ""70"", ""80"", ""90"", ""100"", unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2003853&version=4.2,
Menopause Status,Text term used to describe the patient's menopause status.,"Premenopausal, Perimenopausal, Postmenopausal, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2434914&version=1.1,
Adverse Event Grade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.","Grade 1, Grade 2, Grade 3, Grade 4, Grade 5",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2944515&version=1.0,
AIDS Risk Factors,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.,"Candidiasis,Coccidioidomycosis,Cryptococcosis,Cytomegalovirus,Encephalopathy,Herpes Simplex Virus,Histoplasmosis,Isosporiasis,Mycobacterium avium Complex,Mycobacterium tuberculosis,Mycobacterium, NOS,Nocardiosis,Pneumocystis Pneumonia,Pneumonia, NOS,Progressive Multifocal Leukoencephalopathy,Salmonella Septicemia,Toxoplasmosis,Wasting Syndrome",,,FALSE,Follow Up,,,
Body Surface Area,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=653&version=6.0,
CD4 Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4182751&version=1.0,
CDC HIV Risk Factors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.","Hemophiliac,Heterosexual Contact,Homosexual Contact,Intravenous Drug User,None,Transfusion Recipient,unknown,Not Reported",,,FALSE,Follow Up,,,
Days to Imaging,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,Follow Up,,,regex match \d+$|Not\sApplicable$|unknown$
Evidence of Recurrence Type,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,"Biopsy with Histologic Confirmation, Convincing Image Source, Positive Biomarkers",,,FALSE,Follow Up,,,
HAART Treatment Indicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,"Yes, No, unknown, Not Reported",,,FALSE,Follow Up,,,
HIV Viral Load,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2649682&version=1.0,
Hormonal Contraceptive Use,The text term used to indicate whether the patient used hormonal contraceptives.,"Current User, Former User, Never Used, unknown, Not Reported",,,FALSE,Follow Up,,,
Hysterectomy Margins Involved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,"Bladder,Macroscopic Parametrium,Microscopic Parametrium,None,Vagina,unknown,Not Reported",,,FALSE,Follow Up,,,
Hysterectomy Type,The text term used to describe the type of hysterectomy the patient had.,"Hysterectomy NOS, Not performed, Radical Hysterectomy, Simple Hysterectomy, unknown, Not Reported",,,FALSE,Follow Up,,,
Imaging Result,The text term used to describe the result of the imaging or scan performed on the patient.,"Positive, Indeterminate, Negative, Not Performed, unknown, Not Reported",,,FALSE,Follow Up,,,
Imaging Type,The text term used to describe the type of imaging or scan performed on the patient.,"99mTc Bone Scintigraphy, CT Scan, MRI, PET",,,FALSE,Follow Up,,,
Immunosuppressive Treatment Type,The text term used to describe the type of immunosuppresive treatment the patient received.,"Anti-TNFTherapy,Azathioprine,Cyclophosphamide,Methotrexate,None,Other,unknown,Not Reported",,,FALSE,Follow Up,,,
Nadir CD4 Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,,,,FALSE,Follow Up,,,
Pregnancy Outcome,The text term used to describe the type of pregnancy the patient had,"Ectopic Pregnancy,Induced Abortion,Live Birth,Miscarriage,Stillbirth,unknown,Not Reported",,,FALSE,Follow Up,,,
Recist Targeted Regions Number,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",,,,FALSE,Follow Up,,,
Recist Targeted Regions Sum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",,,,FALSE,Follow Up,,,
Scan Tracer Used,The text term used to describe the type of tracer used during the imaging or scan of the patient.,"Acetate, Axumin, Choline, PSMA, Sodium Fluoride",,,FALSE,Follow Up,,,
Progression or Recurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes - Progression or Recurrence, No, unknown, Not Reported",,,TRUE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3121376&version=1.0,
Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,,"Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Progression or Recurrence Anatomic Site",,FALSE,Diagnosis,,,
Progression or Recurrence Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161026&version=1.0,
Treatment Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161026&version=1.0,
NCI Atlas Cancer Site,"The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017","Bladder, Brain And Other Nervous System, Female Breast, In situ Female Breast, Cervix Uteri, Less Than Age, Malignant Childhood Neoplasm, Colon And Rectum, Esophagus, Kidney And Renal Pelvis, Leukemia, Liver And Bile Duct, Lung And Bronchus, Cutaneous Melanoma, Non-Hodgkin's Lymphoma, Oral Cavity And Pharynx, Ovary, Pancreas, Prostate Gland, Stomach, Thyroid Gland, Uterus",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7639473&version=1.0,
Progression or Recurrence Type,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,"Biochemical, Distant, Local, Regional, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6142385&version=1.0,
Reflux Treatment Type,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,"Antacids, H2 Blockers, Medically Treated, No Treatment, Not Applicable, Not Reported, Proton Pump Inhibitors, Surgically Treated, unknown",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440206&version=1.0,
Risk Factor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,"Alcohol Consumption,Alcoholic Liver Disease,Allergy Animal NOS,Allergy Ant,Allergy Bee,Allergy Cat,Allergy Dairy or Lactose,Allergy Dog,Allergy Eggs,Allergy Food NOS,Allergy Fruit,Allergy Meat,Allergy Mold or Dust,Allergy Nuts,Allergy Processed Foods,Allergy Seafood,Allergy Wasp,Alpha-1 Antitrypsin Deficiency,Autoimmune Atrophic Chronic Gastritis,Barrett's Esophagus,Beckwith-Wiedemann,Behcet's Disease,Cancer,Cholelithiasis,Chronic Hepatitis,Cirrhosis,Colon Polyps,Common variable immune deficiency (CVID),Denys-Drash Syndrome,Diabetes NOS,Diabetes Type I,Diabetes Type II,Diet,Diverticulitis,Endometriosis,Endosalpingiosis,Eczema,Epstein-Barr Virus,Familial Adenomatous Polyposis,Fanconi Anemia,Fibrosis,Gastric Polyp(s),Gilbert's Syndrome,Gorlin Syndrome,Hashimoto's Thyroiditis,Hay Fever,Headache,Helicobacter Pylori-Associated Gastritis,Hematologic Disorder NOS,Hemihypertrophy,Hemochromatosis,Hepatic Encephalopathy,Hepatitis B Infection,Hepatitis C Infection,Hepatitis NOS,High Grade Dysplasia,HIV,Human Papillomavirus Infection,Hypospadias,Intestinal Metaplasia,Iron Overload,Li-Fraumeni Syndrome,Low Grade Dysplasia,Lymphocytic Thyroiditis,Lynch Syndrome,Myasthenia Gravis,Nonalcoholic Fatty Liver Disease,Nonalcoholic Steatohepatitis,Obesity,Oral Contraceptives,Pancreatitis,Parasitic Disease of Biliary Tract,Primary Sclerosing Cholangitis,Recurrent Pyogenic Cholangitis,Reflux Disease,Rheumatoid Arthritis,Rubinstein-Taybi Syndrome,Sarcoidosis,Seizure,Sensory Changes,Serous tubal intraepithelial carcinoma (STIC),Steatosis,Tattoo,Thyroid Nodular Hyperplasia,Tobacco NOS,Tobacco Smokeless,Tobacco Smoking,Turcot Syndrome,Undescended Testis,Vision Changes,Wagr Syndrome,unknown,Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6142389&version=1.0,
Risk Factor Treatment,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.,"Yes, No, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6514356&version=1.0,
Viral Hepatitis Serologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,"HBV Core Antibody, HBV DNA, HBV Genotype, HBV Surface Antibody, HCV Genotype, Hepatitis B Surface Antigen, Hepatitis C Antibody, Hepatitis C Virus RNA, unknown, Not Reported",,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4395982&version=1.0,
Weight,The weight of the patient measured in kilograms.,,,,FALSE,Follow Up,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=651&version=4.0,
Days to Treatment End,Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable',,,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154725&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Days to Treatment Start,Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable',,,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154726&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Initial Disease Status,The text term used to describe the status of the patient's malignancy when the treatment began.,"Initial Diagnosis, Progressive Disease, Recurrent Disease, Residual Disease, unknown, Not Reported",,,FALSE,Therapy,,,
Regimen or Line of Therapy,The text term used to describe the regimen or line of therapy.,,,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161024&version=1.0,
Therapeutic Agents,Text identification of the individual agent(s) used as part of a treatment regimen.,,,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2975232&version=1.0,
Treatment Effect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,"Complete Necrosis (No Viable Tumor), Incomplete Necrosis (Viable Tumor Present), No Necrosis, unknown, Not Reported",,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6514354&version=1.0,
Treatment Intent Type,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],"Adjuvant, Cancer Control, Cure, Neoadjuvant, Palliative, Prevention, unknown, Not Reported",,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2793511&version=1.0,
Treatment or Therapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,"yes, no, unknown, Not Reported",,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4231463&version=1.0,
Treatment Outcome,Text term that describes the patient's final outcome after the treatment was administered.,"Complete Response, Mixed Response, No Measurable Disease, No Response, Partial Response, Persistent Disease, Progressive Disease, Stable Disease, Treatment Ongoing, Treatment Stopped Due to Toxicity, Very Good Partial Response, unknown, Not Reported",,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5102383&version=1.0,
Treatment Type,Text term that describes the kind of treatment administered.,"Ablation Cryo,Ablation Ethanol Injection,Ablation Microwave,Ablation NOS,Ablation Radiofrequency,Ablation Radiosurgical,Ancillary Treatment,Antiseizure Treatment,Bisphosphonate Therapy,Blinded Study Treatment unknown,Brachytherapy High Dose,Brachytherapy Low Dose,Brachytherapy NOS,Chemoembolization,Chemoprotectant,Chemotherapy,Concurrent Chemoradiation,Cryoablation,Embolization,Ethanol Injection Ablation,External Beam Radiation,Hormone Therapy,I-131 Radiation Therapy,Internal Radiation,Immunotherapy (Including Vaccines),Isolated Limb Perfusion (ILP),Organ Transplantation,Other,Pharmaceutical Therapy NOS,Pleurodesis,Radiation 2D Conventional,Radiation 3D Conformal,Radiation Combination,Radiation Cyberknife,Radiation External Beam,Radiation Implants,Radiation Intensity-Modulated Radiotherapy,Radiation Internal,Radiation Proton Beam,Radiation Radioisotope,Radiation Stereotactic/Gamma Knife/SRS,Radiation Systemic,Radiation Therapy NOS,Radioactive Iodine Therapy,Radioembolization,Radiosensitizing Agent,Stem Cell Treatment,Stem Cell Transplantation Autologous,Stem Cell Transplantation Double Autologous,Stem Cell Transplantation Allogeneic,Stem Cell Transplantation Non-Myeloablative,Stem Cell Transplantation Syngenic,Stem Cell Transplantation Haploidentical,Stem Cell Transplantation NOS,Stereotactic Radiosurgery,Steroid Therapy,Surgery,Targeted Molecular Therapy,unknown,Not Reported",,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5102381&version=1.0,list like
Chemo Concurrent to Radiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,"Yes, No, unknown, Not Reported",,,FALSE,Therapy,,,
Number of Cycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,,,,FALSE,Therapy,,,
Reason Treatment Ended,The text term used to describe the reason a specific treatment or regimen ended.,"Adverse Therapy Event, Course of Therapy Completed, Death, Disease Progression, Other, Withdrawal by Subject",,,FALSE,Therapy,,,
Treatment Arm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,"A081105, E4512, EA5142",,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7068995&version=1.0,
Treatment Dose,The numeric value used to describe the dose of an agent the patient received.,,,,FALSE,Therapy,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2182728&version=3.0,
Treatment Dose Units,The text term used to describe the dose units of an agent the patient received.,"cGy, Gy",,,FALSE,Therapy,,,
Treatment Effect Indicator,The text term used to indicate whether the treatment had an effect on the patient.,"Yes, No, Not Reported, unknown",,,FALSE,Therapy,,,
Treatment Frequency,The text term used to describe the frequency the patient received an agent or regimen.,"Every Hour,Five Times Daily,Four Times Daily,Three Times Daily,Twice Daily,Every 24 Hours,Every Other Day,Twice Weekly,Once Weekly,unknown,Not Reported",,,FALSE,Therapy,,,
Sentinel Lymph Node Count,Numeric count of sentinel lymph nodes.,,,,FALSE,Diagnosis,,,
Sentinel Node Positive Assessment Count,The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.,,,,FALSE,Diagnosis,,,
Tumor Extranodal Extension Indicator,The indicator to determine extranodal involvement or extent of the disease.,"Absent,Indeterminate,NO, YES, No source documentation,Not applicable,Not sampled or dissected,Present,Present - extensive,Present - minimal,UNKNOWN,Unspecified",,,FALSE,Diagnosis,,,
Satellite Metastasis Present Indicator,A yes/no indicator to ask if intransit metastases or satellite lesions are present.,"Yes, No, unknown",,,FALSE,Diagnosis,,,
Other Biopsy Resection Site,A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1),,,,FALSE,Diagnosis,,,
Extent of Tumor Resection,"The degree to which the lesion has been cut out, or resected.","Gross Total Resection, Open Biopsy, Subtotal Resection, Extensive Subtotal, Minor, Optimal debulking, Other, Partial debulking, Segmental, Suboptimal, Suboptimal debulking, NTR, unknown, Not Reported, Not Applicable      ",,,FALSE,Diagnosis,,,
Precancerous Condition Type,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).,"Ductal Carcinoma In Situ,Pancreatic Intraductal Papillary-Mucinous Neoplasm,Atypical Adenomatous Lung Hyperplasia,Other,Pancreatic Intraepithelial Neoplasia,Prostatic Intraepithelial Neoplasia,Melanocytic hyperplasia,Atypical melanocytic proliferation,Melanoma in situ,Superficial spreading,Melanoma in situ,Lentigo maligna type,Melanoma in situ,Acral-lentiginous,Melanoma in situ arising in a giant congenital nevus,Persistent melanoma in situ,Melanoma in situ not otherwise classified,Scar - no residual melanoma,Invasive melanoma - superficial spreading,Invasive melanoma - nodular type,Invasive melanoma - lentigo maligna,Invasive melanoma - acral lentiginous,Invasive melanoma - desmoplastic,Invasive melanoma - nevoid,Invasive melanoma,Normal WDA,Reserve cell hyperplasia,Squamous metaplasia - mature,Squamous metaplasia - immature,Mild dysplasia,Moderate dysplasia,Severe dysplasia,Atypical adenomatous hyperplasia,Adenocarcinoma in situ - non mucinous,Adenocarcinoma in situ - mucinous,Benign tumor NOS,Hamartoma,Carcinoma NOS, Normal, Squamous carcinoma in situ, Neuroendocrine cell hyperplasia, No diagnosis possible, Not Applicable",,,FALSE,Diagnosis,,,
Prior Sites of Radiation,The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.,"Abdomen total,Abdominal Wall,Acetabulum,Adenoid,Adipose,Adrenal,Alveolar Ridge,Amniotic Fluid,Ampulla of Vater,Anal Sphincter,Ankle,Anorectum,Antecubital Fossa,Antrum,Anus,Aorta,Aortic Body,Appendix,Aqueous Fluid,Arm,Artery,Ascending Colon,Ascending Colon Hepatic Flexure,Ascites,Auditory Canal,Autonomic Nervous System,Axilla,Back,Bile Duct,Bladder,Blood,Blood Vessel,Body total,Bone,Bone Marrow,Bone non-spine,Bowel,Brain,Brain Stem,Breast,Broad Ligament,Bronchiole,Bronchus,Brow,Buccal Cavity,Buccal Mucosa,Buttock,Calf,Capillary,Cardia,Carina,Carotid Artery,Carotid Body,Cartilage,Cecum,Cell-Line,Central Nervous System,Cerebellum,Cerebral Cortex,Cerebrospinal Fluid,Cerebrum,Cervical Spine,Cervix,Chest,Chest Wall,Chin,Clavicle,Clitoris,Colon,Colon Mucosa Only,Common Duct,Conjunctiva,Connective Tissue,Dermal,Descending Colon,Diaphragm,Distant Site,Duodenum,Ear,Ear Canal,Ear Pinna (External),Elbow,Endocrine Gland,Epididymis,Epidural Space,Epitrochlear,Esophagogastric Junction,Esophagus,Esophagus Mucosa Only,Eye,Fallopian Tube,Femoral Artery,Femoral Vein,Femur,Fibroblasts,Fibula,Finger,Floor of Mouth,Fluid,Foot,Forearm,Forehead,Foreskin,Frontal Cortex,Frontal Lobe,Fundus of Stomach,Gallbladder,Ganglia,Gastroesophageal Junction,Gastrointestinal Tract,Gastrointestinal Intestine,Genitourinary NOS,Groin,Gum,Hand,Hard Palate,Head Face Or Neck Nos,Head and Neck,Heart,Hepatic,Hepatic Duct,Hepatic Vein,Hilar,Hip,Hippocampus,Humerus,Hypopharynx,Ileocecal Valve,Ileum,Ilium,Index Finger,Ischium,Islet Cells,Jaw,Jejunum,Joint,Kidney,Knee,Lacrimal Gland,Large Bowel,Laryngopharynx,Larynx,Leg,Leptomeninges,Ligament,Lip,Liver,Lumbar Spine,Lung,Lymph Node,Lymph Node(s) Axilla,Lymph Node(s) Cervical,Lymph Node(s) Distant,Lymph Node(s) Epitrochlear,Lymph Node(s) Femoral,Lymph Node(s) Hilar,Lymph Node(s) Iliac-Common,Lymph Node(s) Iliac-External,Lymph Node(s) Inguinal,Lymph Node(s) Internal Mammary,Lymph Node(s) Mammary,Lymph Node(s) Mediastinal,Lymph Node(s) Mesenteric,Lymph Node(s) Occipital,Lymph Node(s) Paraaortic,Lymph Node(s) Parotid,Lymph Node(s) Pelvic,Lymph Node(s) Popliteal,Lymph Node(s) Regional,Lymph Node(s) Retroperitoneal,Lymph Node(s) Scalene,Lymph Node(s) Splenic,Lymph Node(s) Subclavicular,Lymph Node(s) Submandibular,Lymph Node(s) Supraclavicular,Mandible,Mantle,Maxilla,Mediastinal Soft Tissue,Mediastinum,Mesentery,Mesothelium,Middle Finger,Mitochondria,Muscle,Nails,Nasal Cavity,Nasal Soft Tissue,Nasopharynx,Neck,Nerve,Nerve(s) Cranial,Occipital Cortex,Ocular Orbits,Omentum,Oral Cavity,Oral Cavity Mucosa Only,Oropharynx,Other,Ovary,Palate,Pancreas,Parametrium,Paraspinal Ganglion,Parathyroid,Parotid Gland,Patella,Pelvis,Penis,Pericardium,Periorbital Soft Tissue,Peritoneal Cavity,Peritoneum,Pharynx,Pineal,Pineal Gland,Pituitary Gland,Placenta,Pleura,Popliteal Fossa,Pouch,Primary Tumor Field,Primary tumor site,Prostate,Prostate Bed,Prostate Seminal Vesicles and Lymph Nodes,Pylorus,Rectosigmoid Junction,Rectum,Regional Site,Retina,Retro-Orbital Region,Retroperitoneum,Rib,Ring Finger,Round Ligament,Sacrum,Salivary Gland,Scalp,Scapula,Sciatic Nerve,Scrotum,Seminal Vesicle,Shoulder,Sigmoid Colon,Sinus,Sinus(es) Maxillary,Skeletal Muscle,Skin,Skin lower extremity local,Skin total,Skin trunk local,Skin upper extremity local,Skull,Small Bowel,Small Bowel Mucosa Only,Small Finger,Soft Tissue,Spinal Column,Spinal Cord,Spine,Spleen,Splenic Flexure,Sternum,Stomach,Stomach Mucosa Only,Subcutaneous Tissue,Synovium,Temporal Cortex,Tendon,Testis,Thigh,Thoracic Spine,Thorax,Throat,Thumb,Thymus,Thyroid,Tibia,Tongue,Tonsil,Tonsil (Pharyngeal),Trachea / Major Bronchi,Transverse Colon,Trunk,Umbilical Cord,unknown,Ureter,Urethra,Urinary Tract,Uterus,Uvula,Vagina,Vas Deferens,Vein,Venous,Vertebra,Vulva,White Blood Cells,Wrist,Not Reported",,,FALSE,Therapy,,,
Immunosuppression,The indicator that describes whether or not immunosuppressive therapy was administered.,"Yes, No, unknown, Not Applicable, Not Done",,,FALSE,Therapy,,,
Concomitant Medication Received Type,An enumerated list of the type of concomitant medication received by the patient.,"Anticoagulant agents,Anticonvulsant,Antifungal,Antiplatelet agents,Antidepressants-Moderate CYP2D6 inhibitors,Antidepressants-Strong CYP2D6 inhibitors,Antidepressants-weak CYP2D2 inhibitors or non-inhibitors,Anxiolytics or sedatives,Aspirin,Bisphosphonates for treatment/prevention of bone loss,Corticosteroid,COX-2 inhibitor,Decadron,Diabetes-Insulin,Diabetes-Metformin containing agents,Growth factor,Intravaginal estrogen preparations,Lipid-lowering drugs,Non-prescription supplements for memory,Non-prescription supplements for relief of hot flashes,Non-steroidal anti-inflammatory agents,Opioids,Other,Prescription medications for memory,Prescription medications for relief of hot flashes,Prophylactic antiplatelet therapy,Tricyclic antidepressants,Not Applicable,unknown,Not Reported",,,FALSE,Therapy,,,
Family Member Vital Status Indicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),"Vital Status Alive, Vital Status Dead, unknown, Not Reported",,,FALSE,Family History,,,
COVID19 Occurrence Indicator,The indicator that describes whether or not a COVID-19 infectious disorder occurred.,"Yes, No, unknown, Not Applicable, Not Done",,,FALSE,Exposure,,,
COVID19 Current Status,The patient's current COVID-19 status of sign or symptom events or interventions,"Patient currently has symptoms, Patient had symptoms but now is fully recovered, Patient never had any symptoms of COVID-19, Status unknown due to general COVID-19 related travel restrictions, Status unknown due to lack of disease/tumor assessment due to COVID-19 diagnosis, Status unknown due to other reasons",,,FALSE,Exposure,,,
COVID19 Positive Lab Test Indicator,The indicator that describes whether or not there was a COVID-19 positive test result.,"Yes, No, unknown, Not Applicable, Not Done",,,FALSE,Exposure,,,
COVID19 Antibody Testing,Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.,"SARS-CoV-2 IgM antibody positive, SARS-CoV-2 IgG antibody positive, SARS-CoV-2 IgG/IgM antibody positive, SARS-CoV-2 IgM antibody negative, SARS-CoV-2 IgG antibody negative, SARS-CoV-2 IgG/IgM antibody negative, unknown, Not Applicable, Not Done",,,FALSE,Exposure,,,
COVID19 Complications Severity,Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.,"Cardiac complications, Pulmonary complications, Systemic complications, Other, Not Applicable, unknown",,,FALSE,Exposure,,,
COVID19 Cancer Treatment Followup,Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder,"Yes, No, unknown, Not Applicable",,,FALSE,Exposure,,,
Ecig vape use,"Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)","Current, Former, Never, unknown",,,FALSE,Exposure,,,
Ecig vape 30 day use num,Number of days e-cigarettes or vaping device was used in the last 30 days,,,,FALSE,Exposure,,,
Ecig vape times per day,e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes),,,,FALSE,Exposure,,,
Type of smoke exposure cumulative years,The number of cumulative years of the patient's specific type of smoke exposure,,,,FALSE,Exposure,,,
Chewing tobacco daily use count,"The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.",,,,FALSE,Exposure,,,
Second hand smoke exposure years,The number of cumulative years of the patient's exposure to second-hand cigarette smoke,,,,FALSE,Exposure,,,
Known Genetic Predisposition Mutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,"Yes, No, unknown",,,FALSE,Family History,,,
Hereditary Cancer Predisposition Syndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,"Alpha-1 antitrypsin,Attenuated familial adenomatous polyposis,BAP1 mutant disease,Beckwith-Wiedemann,Biliary disorder,Birt-Hogg-Dube syndrome,Carney complex,Cirrhosis unknown etiology,Constitutional mismatch repair deficiency,Familial adenomatous polyposis,Familial gastrointestinal stromal tumor,Familial pancreatic cancer,Familial prostate cancer,Familial renal cancer,Fanconi anemia,Glycogen Storage Disease,Gorlin syndrome,Hereditary breast–ovarian cancer syndrome,Hereditary diffuse gastric cancer ,Hereditary leiomyoma-renal cell carcinoma,Hereditary melanoma,Hereditary mixed polyposis syndrome,Hereditary papillary RCC ,Hereditary papillary renal cell carcinoma,Hereditary paraganglioma–pheochromocytoma syndrome,Hereditary renal oncocytoma,Hereditary retinoblastoma ,Juvenile polyposis syndrome,Li-Fraumeni syndrome,Lynch syndrome,Melanoma–astrocytoma syndrome,Multiple endocrine neoplasia type I,Multiple endocrine neoplasia type II,MUTYH-associated polyposis,Nevoid basal cell carcinoma syndrome ,Not Applicable ,Not Reported,Peutz–Jeghers syndrome,Cowden syndrome,Rhabdoid tumor predisposition syndrome type I,Rhabdoid tumor predisposition syndrome type II,Rubinstein-Taybi syndrome,SDH associated renal cancer,Serrated polyposis syndrome,Tuberous sclerosis complex ,Turcot syndrome,Tyrosinemia,unknown,von Hippel-Lindau Syndrome",,,FALSE,Family History,,,
Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation",,,FALSE,Family History,,,
Mutational Signatures,"Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ","UV light induced mutations,Alkylating Agents (Temozolomide) induced mutations,Tobacco use associated mutations,age of cancer diagnosis,transcriptional strand bias,microsatellite instability (additions and deletions),methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine) ,Activation Induced Deaminases (AID) associated mutations,APOBEC enzymes associated mutations,altered activity of the error-prone polymerase POLε (POLE) ,localized substitution hypermutation (kataegis),DNA MMR Deficiency,Ig gene hypermutation,Signature 1A,Signature 1B,Signature 2,Signature 3,Signature 4,Signature 5,Signature 6,Signature 7,Signature 8,Signature 9,Signature 10,Signature 11,Signature 12,Signature 13,Signature 14,Signature 15,Signature 16,Signature 17,Signature 18,Signature 19,Signature 20,Signature 21,Other,Data not available,Not Applicable,Not Reported,unknown",,,FALSE,Molecular Test,,,
Mismatch Repair System Status,The text that best describes the condition or state of MMR (mismatch repair system) in the patient,"Mismatch repair deficiency MMRD, Mismatch repair proficiency MMPP, Microsatellite instability high MSIH, Microsatellite stable MSS, unknown or other",,,FALSE,Molecular Test,,,
Lab Tests for MMR Status,Laboratory tests used to evaluate the status of mismatch repair pathways,"IHC staining for mismatch repair proteins, PCR to evaluate microsatellite instability, MLH1 promoter methylation analysis, BRAF sequencing, Other, Not Applicable, unknown",,,FALSE,Molecular Test,,,
Mode of Cancer Detection,"Text term used to describe the mode of cancer detection, like standard of care screening or random detection","Standard of Care Screening, Clinical Examination of unrelated cancer symptoms, Incidentaloma, Interval Cancer, Data not available",,,FALSE,Diagnosis,,,
Gene Symbol,"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,Molecular Test,,,
Molecular Analysis Method,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.,"Comparative Genomic Hybridization,Cytogenetics NOS,FISH,Flow Cytometry,IHC,ISH,Karyotype,Microarray,Microsatellite Analysis,Nuclear Staining,Other,RNA Sequencing,RT-PCR,Sequencing NOS,Southern Blotting,Targeted Sequencing,WGS,WXS,unknown,Not Reported,Not Applicable",,,TRUE,Molecular Test,,,
Test Result,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.,"Abnormal NOS,Copy Number Reported,Equivocal,High,Intermediate,Loss of Expression,Low,Negative,Normal,Overexpressed,Positive,Test Value Reported,unknown,Not Reported,Not Applicable",,,TRUE,Molecular Test,,,
AA Change,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,Molecular Test,,,
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.,"BCL6, CA-125, CA19-9, CCND1, CD10, CD117, CD138, CD14, CD15, CD19, CD20, CD22, CD23, CD25, CD3, CD30, CD33, CD34, CD45, CD5, CD56, CD7, CD79A, CEA, HLA-DR, Mesothelin, NSE, Squamous Cell Carcinoma Antigen, unknown, Not Reported",,,FALSE,Molecular Test,,,
Clinical Biospecimen Type,"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.","Blood, Bone Marrow, Buccal Mucosa, Buffy Coat, Cerebrospinal Fluid, Connective Tissue, Embryonic Fluid, Embryonic Tissue, Feces, Granulocyte, Muscle Tissue, Nerve Tissue, Peritoneal Fluid, Plasma, Pleural Fluid, Saliva, Serum, Skin, Soft Tissue, Tissue NOS, Uninvolved Tissue NOS, Urine, unknown, Not Reported",,,FALSE,Molecular Test,,,
Blood Test Normal Range Upper,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,Molecular Test,,,
Blood Test Normal Range Lower,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,Molecular Test,,,
Cell Count,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,Molecular Test,,,
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.","chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chrM,chrX,chrY,unknown,Not Reported",,,FALSE,Molecular Test,,,
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.,"Clonal, Non-clonal",,,FALSE,Molecular Test,,,
Copy Number,"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,Molecular Test,,,
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,Molecular Test,,,
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,Molecular Test,,,
Histone Family,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.","H1, H2A, H2B, H3, H4, unknown, Not Reported",,,FALSE,Molecular Test,,,
Histone Variant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.","CENP-A, H2A-Bbd, H2A.X, H2A.Z,H2A.Z.1, H2A.Z.2, H2A.Z.2.2, H3.1, H3.2, H3.3, H3.5, H3.X, H3.Y, H3t (H3.4), mH2A, mH2A.1, mH2A.2, unknown, Not Reported",,,FALSE,Molecular Test,,,
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,Molecular Test,,,
Laboratory Test,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.","Absolute Neutrophil,Albumin,Alpha Fetoprotein,B-cell genotyping,Basophil,Beta 2 Microglobulin,Blood Urea Nitrogen,C-Reactive Protein,Calcium,Cellularity,Circulating Tumor Cells,Creatinine,Eosinophil,Epstein-Barr Virus,Glucose,Hematocrit,Hemoglobin,HPV-E6/E7,Human Chorionic Gonadotropin,Human Papillomavirus,Immunoglobulin A,Immunoglobulin G,Immunoglobulin M,Lactate Dehydrogenase,Leukocytes,Luteinizing Hormone,Lymphoblasts,Lymphocytes,M Protein,Metamyelocytes,Myeloblasts,Myelocytes,Neutrophil Bands,Platelets,Prolymphocytes,Promonocytes,Promyelocytes,Segmented Neutrophil,Serum Free Immunoglobulin Light Chain, Kappa,Serum Free Immunoglobulin Light Chain, Lambda,Serum Free Immunoglobulin Light Chain, NOS,Testosterone,Total Bilirubin,Total Protein,unknown,Not Reported",,,FALSE,Molecular Test,,,
Loci Abnormal Count,Numeric value used to describe the number of loci determined to be abnormal.,,,,FALSE,Molecular Test,,,
Loci Count,Numeric value used to describe the number of loci tested.,,,,FALSE,Molecular Test,,,
Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,,,,FALSE,Molecular Test,,,
Mismatch Repair Mutation,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.,"Yes, No, unknown, Not Reported",,,FALSE,Molecular Test,,,
Molecular Consequence,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.,"3 Prime UTR Variant, 5 Prime UTR Variant, Coding Sequence Variant, Downstream Gene Variant, Feature Elongation, Feature Truncation, Frameshift Variant, Incomplete Terminal Codon Variant, Inframe Deletion, Inframe Insertion, Intergenic Variant, Intron Variant, Mature miRNA Variant, Missense Variant, NMD Transcript Variant, Non-coding Transcript Exon Variant, Non-coding Transcript Variant, Protein Altering Variant, Regulatory Region Ablation, Regulatory Region Amplification, Regulatory Region Variant, Splice Acceptor Variant, Splice Donor Variant, Splice Region Variant, Start Lost, Stop Gain, Stop Lost, Stop Retained Variant, Synonymous Variant, TF Binding Site Variant, TFBS Ablation, TFBS Amplification, Transcript Ablation, Transcript Amplification, Upstream Gene Variant",,,FALSE,Molecular Test,,,
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).,"Benign, Likely Benign, Likely Pathogenic, Pathogenic, Uncertain Significance",,,FALSE,Molecular Test,,,
Ploidy,Text term used to describe the number of sets of homologous chromosomes.,"Aneuploid, Diploid, Hyperdiploid, Hypodiploid, Near Diploid, Tetraploid, unknown, Not Reported",,,FALSE,Molecular Test,,,
Second Exon,"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,Molecular Test,,,
Second Gene Symbol,"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,Molecular Test,,,
Specialized Molecular Test,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,Molecular Test,,,
Test Analyte Type,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.,"DNA, mRNA, miRNA, Protein Analyte, Total RNA, unknown, Not Reported",,,FALSE,Molecular Test,,,
Test Units,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,Molecular Test,,,
Test Value,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,Molecular Test,,,
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,Molecular Test,,,
Variant Origin,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.,"Germline, Somatic, unknown",,,FALSE,Molecular Test,,,
Variant Type,The text term used to describe the type of genetic variation.,"Alleles, Amplification, Chrimerism, Conversion, Deletion, Deletion-Insertion, Duplication, Extension, Gain, Hypermethylation, Insertion, Inversion, Loss, Methylation, Mosaicism, Other, Partial Methylation, Rearrangement, Repeated Sequences, Splice, Substitution, Translocation, unknown, Not Reported",,,FALSE,Molecular Test,,,
Zygosity,The text term used to describe the zygosity of a specific genetic variant.,"Heterozygous, Hemizygous, Homozygous, Nullizygous, unknown, Not Reported",,,FALSE,Molecular Test,,,
Cog Neuroblastoma Risk Group,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.,"High Risk, Intermediate Risk, Low Risk, unknown, Not Reported",,,FALSE,Diagnosis,,,
Cog Rhabdomyosarcoma Risk Group,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).","High Risk, Intermediate Risk, Low Risk, unknown, Not Reported",,,FALSE,Diagnosis,,,
Gleason Grade Group,"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.","Group 1, Group 2, Group 3, Group 4, Group 5",,,FALSE,Diagnosis,,,
Gleason Grade Tertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,"Pattern 4, Pattern 5",,,FALSE,Diagnosis,,,
Gleason Patterns Percent,"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,,,
Greatest Tumor Dimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,,,,FALSE,Diagnosis,,,
IGCCCG Stage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.","Good Prognosis, Intermediate Prognosis, Poor Prognosis, unknown, Not Reported",,,FALSE,Diagnosis,,,
INPC Grade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).","Differentiating, Poorly Differentiated, Undifferentiated,unknown, Not Reported",,,FALSE,Diagnosis,,,
INPC Histologic Group,"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.","Favorable, Unfavorable, unknown, Not Reported",,,FALSE,Diagnosis,,,
INRG Stage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).","L1, L2, M, Ms, unknown, Not Reported",,,FALSE,Diagnosis,,,
INSS Stage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).","Stage 1, Stage 2A, Stage 2B, Stage 3, Stage 4, Stage 4S, unknown, Not Reported",,,FALSE,Diagnosis,,,
International Prognostic Index,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.","Low Risk, Low-Intermediate Risk, High-Intermediate Risk, High Risk",,,FALSE,Diagnosis,,,
IRS Group,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).","Group I,Group Ia,Group Ib,Group II, Group IIa,Group IIc,Group III,Group IIIa,Group IIIb,Group IV,unknown,Not Reported",,,FALSE,Diagnosis,,,
IRS Stage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).","1,2,3,4,unknown,Not Reported",,,FALSE,Diagnosis,,,
ISS Stage,The multiple myeloma disease stage at diagnosis.,"I,II,III, Not Reported, unknown",,,FALSE,Diagnosis,,,
Lymph Node Involved Site,The text term used to describe the anatomic site of lymph node involvement.,"Axillary,Cervical,Epitrochlear,Femoral,Hilar,Iliac-common,Iliac-external,Iliac, NOS,Inguinal,Mediastinal,Mesenteric,None,Occipital,Paraaortic,Parotid,Popliteal,Retroperitoneal,Splenic,Submandibular,Supraclavicular,unknown,Not Reported",,,FALSE,Diagnosis,,,
Margin Distance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,,,,FALSE,Diagnosis,,,
Margins Involved Site,The text term used to describe the anatomic sites that were involved in the survival margins.,"Gerota Fascia, Parenchyma, Perinephric Fat, Renal, Renal Capsule, Renal Sinus, Renal Vein, Ureter",,,FALSE,Diagnosis,,,
Medulloblastoma Molecular Classification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,"Not Determined, Non-WNT/non-SHH Activated, SHH-Activated, WNT-Activated, unknown, Not Reported",,,FALSE,Diagnosis,,,
Micropapillary Features,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,"Absent, Present, unknown, Not Reported",,,FALSE,Diagnosis,,,
Mitosis Karyorrhexis Index,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,"High, Intermediate, Low, unknown, Not Reported",,,FALSE,Diagnosis,,,
Non Nodal Regional Disease,The text term used to describe whether the patient had non-nodal regional disease.,"Absent, Indeterminate, Present, unknown, Not Reported",,,FALSE,Diagnosis,,,
Non Nodal Tumor Deposits,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.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,,
Ovarian Specimen Status,The text term used to describe the physical condition of the involved ovary.,"Ovarian Capsule Intact, Ovarian Capsule Ruptured, Ovarian Capsule Fragmented, unknown, Not Reported",,,FALSE,Diagnosis,,,
Ovarian Surface Involvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,"Absent, Present, Indeterminate, unknown, Not Reported",,,FALSE,Diagnosis,,,
Pregnant at Diagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,,
Primary Gleason Grade,"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.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5",,,FALSE,Diagnosis,,,
Secondary Gleason Grade,"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.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5",,,FALSE,Diagnosis,,,
Supratentorial Localization,Text term to specify the location of the supratentorial tumor.,"Cerebral Cortex, Deep Gray, Spinal Cord, White Matter, unknown, Not Reported",,,FALSE,Diagnosis,,,
Tumor Depth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",,,,FALSE,Diagnosis,,,
WHO CNS Grade,WHO CNS Grade,"Grade I, Grade II, Grade III, Grade IV, Grade Not Assigned, unknown, Not Reported",,,FALSE,Diagnosis,,,
WHO NTE Grade,WHO NTE Grade,"G1, G2, G3, GX, unknown, Not Reported",,,FALSE,Diagnosis,,,
Age at Diagnosis,Age at the time of diagnosis expressed in number of days since birth.,,,,TRUE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3225640&version=2.0,
Days to Last Follow up,"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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3008273&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Days to Last Known Disease Status,"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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3008273&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
Last Known Disease Status,Text term that describes the last known state or condition of an individual's neoplasm.,"Distant met recurrence/progression, Loco-regional recurrence/progression, Biochemical evidence of disease without structural correlate, Tumor free, unknown tumor status, With tumor, Not Reported, Not Allowed To Collect, Not Applicable",,,TRUE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2759550&version=1.0,
Primary Diagnosis,"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).","Acinar cell carcinoma,Acute basophilic leukaemia,Acute leukemia Burkitt type,Acute leukemia NOS,Acute lymphatic leukemia,Acute lymphoblastic leukemia-lymphoma NOS,Acute lymphoblastic leukemia mature B-cell type,Acute lymphoblastic leukemia NOS,Acute lymphoblastic leukemia precursor cell type,Acute lymphocytic leukemia,Acute lymphoid leukemia,Acute myeloid leukemia minimal differentiation,Acute myeloid leukemia MLL,Acute myeloid leukemia NOS,Acute myelomonocytic leukemia,Acute promyelocytic leukemia NOS,Adenocarcinoid tumor,Adenocarcinoma combined with other types of carcinoma,Adenocarcinoma in a polyp NOS,Adenocarcinoma in adenomatous polyp,Adenocarcinoma in polypoid adenoma,Adenocarcinoma in situ in a polyp NOS,Adenocarcinoma in situ in adenomatous polyp,Adenocarcinoma in situ in tubular adenoma,Adenocarcinoma in situ mucinous,Adenocarcinoma in situ non-mucinous,Adenocarcinoma in situ NOS,Adenocarcinoma in tubular adenoma,Adenocarcinoma in villous adenoma,Adenocarcinoma of anal ducts,Adenocarcinoma of anal glands,Adenocarcinoma diffuse type,Adenocarcinoma endocervical type,Adenocarcinoma intestinal type,Adenocarcinoma metastatic NOS,Adenocarcinoma NOS,Adenocarcinoma pancreatobiliary type,Adult rhabdomyoma,Adult T-cell lymphoma,Adult T-cell lymphoma/leukemia,Astrocytoma anaplastic,Astrocytoma low grade,Astrocytoma NOS,B cell lymphoma NOS,B lymphoblastic leukemia/lymphoma with hyperdiploidy,B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL),B lymphoblastic leukemia/lymphoma NOS,B-ALL,B-cell lymphocytic leukemia/small lymphocytic lymphoma,Basal cell adenocarcinoma,Basal cell adenoma,Basal cell carcinoma NOS,Basal cell epithelioma,Basal cell tumor,Basophil adenocarcinoma,Basophil adenoma,Basophil carcinoma,Bile duct adenocarcinoma,Bile duct adenoma,Bile duct carcinoma,Bile duct cystadenocarcinoma,Bile duct cystadenoma,Bronchial adenoma carcinoid,Bronchial adenoma cylindroid,Bronchial adenoma NOS,Bronchial-associated lymphoid tissue lymphoma,Bronchio-alveolar carcinoma mixed mucinous and non-mucinous,Bronchio-alveolar carcinoma mucinous,Bronchiolar adenocarcinoma,Bronchiolar carcinoma,Bronchiolo-alveolar adenocarcinoma NOS,Bronchiolo-alveolar carcinoma Clara cell,Bronchiolo-alveolar carcinoma Clara cell and goblet cell type,Bronchiolo-alveolar carcinoma goblet cell type,Bronchiolo-alveolar carcinoma indeterminate type,Bronchiolo-alveolar carcinoma non-mucinous,Bronchiolo-alveolar carcinoma NOS,Burkitt cell leukemia,Burkitt lymphoma NOS (Includes all variants),Burkitt tumor,Burkitt-like lymphoma,c-ALL,Cancer,Capillary hemangioma,Capillary lymphangioma,Carcinoma in a polyp NOS,Carcinoma in adenomatous polyp,Carcinoma in pleomorphic adenoma,Carcinoma in situ in a polyp NOS,Carcinoma in situ in adenomatous polyp,Carcinoma in situ NOS,Carcinoma anaplastic NOS,Carcinoma diffuse type,Carcinoma intestinal type,Carcinoma metastatic NOS,Carcinoma NOS,Carcinosarcoma NOS,Carcinoma undifferentiated NOS,Cementoma NOS,Central neuroblastoma,Central neurocytoma,Cerebellar liponeurocytoma,Cerebellar sarcoma NOS,Cervical intraepithelial neoplasia grade III,Cervical intraepithelial neoplasia low grade,Chondroma NOS,Chondrosarcoma grade 2/3,Chronic granulocytic leukemia BCR/ABL,Chronic granulocytic leukemia NOS,Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive,Chronic leukemia NOS,Chronic lymphatic leukemia,Chronic lymphocytic leukemia,Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL),Chronic lymphoid leukemia,Chronic monocytic leukemia,Chronic myelocytic leukemia NOS,Chronic myelogenous leukemia BCR-ABL positive,Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive,Chronic myeloid leukemia NOS,Chronic myelomonocytic leukemia in transformation,Chronic myelomonocytic leukemia NOS,Chronic myelomonocytic leukemia Type 1,Chronic myelomonocytic leukemia Type II,Chronic myeloproliferative disease NOS,Chronic myeloproliferative disorder,Chronic neutrophilic leukemia,Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis,Classical Hodgkin lymphoma lymphocyte depletion NOS,Classical Hodgkin lymphoma lymphocyte depletion reticular,Classical Hodgkin lymphoma lymphocyte-rich,Classical Hodgkin lymphoma mixed cellularity NOS,Classical Hodgkin lymphoma nodular sclerosis cellular phase,Classical Hodgkin lymphoma nodular sclerosis grade 1,Classical Hodgkin lymphoma nodular sclerosis grade 2,Classical Hodgkin lymphoma nodular sclerosis NOS,Combined hepatocellular carcinoma and cholangiocarcinoma,Combined large cell neuroendocrine carcinoma,Combined small cell carcinoma,Combined small cell-adenocarcinoma,Combined small cell-large carcinoma,Combined small cell-squamous cell carcinoma,Combined/mixed carcinoid and adenocarcinoma,Composite Hodgkin and non-Hodgkin lymphoma,Dermal nevus,Dermatofibroma NOS,Diffuse astrocytoma IDH-mutant,Diffuse astrocytoma IDH-wildtype,Diffuse astrocytoma low grade,Diffuse large B-cell lymphoma NOS,Diffuse melanocytosis,Duct adenocarcinoma NOS,Duct adenoma NOS,Duct carcinoma desmoplastic type,Duct carcinoma NOS,Duct cell carcinoma,Ductal carcinoma in situ NOS,Ductal carcinoma NOS,Dysplastic nevus,Endometrial sarcoma NOS,Endometrioid adenocarcinoma NOS,Endometrioid adenofibroma NOS,Endometrioid adenoma NOS,Endometrioid carcinoma NOS,Eosinophil adenocarcinoma,Eosinophil adenoma,Eosinophil carcinoma,Eosinophilic granuloma,Eosinophilic leukemia,Ependymoma NOS,Epidermoid carcinoma in situ NOS,Epidermoid carcinoma NOS,Epithelial tumor benign,Epithelial tumor malignant,Esophageal glandular dysplasia (intraepithelial neoplasia) high grade,Esophageal glandular dysplasia (intraepithelial neoplasia) low grade,Esophageal intraepithelial neoplasia high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) low grade,Ewing sarcoma,Ganglioglioma NOS,Familial adenomatous polyposis,Gastrin cell tumor,Gastrin cell tumor malignant,Gastrinoma malignant,Gastrinoma NOS,Gastrointestinal stromal tumor malignant,Glioblastoma,Glioma malignant,Glioma NOS,Haemangioblastoma,Haemangiosarcoma,Hepatocarcinoma,Hepatocellular adenoma,Hepatocellular carcinoma NOS,Hepatocholangiocarcinoma,Hepatoid adenocarcinoma,Hepatoid carcinoma,Hodgkin disease NOS,Hodgkin granuloma,Hodgkin lymphoma mixed cellularity NOS,Hodgkin lymphoma nodular sclerosis NOS,Hodgkin lymphoma NOS,Hodgkin paragranuloma NOS,Hodgkin sarcoma,Infiltrating basal cell carcinoma NOS, Infiltrating duct carcinoma NOS, Infiltrating duct and colloid carcinoma,Infiltrating duct and cribriform carcinoma,Inflammatory adenocarcinoma,Inflammatory carcinoma,Interstitial cell tumor benign,Interstitial cell tumor malignant,Interstitial cell tumor NOS,Intracystic papilloma,Intradermal nevus,Intraductal adenocarcinoma noninfiltrating NOS,Intraductal and lobular carcinoma,Intraductal carcinoma and lobular carcinoma in situ,Intraductal carcinoma clinging,Intraductal carcinoma noninfiltrating NOS,Intraductal carcinoma NOS,Intraductal carcinoma solid type,Intraductal micropapillary carcinoma,Intraductal papillary adenocarcinoma with invasion,Intraductal papillary adenocarcinoma NOS,Intraductal papillary carcinoma,Intraductal tubular-papillary neoplasm high grade,Intraductal tubular-papillary neoplasm low grade,Intraductal tubulopapillary neoplasm,Intraepidermal carcinoma NOS,Intraepidermal squamous cell carcinoma Bowen type,Intravascular B-cell lymphoma,Juvenile myelomonocytic leukemia,Kaposi sarcoma,Large cell carcinoma NOS,Liposarcoma differentiated,Liposarcoma NOS,Liposarcoma well differentiated,Liver cell adenoma,Liver cell carcinoma,Lobular adenocarcinoma,Lobular and ductal carcinoma,Lobular carcinoma in situ NOS,Lobular carcinoma noninfiltrating,Lobular carcinoma NOS,Lymphatic leukemic NOS,Lymphoblastic leukemia NOS,Lymphoblastoma,Lymphocytic leukemia NOS,Lymphoma NOS,Malignancy,Malignant lymphoma diffuse NOS,Malignant lymphoma Hodgkin,Malignant lymphoma immunoblastic NOS,Malignant lymphoma large B-cell diffuse NOS,Malignant lymphoma large B-cell NOS,Malignant lymphoma large cell NOS,Malignant lymphoma lymphoblastic NOS,Malignant lymphoma lymphocytic diffuse NOS,Malignant lymphoma lymphocytic nodular NOS,Malignant lymphoma lymphocytic NOS,Malignant lymphoma mixed cell type diffuse,Malignant lymphoma mixed cell type follicular,Malignant lymphoma mixed cell type nodular,Malignant lymphoma nodular NOS,Malignant lymphoma non-Hodgkin NOS,Malignant lymphoma NOS,Malignant lymphoma small B lymphocytic NOS,Malignant melanoma in congenital melanocytic nevus,Malignant melanoma in giant pigmented nevus,Malignant melanoma in Hutchinson melanotic freckle,Malignant melanoma in junctional nevus,Malignant melanoma in precancerous melanosis,Malignant melanoma NOS,Malignant melanoma regressing,Mammary carcinoma in situ,Medullary adenocarcinoma,Medullary carcinoma NOS,Medullary osteosarcoma,Medulloblastoma NOS,Melanoameloblastoma,Melanocytic nevus,Melanocytoma eyeball,Melanocytoma NOS,Melanoma in situ,Melanoma malignant of soft parts,Melanoma NOS,Melanotic medulloblastoma,Melanotic MPNST,Melanotic neuroectodermal tumor,Melanotic neurofibroma,Melanotic progonoma,Melanotic psammomatous MPNST,Melanotic schwannoma,Meningeal melanocytoma,Meningeal melanoma,Meningioma anaplastic,Meningioma malignant,Meningioma NOS,Micropapillary carcinoma NOS,Mixed adenocarcinoma and epidermoid carcinoma,Mixed adenocarcinoma and squamous cell carcinoma,Mixed medullary-follicular carcinoma,Mixed medullary-papillary carcinoma,Mixed pancreatic endocrine and exocrine tumor malignant,Mixed pineal tumor,Mixed small cell carcinoma,Mixed squamous cell and glandular papilloma,Mixed tumor malignant NOS,Mixed tumor NOS,Monocytic leukemia NOS,Mucosal-associated lymphoid tissue lymphoma,Mucous adenocarcinoma,Multiple myeloma,Myelocytic leukemia NOS,Myeloid leukemia NOS,Myeloma NOS,Myoepithelioma,Neoplasm benign,Neoplasm malignant,Neoplasm malignant uncertain whether primary or metastatic,Neoplasm metastatic,Neoplasm NOS,Neoplasm secondary,Neoplasm uncertain whether benign or malignant,Nephroblastoma NOS,Neuroblastoma NOS,Neuroendocrine carcinoma NOS,Neuroepithelioma NOS,Neurofibroma NOS,Neurofibromatosis NOS,Neurofibrosarcoma,Neurosarcoma,Nevus NOS,Non-Hodgkin lymphoma NOS,Non-invasive low grade serous carcinoma,Non-lymphocytic leukemia NOS,Non-small cell carcinoma,Nonpigmented nevus,Not Reported,Oat cell carcinoma,Osteoblastoma malignant,Osteoblastoma NOS,Osteosarcoma NOS,Paget disease and infiltrating duct carcinoma of breast,Paget disease and intraductal carcinoma of breast,Paget disease of breast,Paget disease extramammary,Paget disease mammary,Pagetoid reticulosis,Pancreatic endocrine tumor benign,Pancreatic endocrine tumor malignant,Pancreatic endocrine tumor nonfunctioning,Pancreatic endocrine tumor NOS,Pancreatic microadenoma,Pancreatobiliary neoplasm non-invasive,Pancreatobiliary-type carcinoma,Pancreatoblastoma,Papillary adenocarcinoma follicular variant,Papillary adenocarcinoma NOS,Papillary adenofibroma,Papillary adenoma NOS,Papillary and follicular carcinoma,Papillary carcinoma in situ,Papillary carcinoma NOS,Papillary cystadenoma NOS,Papillary epidermoid carcinoma,Papillary glioneuronal tumor,Papillary meningioma,Papillary microcarcinoma,Papillary renal cell carcinoma,Papillary serous adenocarcinoma,Papillary serous cystadenocarcinoma,Papillary serous cystadenoma NOS,Papillary squamous cell carcinoma,Papillary squamous cell carcinoma in situ,Papillary transitional cell carcinoma,Papillary tumor of the pineal region,Papillary urothelial carcinoma,Papilloma of bladder,Papilloma NOS,Papillomatosis glandular,Papillomatosis NOS,Papillotubular adenocarcinoma,Papillotubular adenoma,Paraganglioma benign,Paraganglioma malignant,Paraganglioma NOS,Peripheral T-cell lymphoma large cell,Peripheral T-cell lymphoma NOS,Pigmented adenoma,Pigmented basal cell carcinoma,Pigmented nevus NOS,Pituitary adenoma NOS,Pituitary carcinoma NOS,Pleomorphic adenoma,Pleomorphic carcinoma,Pleomorphic lipoma,Pleomorphic liposarcoma,Pleomorphic lobular carcinoma,Pleomorphic lobular carcinoma in situ,Precancerous melanosis NOS,Precursor B-cell lymphoblastic leukemia,Precursor B-cell lymphoblastic lymphoma,Precursor cell lymphoblastic leukemia NOS,Precursor T-cell lymphoblastic leukemia,Precursor T-cell lymphoblastic lymphoma,Preleukemia,Preleukemic syndrome,Primary amyloidosis,Pro-B ALL,Pro-T ALL,Prostatic intraepithelial neoplasia grade III,Pulmonary adenomatosis,Pulmonary artery intimal sarcoma,Pulmonary blastoma,Renal carcinoma collecting duct type,Renal cell adenocarcinoma,Renal cell carcinoma chromophobe type,Renal cell carcinoma NOS,Renal cell carcinoma sarcomatoid,Renal cell carcinoma spindle cell,Renal cell carcinoma unclassified,Renal medullary carcinoma,Rhabdoid meningioma,Rhabdoid sarcoma,Rhabdoid tumor NOS,Rhabdomyoma NOS,Rhabdomyosarcoma with ganglionic differentiation,Rhabdomyosarcoma NOS,Rhabdosarcoma,Rodent ulcer,Sarcoma NOS,Sclerosing hemangioma,Sclerosing hepatic carcinoma,Secondary carcinoma,Secretory carcinoma of breast,Serous cystadenocarcinoma NOS,Serous surface papillary carcinoma,High-grade serous carcinoma,Skin appendage carcinoma,Small cell carcinoma NOS,Small cell neuroendocrine carcinoma,Small cell osteosarcoma,Small cell sarcoma,Small congenital nevus,Spindle cell carcinoma NOS,Spindle cell melanoma NOS,Splenic B-cell lymphoma/leukemia unclassifiable,Splenic diffuse red pulp small B-cell lymphoma,Splenic lymphoma with villous lymphocytes,Splenic marginal zone B-cell lymphoma,Splenic marginal zone lymphoma NOS,Squamous cell carcinoma in situ NOS,Squamous cell carcinoma adenoid,Squamous cell carcinoma clear cell type,Squamous cell carcinoma NOS,T lymphoblastic leukemia/lymphoma,T-cell large granular lymphocytic leukemia,T-cell large granular lymphocytosis,T-cell lymphoma NOS,Teratoma malignant NOS,Teratoma NOS,Therapy related myeloid neoplasm,Transitional carcinoma,Transitional cell carcinoma,Transitional cell carcinoma in situ,Tubular adenocarcinoma,Tubular adenoma NOS,Tubular androblastoma with lipid storage,Tubular androblastoma NOS,Tubular carcinoid,Tubular carcinoma,Tubulo-papillary adenoma,Tubulocystic renal cell carcinoma,Tubulolobular carcinoma,Tubulopapillary adenocarcinoma,Tubulovillous adenoma NOS,Tumor cells benign,Tumor cells malignant,Tumor cells NOS,Tumor cells uncertain whether benign or malignant,Tumor embolus,Tumor benign,Tumor malignant NOS,Tumor metastatic,Tumor NOS,Tumor secondary,Tumorlet benign,Typical carcinoid,Unclassified tumor benign,Unclassified tumor borderline malignancy,Unclassified tumor malignant,Unclassified tumor malignant uncertain whether primary or metastatic,Unclassified tumor uncertain whether benign or malignant,Undifferentiated epithelioid sarcoma,Undifferentiated high-grade pleomorphic sarcoma,Undifferentiated leukaemia,Undifferentiated pleomorphic sarcoma,Undifferentiated round cell sarcoma,Undifferentiated sarcoma,Undifferentiated spindle cell sarcoma,Undifferentiated uterine sarcoma,unknown",,,TRUE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161032&version=1.0,
Prior Malignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,"Yes, No, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3382736&version=2.0,
Prior Treatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,"Yes, No, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,,
Site of Resection or Biopsy,"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).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Paraspinal,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,TRUE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161034&version=1.0,
Tissue or Organ of Origin,"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).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Paraspinal,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,TRUE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161035&version=1.0,
Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Intermediate Grade, Low Grade, unknown, Not Reported, Not Applicable",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2785839&version=2.0,
AJCC Clinical M,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,"M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440331&version=1.0,
AJCC Clinical N,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,"N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440330&version=1.0,
AJCC Clinical Stage,"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.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440332&version=1.0,
AJCC Clinical T,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,"T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440328&version=1.0,
AJCC Pathologic M,"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).","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3045439&version=1.0,
AJCC Pathologic N,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.,"N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3203106&version=1.0,
AJCC Pathologic Stage,"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.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3203222&version=1.0,
AJCC Pathologic T,"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).","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3045435&version=1.0,
AJCC Staging System Edition,"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.","1st, 2nd, 3rd, 4th, 5th, 6th, 7th, 8th, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2722309&version=1.0,
Anaplasia Present,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,"Yes - Anaplasia Present, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6059599&version=1.0,
Yes - Anaplasia Present,Indicates anaplasia is present,,Anaplasia Present Type,,FALSE,Diagnosis,,,
Anaplasia Present Type,"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.","Absent, Diffuse, Equivocal, Focal, Present, Sclerosis, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4925534&version=1.0,
Best Overall Response,The best improvement achieved throughout the entire course of protocol treatment.,"AJ-Adjuvant Therapy, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal Response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, VGPR-Very Good Partial Response",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2003324&version=4.0,
Breslow Thickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.",,,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=64809&version=3.0,
Classification of Tumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,"Primary, Metastasis, Recurrence, Other, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3288124&version=1.0,
Days to Diagnosis,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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6154733&version=1.0,regex match \d+$|Not\sApplicable$|unknown$
First Symptom Prior to Diagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,"Altered Mental Status, Headaches, Motor or Movement Changes, Seizures, Sensory Changes, Visual Changes, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6133605&version=1.0,
Gross Tumor Weight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",,,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6133606&version=1.0,
Laterality,"For tumors in paired organs, designates the side on which the cancer originates.","Bilateral, Left, Midline, Right, Unilateral, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=827&version=3.0,
Lymph Nodes Positive,The number of lymph nodes involved with disease as determined by pathologic examination.,,,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=89&version=3.0,
Lymph Nodes Tested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,,,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3&version=3.0,
Lymphatic Invasion Present,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement","Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=64171&version=3.0,
Metastasis at Diagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,"Distant Metastasis, Metastasis NOS, No Metastasis, Regional Metastasis, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6133614&version=1.0,
Metastasis at Diagnosis Site,Text term to identify an anatomic site in which metastatic disease involvement is found.,"Abdomen, Adrenal Gland, Ascites, Bone, Bone Marrow, Brain, Cerebrospinal Fluid, Central Nervous System, Colon, Distant Nodes, Distant Organ, Groin, Kidney, Liver,  Lung, Lymph Node, Axillary, Lymph Node, Inguinal, Lymph Node NOS, Mediastinum,  Omentum, Ovary, Pelvis, Peritoneal Cavity,  Peritoneum,  Pleura, Scalp, Skin, Small Intestine, Soft Tissue, Spinal Cord, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3029815&version=1.0,
Method of Diagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,"Autopsy,Biopsy,Blood Draw,Bone Marrow Aspirate,Core Biopsy,Cytology,Cystoscopy,Debulking,Diagnostic Imaging,Dilation and Curettage Procedure,Enucleation,Excisional Biopsy,Fine Needle Aspiration,Incisional Biopsy,Laparoscopy,Laparotomy,Other,Pap Smear,Physical Exam,Pathologic Review,Surgical Resection,Thoracentesis,Ultrasound Guided Biopsy,unknown,Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161031&version=1.0,
Mitotic Count,"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,,,
Percent Tumor Invasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,,,,FALSE,Diagnosis,,,
Peritoneal Fluid Cytological Status,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,"Atypical, Malignant, Non-Malignant, Unsatisfactory, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6690681&version=1.0,
Perineural Invasion Present,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=64181&version=3.0,
Residual Disease,Text terms to describe the status of a tissue margin following surgical resection.,"R0, R1, R2, RX, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2608702&version=1.0,
Synchronous Malignancy,"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.","Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6142390&version=1.0,
Tumor Confined to Organ of Origin,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.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4925494&version=1.0,
Tumor Focality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,"Multifocal, Unifocal, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3174022&version=1.0,
Tumor Largest Dimension Diameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",,,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=64215&version=3.0,
Vascular Invasion Present,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,"Yes - Vascular Invasion Present, No, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=64358&version=3.0,
Yes - Vascular Invasion Present,Indicates venous invasion was detected by surgery or presence in a tumor specimen,,Vascular Invasion Type,,FALSE,Diagnosis,,,
Vascular Invasion Type,Text term that represents the type of vascular tumor invasion.,"Extramural, Intramural, Macro, Micro, No Vascular Invasion, unknown, Not Reported",,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3168001&version=1.0,
Year of Diagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,,,,FALSE,Diagnosis,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2896960&version=1.0,
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,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3226275&version=1.0,
Topography Code,"Topography Code, indicating site within the body, based on ICD-O-3.","C00.0, C00.1, C00.2, C00.3, C00.4, C00.5, C00.6, C00.8, C01.9, C02.0, C02.1, C02.2, C02.3, C02.4, C02.8, C02.9, C03.0, C03.1, C03.9, C04.0, C04.1, C04.8, C04.9, C05.0, C05.1, C05.2, C05.8, C05.9, C06.0, C06.1, C06.2, C06.8, C06.9, C07.9, C08.0, C08.1, C08.8, C08.9, C09.0, C09.1, C09.8, C09.9, C10.0, C10.1, C10.2, C10.3, C10.4, C10.8, C10.9, C11.0, C11.1, C11.2, C11.3, C11.8, C11.9, C12.9, C13.0, C13.1, C13.2, C13.8, C13.9, C14.0, C14.2, C14.8, C15.0, C15.1, C15.2, C15.3, C15.4, C15.5, C15.8, C15.9, C16.0, C16.1, C16.2, C16.3, C16.4, C16.5, C16.6, C16.8, C16.9, C17.0, C17.1, C17.2, C17.3, C17.8, C17.9, C18.0, C18.1, C18.2, C18.3, C18.4, C18.5, C18.6, C18.7, C18.8, C18.9, C19.9, C20.9, C21.0, C21.1, C21.2, C21.8, C22.0, C22.1, C23.9, C24.0, C24.1, C24.8, C24.9, C25.0, C25.1, C25.2, C25.3, C25.4, C25.7, C25.8, C25.9, C26.0, C26.8, C26.9, C30.0, C30.1, C31.0, C31.1, C31.2, C31.3, C31.8, C31.9, C32.0, C32.1, C32.2, C32.3, C32.8, C32.9, C33.9, C34.0, C34.1, C34.2, C34.3, C34.8, C34.9, C37.9, C38.0, C38.1, C38.2, C38.3, C38.4, C38.8, C39.0, C39.8, C39.9, C40.0, C40.1, C40.3, C40.8, C40.9, C41.0, C41.1, C41.2, C41.3, C41.4, C41.8, C41.9, C42.0, C42.1, C42.2, C42.3, C42.4, C44.0, C44.1, C44.2, C44.3, C44.4, C44.5, C44.6, C44.7, C47.0, C47.1, C47.2, C47.3, C47.4, C47.5, C47.6, C47.8, C47.9, C48.0, C48.1, C48.2, C48.8, C49.0, C49.1, C49.2, C49.3, C49.4, C49.5, C49.6, C49.8, C49.9, C50.0, C50.1, C50.2, C50.3, C50.4, C50.5, C50.6, C50.8, C50.9, C51.0, C51.1, C51.2, C51.8, C51.9, C52.9, C53.0, C53.1, C53.8, C53.9, C54.0, C54.1, C54.2, C54.3, C54.8, C54.9, C55.9, C56.9, C57.0, C57.1, C57.2, C57.3, C57.4, C57.7, C57.8, C57.9, C60.0, C60.1, C60.2, C60.8, C60.9, C61.9, C62.0, C62.1, C62.9, C63.0, C63.1, C63.2, C63.7, C63.8, C63.9, C64.9, C65.9, C66.9, C67.0, C67.1, C67.2, C67.4, C67.6, C67.7, C67.8, C67.9, C68.0, C68.1, C68.8, C68.9, C69.0, C69.1, C69.2, C69.3, C69.4, C69.5, C69.6, C69.8, C69.9, C70.0, C70.1, C70.9, C71.0, C71.1, C71.2, C71.3, C71.4, C71.5, C71.6, C71.7, C71.8, C71.9, C72.0, C72.1, C72.2, C72.3, C72.4, C72.5, C72.8, C72.9, C73.9, C74.0, C74.1, C74.9, C75.0, C75.1, C75.2, C75.3, C75.4, C75.5, C75.8, C75.9, C76.0, C76.1, C76.2, C76.3, C76.4, C76.5, C76.7, C76.8, C77.0, C77.1, C77.2, C77.3, C77.4, C77.5, C77.8, C77.9, C80.9,unknown,Not Reported",,,FALSE,Diagnosis,,,
Additional Topography,Topography not included in the ICD-O-3 Topography codes.,"Skin of scalp, Skin of eye lid, Skin of nose, Skin of lip, Skin of ear, Skin of neck, Skin of other parts of face, Skin of chest, Skin of back, Skin of abdomen, Skin of trunk, Skin of breast, Skin of upper limb and shoulder, Skin of palm, Skin of lower limb and hip, Skin of sole, Skin of penis, Skin of scrotum, Skin of vulva, Skin NOS, Hilar Airway, Peri-tumoral Airway, Not Reported",,,FALSE,Diagnosis,,,
Lung Cancer Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer","Low Dose Computed Tomography (LDCT), Chest X-ray, Chest CT, unknown, Data not available, Other",,,FALSE,Lung Cancer Tier 3,,,
Lung Cancer Participant Procedure History,Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.,"Lobectomy Bilateral, Lobectomy Left, Lobectomy Right, Lung Wedge Resection Bilateral, Lung Wedge Resection Left, Lung Wedge Resection Multiple, Lung Wedge Resection Right, Pneumonectomy Left, Pneumonectomy Right, Endobronchial biopsy, Mediastinoscopy, VATS Sclerosis, Brain resection, Segmentectomy, unknown, Other, Not Reported",,,FALSE,Lung Cancer Tier 3,,,
Lung Adjacent Histology Type,The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth,"Lung adenocarcinoma, Adenosquamous carcinoma, Carcinoid tumor and lung atypical carcinoid tumor, Lung adenocarcinoma in situ, Large cell lung carcinoma, Large cell neuroendocrine carcinoma, Lung lymphoepithelioma-like carcinoma, Bronchioalveolar carcinoma, Thoracic NUT carcinoma, Sarcomatoid carcinoma, Small cell lung carcinoma, Squamous cell lung carcinoma, Lung squamous cell carcinoma in situ, Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,,
Lung Tumor Location Anatomic Site,Anatomic location of the tumor inside the lung,"Main carina, Left, Right, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,,
Lung Tumor Lobe Bronchial Location,Anatomic lobe and bronchial location of the tumor inside the lung,"Upper lobe, Middle lobe, Lower lobe, Stump, Bronchus, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,,
Current Lung Cancer Symptoms,Reported lung cancer related symptoms person is currently experiencing,"asbestosis, productive cough, non-productive cough, wheezing, rhonci, crackles, hemoptysis, dyspnea, unexplained weight loss, unexplained loss of energy/fatigue, chest pain or discomfort, dysphagia, pneumonia, hoarseness/laryngitis/vocal cord inflammation, air entry decreased/fair/poor/diminished, fair/poor aeration, shallow inspiration, breath sounds coarse/diminished, dullness to percussion, abnormal breath sounds, clear lungs to auscultation or percussion, unlabored/normal breathing, cold symptoms/flu/sinus/nasal congestion, sinus pain/infection, finger clubbing, no evidence of lung cancer recurrence, patient is NED, oxygen supplemental-portable O2 at night or continuous, prolonged expiration-long/forced expiratory phase, Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,,
Lung Topography,Lung PCA specific topography (not covered in previous tiers),"MC-Carina between right and left lungs (main carina), TR -Trachea (airway wall between tracheo-esophageal bifurcation and main carina), Carina NOS (Carina not otherwise specified), LUDB-Carina between the lingula and upper division left upper lobe, Carina between LUDB orifice and lingula orifice, LUDB-orifice airway wall between LUDB and LB3(LB1+2 carinae), Lingula orifice airway wall between LUDB and LB4/5 carinae, RMB-Right mainstem bronchus(airway wall between MC & RUL carina), LMB-Left mainstem bronchus(airway wall between MC & LUL carina), RL NOS (Right lung not otherwise specified), RB1/2 - Carina between apical and posterior segments right upper lobe (Carina between RB1 orifice and RB2 orifice), RB6A/B - Carina between apical and lateral subsegments superior segment RLL, RB6A/C - Carina between apical and medial subsegments superior segment RLL, RB6B/C - Carina between medial and lateral subsegments superior segment RLL, RB7A/B - Carina between medial and lateral subsegments medial basal segment RLL, RB8/9 - Carina between anterior and lateral segments RLL (Carina between RB8 orifice and RB9 orifice), RB8A/B - Carina between medial and lateral subsegments anterior segment RLL, RB9/10 - Carina between lateral and posterior segments RLL, RB9A/B - Carina between medial and lateral subsegments lateral segment RLL, RB10A/B - Carina between medial and lateral subsegments posterior segment RLL, RB10A/C - Carina between medial and apical subsegments posterior segment RLL, RB1A/B - Carina between medial and lateral subsegments apical segment RUL, RB10B/C - Carina between medial and lateral subsegments posterior segment RLL, RB6 - Carina of superior segment RLL (Carina between RB6 orifice and lower portion of RLL orifice), RB6 orifice Airway wall between RB6 and RB6A/B/C carinae, Bronchus Intermedius Bronchus (airway wall) between right upper and right middle lobes, RB1/3 - Carina between apical and anterior segments RUL (Carina between RB1 orifice and RB3 orifice), RB2/3 - Carina between anterior and posterior segments RUL (Carina between RB2 orifice and RB3 orifice), RB2A/B - Carina between the medial and lateral subsegments of the posterior segment (RUL), RB3A/B - Carina between the medial and lateral subsegments of the anterior segment RUL, RB4/5 - Carina between the lateral and medial segments right middle lobe (Carina between RB4 orifice and RB5 orifice), RB4A/B - Carina between the medial and lateral subsegments of the lateral segment of the right middle lobe, RB5A/B - Carina between the medial and lateral subsegments of the medial segment of the right middle lobe, RUL Carinae between RUL orifice and bronchus intermedius, RUL orifice Airway wall between RUL and RB1/RB2/RB3, RB1 orifice Apical segment - right upper lobe(airway wall between RB1 and RB1A/B carinae), RB2 orifice Posterior segment - right upper lobe(airway wall between RB2 and RB2A/B carinae), RB3 orifice Anterior segment - right upper lobe(airway wall between RB3 and RB3A/B carinae), RML - Carina between RML orifice and RLL orifice, RML orifice Airway wall between RML and RB4/5, RB4 orifice Lateral segment right middle lobe (airway wall between RB4 and RB4A/B carinae), RB5 orifice Medial segment right middle lobe (airway wall between RB5 and RB5A/B carinae), RLL orifice Airway wall between RML and RB6-10 carinae, RB7 Medial basal segment right lower lobe (Carina at RB7 orifice takeoff from RLL orifice), RB7 orifice Airway wall between RB7 and RB7A/B carinae, RB8 orifice Anterior segment right lower lobe(airway wall between RB8 and RB8A/B carinae), RB9 orifice Lateral segment right lower lobe(airway wall between RB9 and RB9A/B carinae), RB10 Posterior segment right lower lobe (Carina at RB10 orifice takeoff from RLL orifice), RB10 orifice Airway wall between RB10 and RB10A/B carinae, LL NOS (Left lung not otherwise specified), LB1/2  Carina between apical and posterior segment left upper lobe (Carina between LB1 orifice and LB2 orifice), LB4/5  Carina between superior and inferior segment lingula (Carina between LB4 orifice and LB5 orifice), LB4A/B  Carina between medial and lateral subsegments superior segment lingula, LB5A/B  Carina between the medial and lateral subsegments inferior segment lingula, LB6A/B  Carina between the superior and lateral subsegments superior segment LLL, LB6A/C  Carina between the superior and medial subsegments of superior segment LLL, LB6B/C  Carina between the medial and lateral subsegments of the superior segment LLL, LB8/9  Carina between the anterior and lateral segments LLL (Carina between LB8 orifice and LB9 orifice), LB8A/B  Carina between the medial and lateral subsegments of the anterior segment LLL, LB9/10  Carina between the lateral and posterior segments LLL (Carina between LB9 orifice and LB10 orifice), LB9A/B  Carina between the medial and lateral subsegments of the lateral segment LLL, LB1A/B  Carina between the lateral and medial subsegments of the apical segment of the LUL, LB10A/B  Carina between the apical and lateral subsegments of the posterior segment of the LLL, LB10A/C  Carina between the apical and medial segments of the posterior segment of the LLL, LB10B/C  Carina between the medial and lateral subsegments of the posterior segment of the LLL, LB1+2 orifice  The apico-posterior segment of the left upper lobe (airway wall between LB1+2/3 carina and LB1 or LB2), LB6  The superior segment of the left lower lobe (Carina between LB6 orifice and lower portion of LLL orifice), LB6 orifice Airway wall between LB6 and LB6A/B carinae, LB1A/C  Carina between the apical and lateral subsegments of the apical segment left upper lobe, LB1B/C  Carina between the medial and lateral subsegments of the apical segment of the left upper lobe, LB2A/B  Carina between the apical and lateral subsegments of the posterior segment of the left upper lobe, LB2A/C  Carina between the apical and medial subsegments of the posterior segment of the left upper lobe, LB2B/C  Carina between the medial and lateral subsegments of the posterior segment left upper lobe, LB1+2/3  Carina between the apico-posterior and anterior segments of the left upper lobe (Carina between LB1+2 orifice and LB3 orifice), LB3A/B Carina between the apical and lateral subsegments of the anterior segment of the left upper lobe , LUL Carina between the LUL orifice and LLL orifice (airways), LUL orifice Airway wall between LUL and LUDB, LB3 orifice Anterior segment left upper lobe(airway wall between LB3 and LB3A/B carinae), LB4 orifice Superior segment lingula(airway wall between LB4 and LB4A/B carinae), LB5 orifice Inferior segment lingula(airway wall between LB5 and LB5A/B carinae), LLL orifice Airway wall between LUL carina and LB6-10 carinae, LB9 orifice Lateral segment left lower lobe(airway wall between LB9 and LB9A/B carinae), LB8 orifice Anterior segment left lower lobe(airway wall between LB8 and LB8A/B carinae), LB10 orifice  Posterior segment left lower lobe(airway wall between LB10 and LB10A/B carinae), Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,,
Lung Cancer Harboring Genomic Aberrations,Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2),"G12A KRAS mutation, G12C KRAS mutation, G12D KRAS mutation, G12R KRAS mutation, G12S KRAS mutation, G12V KRAS mutation, G13D KRAS mutation, G13R KRAS mutation, G13C KRAS mutation, G13A KRAS mutation, G13V KRAS mutation, Q61L KRAS mutation, Q61H KRAS mutation, A146T KRAS mutation, G719X EGFR mutation, T790M EGFR mutation, C797S EGFR mutation, L858R EGFR mutation, L861Q EGFR mutation, Exon 19 deletion, Exon 20 insertion, EML4-ALK translocation-variant 1, EML4-ALK translocation-variant 2, EML4-ALK translocation-variant 3, EML4-ALK translocation-variant 4, EML4-ALK translocation-variant 5, V600E BRAF mutation, V600D BRAF mutation, V600K BRAF mutation, V600R BRAF mutation, K601E BRAF mutation, D963 splice MET mutation, D1010N MET mutation, D1010 splice MET mutation, Intron 13 mutation, Intron 14 mutation, Exon 14 mutation, Exon 14 deletion, Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,,
Colorectal Cancer Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer","Fecal occult blood test, Sigmoidoscopy, Colonoscopy, Virtual colonoscopy, DNA stool test, Other, unknown, Data not available",,,FALSE,Colorectal Cancer Tier 3,,,
History of Prior Colon Polyps,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,,
Family Colon Cancer History Indicator,The indicator to designate if any first degree relative has a history of colorectal cancer.,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,,
Family Medical History Colorectal Polyp Diagnosis,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,,
Immediate Family History Endometrial Cancer,Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.,"Before age 50, Not before age 50, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Immediate Family History Ovarian Cancer,Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.,"Before age 50, Not before age 50, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Patient Inflammatory Bowel Disease Personal Medica History,"The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).","Yes - Crohn's disease, Yes - Ulcerative colitis, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Patient Colonoscopy Performed Indicator,The yes/no indicator that records if the subject has undergone a previous colonoscopy.,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,,
Colorectal Cancer Tumor Border Configuration,The description of the border configuration of a colorectal tumor at pathologic assessment.,"Indeterminate, Infiltrating, Other, Pushing, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
MLH1 Promoter Methylation Status,Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.,"Absent, Indeterminate, Not Assessed, Present",,,FALSE,Colorectal Cancer Tier 3,,,
Colorectal Cancer KRAS Indicator,The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Colon Polyp Occurence Indicator,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Family History Colorectal Polyp,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Colorectal Polyp New Indicator,A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Colorectal Polyp Shape,Shape of polyp identified in the participant,"Pedunculated, Sessile, Flat, Not stated, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Size of Polyp Removed,Size of the polyp removed in cm,,,,FALSE,Colorectal Cancer Tier 3,,,
Colorectal Polyp Count,The total number of polyps detected,,,,FALSE,Colorectal Cancer Tier 3,,,
Colorectal Polyp Type,Type of polyp found in the participant,"Adenoma, Hyperplastic, Mixed, Papillomatous, Normal, Cancer, Other, unknown",,,FALSE,Colorectal Cancer Tier 3,,,
Colorectal Polyp Adenoma Type,Type of adenoma associated with the polyp,"Tubular, Villous, Tubulovillous, Sessile serrated, Traditional serrated, Serrated not specified, Not stated, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,,
Breast Carcinoma Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.","Clinical Exam, Data not available, Nipple Discharge, Other, Screening Mammography, Screening MRI, Self exam, unknown",,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma Histology Category,Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.,"Infiltrating ductal carcinoma, Infiltrating lobular carcinoma, Invasive mammary carcinoma NOS, Invasive mixed ductal and lobular carcinoma, Other",,,FALSE,Breast Cancer Tier 3,,,
Invasive Lobular Breast Carcinoma Histologic Category,The histologic subtype for an infiltrating lobular carcinoma of the breast.,"Alveolar type, Classical type, Data not available, Pleomorphic type, unknown",,,FALSE,Breast Cancer Tier 3,,,
Invasive Ductal Breast Carcinoma Histologic Category,The histologic subtype for the most common type of invasive breast carcinoma.,"Classical type, Invasive carcinoma-type cannot be determined, Invasive cribriform carcinoma, Invasive micropapillary carcinoma, Invasive papillary carcinoma, Invasive tubular carcinoma, Medullary carcinoma, Mucinous carcinoma, Tubulolobular carcinoma, Other, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
Breast Biopsy Procedure Finding Type,Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.,"Atypical hyperplasia, DCIS, LCIS, Cancer, No cancer, Other",,,FALSE,Breast Cancer Tier 3,,,
Breast Quadrant Site,The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.,"Upper outer quadrant, Lower outer quadrant, Upper inner quadrant, Lower inner quadrant, Central, Nipple, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
Breast Cancer Assessment Tests,Text term to identify assessment tests done in participants during diagnosis,"Estrogen receptor IHC, Progesterone receptor IHC, HER2 IHC, HER2 FISH-CISH, HER2 FISH, Other, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
Breast Cancer Genomic Test Performed,Text term that represents the name of the genomic test performed for breast cancer.,"Oncotype, MammaPrint, Other, Data not available, unknown, Not performed",,,FALSE,Breast Cancer Tier 3,,,
Mammaprint Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.,"High risk, Intermediate risk, Low risk, Data not available, unknown",,,FALSE,Breast Cancer Tier 3,,,
Oncotype Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.,"High risk, Intermediate risk, Low risk, Data not available, unknown",,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma Estrogen Receptor Status,Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown",,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma Progesteroner Receptor Status,Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown",,,FALSE,Breast Cancer Tier 3,,,
Breast Cancer Allred Estrogen Receptor Score,"The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.","0, 1, 2, 3, 4, 5, 6, 7, 8, 10, unknown",,,FALSE,Breast Cancer Tier 3,,,
Prior Invasive Breast Disease,Text term to indicate prior invasive breast condition in the participant,"DCIS, LCIS, Invasive breast cancer (unrelated to the current cancer), Other, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma ER Status Percentage Value,A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer,,,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma PR Status Percentage Value,A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer,,,,FALSE,Breast Cancer Tier 3,,,
HER2 Breast Carcinoma Copy Number Total,"Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.",,,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma Centromere 17 Copy Number,"Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.",,,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma HER2 Centromere17 Copynumber Total,Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer,,,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma HER2 Chromosome17 Ratio,HER2 chromosome 17 ratio in participants with breast cancer,,,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma Surgical Procedure Name,Text name of a surgical procedure performed for a person with a diagnosis of breast cancer,"Lumpectomy, Radical mastectomy, Modified radical mastectomy, Other, Partial mastectomy, Re-excision, Simple mastectomy, Surgery not performed, unknown",,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma HER2 Ratio Diagnosis,HER2 ratio of the participant at diagnosis,,,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma HER2 Status,Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer,"Positive, Negative, Amplified, Non-amplified, Equivocal, Indeterminate, Not Performed, unknown",,,FALSE,Breast Cancer Tier 3,,,
Hormone Therapy Breast Cancer Prevention Indicator,Did the patient receive hormonal therapy for prevention of breast cancer?,"Yes, No, unknown, Not Applicable",,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma ER Staining Intensity,Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown",,,FALSE,Breast Cancer Tier 3,,,
Breast Carcinoma PR Staining Intensity,Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown",,,FALSE,Breast Cancer Tier 3,,,
Oncotype Score,OncotypeDX recurrence score,,,,FALSE,Breast Cancer Tier 3,,,
Breast Imaging Performed Type,"The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).","Mammogram, Ultrasound, MRI, PET/CT, CT, Multiple imaging modalities, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
Multifocal Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.,"Yes, No, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
Multicentric Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.,"Yes, No, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
BIRADS Mammography Breast Density Category,The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.,"Predominantly fatty, Scattered fibroglandular densities, Heterogeneously dense, Extremely dense, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,,
CNS Tumor Primary Anatomic Site,Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2,"Thalamus, Ventricles, Intracranial/Leptomeningeal, Suprasellar/Hypothalamic/Pituitary, Cerebellar/Posterior fossa, Brain stem-Medulla, Brain stem-Midbrain/Tectum, Brainstem-Pons, Spinal cord-Cervical, Spinal cord-Thoracic, Spinal cord-Lumbar, Optic pathway, Other locations NOS, Paraspinal ganglion, Basal ganglia, Hippocampus, Meninges/Dura, Other lymph nodes",,,FALSE,Neuroblastoma and Glioma Tier 3,,,
Glioma Specific Metastasis Sites,Evidence of active brain metastasis including leptomeningeal involvement,"CSF, Spine, Bone marrow, Brain, Other, Leptomeningeal, Not Applicable",,,FALSE,Neuroblastoma and Glioma Tier 3,,,
Glioma Specific Radiation Field,A description of the location on or within the CNS where radiation was administered in a partcipant with glioma,"Craniospinal, Focal-tumor bed, unknown, Not Applicable",,,FALSE,Neuroblastoma and Glioma Tier 3,,,
Supra Tentorial Ependymoma Molecular Subgroup,Text term to identify the molecular subgroup in a supra tentorial ependymoma,"ST-EPN-RELA, ST-EPN-YAP1, unknown, Not Applicable",,,FALSE,Neuroblastoma and Glioma Tier 3,,,
Infra Tentorial Ependymoma Molecular Subgroup,Text term to identify the molecular subgroup in a infra tentorial ependymoma,"PF-EPN-A, PF-EPN-B, Myxopapillary ependymoma, unknown, Not Applicable",,,FALSE,Neuroblastoma and Glioma Tier 3,,,
Neuroblastoma MYCN Gene Amplification Status,Neuroblastoma MYCN amplification or over-expression status,"Amplified, Not amplified, Not done, unknown",,,FALSE,Neuroblastoma and Glioma Tier 3,,,
Specimen Blast Count Percentage Value,"The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis",,,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,,
NCI ALL Risk Group,The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.,"NCI High Risk, NCI Standard Risk, unknown",,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,,
MRD ALL Diagnostic Sensitivity,The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.,"Optimal, Suboptimal, Indeterminate, unknown",,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,,
CNS Leukemia Status,The status of central nervous system leukemia at the time of diagnosis.,"CNS 1, CNS 2, CNS 3, CNS 2a, CNS 2b, CNS 2c, CNS 3a, CNS 3b, CNS 3c, Not evaluated, unknown",,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,,
Ovarian Cancer Histologic Subtype,Text term to describe the histological subtype of ovarian cancer in the participant,"High-grade serous, Low-grade serous, High-grade endometrioid, Low-grade endometrioid, Clear cell, Mucinous, Sex-cord stromal, Germ cell, Other, unknown, Data not available",,,FALSE,Ovarian Cancer Tier 3,,,
Ovarian Cancer Surgical Outcome,Text term that describes the kind of surgical treatment administered.,"R0 resection,Optimal cytoreduction, Sub-optimal cytoreduction, Other, unknown, Data not available",,,FALSE,Ovarian Cancer Tier 3,,,
Ovarian Cancer Platinum Status,Text term to indicate the status of treatment with platinum in participant with ovarian cancer,"Platinum-refractory, Platinum-sensitive, Platinum-resistant, Data not available, unknown",,,FALSE,Ovarian Cancer Tier 3,,,
Location Extent Extraprostatic Extension,Location and extent of extraprostatic extension,"Left Anterior, Left Lateral, Left Posterolateral, Left Posterior, Left Apex, Left Mid, Left Base, Left Focal, Left Non-focal (established), Right Anterior, Right Lateral, Right Posterolateral, Right Posterior, Right Apex, Right Mid, Right Base, Right Focal, Right Non-focal (established), unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,,
Location Nature Positive Margins,Location and nature of positive margins,"Left Anterior, Left Lateral, Left Posterolateral, Left Posterior, Left Apex, Left Mid, Left Base, Left Focal, Left Extensive, Left Positive in an area of extraprostatic extension (EPE), Left Positive in an area of intraprostatic incision (II), Left Positive where it is difficult to distinguish EPE vs II, Right Anterior, Right Lateral, Right Posterolateral, Right Posterior, Right Apex, Right Mid, Right Base, Right Focal, Right Extensive, Right Positive in an area of extraprostatic extension (EPE), Right Positive in an area of intraprostatic incision (II), Right Positive where it is difficult to distinguish EPE vs II, Bladder neck (block PUM), Vas deferens, Apical margin (block DUM), unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,,
Seminal Vesicle Invasion,An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.,"None, Left, Right, Both sides, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,,
Prostate Carcinoma Histologic Type,The diagnostic subclassification of an invasive prostate carcinoma.,"Prostatic adenocarcinoma (conventional NOS), Prostatic duct adenocarcinoma, Acinar prostate mucinous (colloid) adenocarcinoma, Acinar prostate adenocarcinoma-signet-ring variant, Prostatic adenosquamous carcinoma, Acinar prostate mucinous adenocarcinoma, Prostatic small cell carcinoma, Acinar prostate adenocarcinoma-sarcomatoid variant, Undifferentiated carcinoma NOS, Other",,,FALSE,Prostate Cancer Tier 3,,,
Prostate Cancer Local Extent,The response used to categorize the local extent of disease for prostate cancer.,"Organ Confined, Extraprostatic extension, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,,
Additonal Findings Uninvolved Prostate,"Additional findings, uninvolved prostate","High-grade prostatic intraepithelial neoplasia (PIN), Inflammation, Benign prostatic hyperplasia (BPH), Prostatic Intraductal adenocarcinoma, Other, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,,
Prostate Cancer Cytologic Morphologic Subtypes,Text term that describes various morphological and cytological subtypes in protate tumors.,"prostatic basal cell hyperplasia, prostatic clear cell cribiform hyperplasia, prostatic atypical adenomatous hyperplasia (adenosis or AAH), Low grade prostatic intraepithelial neoplasia (PIN)/(PIN I), High grade prostatic intraepithelial neoplasia (HGPIN)/ (PIN II & PIN III), Other, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,,
Sarcoma Subtype,"The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.","Undifferentiated pleomorphic sarcoma, Leiomyosarcoma (uterine or extra-uterine), Other Synovial Sarcoma Or Malignant Peripheral Nerve Sheath Tumor Sarcoma, Gastrointestinal Stromal Tumor, Liposarcoma, undifferentiated pleomorphic sarcoma or malignant fibrous histiosarcoma, Other, unknown, Not Reported",,,FALSE,Sarcoma Tier 3,,,
Sarcoma Diagnosis Classification Category,"High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.","Bone Sarcoma, Musculoskeletal Sarcoma, Soft Tissue Sarcoma, unknown, Not Reported",,,FALSE,Sarcoma Tier 3,,,
Sarcoma Tumor Extension Type,The field to indicate the organs and structures to which the tumor has become adherent or has invaded.,"Extraosseous, Intracranial, Lymph nodes, Parameningeal, Thoracic cavity, Other, unknown, Not Reported",,,FALSE,Sarcoma Tier 3,,,
Pancreas Precancer Histopathologic Grade,The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.,"IPMN-Adenoma, IPMN-Borderline, IPMN-Carcinoma in situ, IPMN-Invasive carcinoma, PanIN 1, PanIN 1A, PanIN 1B, PanIN 2, PanIN 3, unknown, Not Reported",,,FALSE,Pancreatic Cancer Tier 3,,,
Pancreatic IPMN Pathology Epithelial Subtype,The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen,"Gastric Foveolar, Intestinal, Intraductal Tubopapillary, Pancreatobiliary, Oncocytic, Other, unknown, Not Reported",,,FALSE,Pancreatic Cancer Tier 3,,,
Pancreatic Duct Final Pathology Type,The final pathology result of the pancreatic duct communication type.,"Side-Branch, Main Duct, Mixed, Not Specified, None, Not Reported",,,FALSE,Pancreatic Cancer Tier 3,,,
Cutaneous Melanoma Tumor Infiltrating Lymphocytes,Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.,"Absent, Brisk, Nonbrisk, unknown",,,FALSE,Melanoma Tier 3,,,
Cutaneous Melanoma Tumor Regression Range,Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.,"Absent, Present involving 75% or more, Present involving less than 75%, unknown",,,FALSE,Melanoma Tier 3,,,
Melanoma Specimen Clark Level Value,Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.,"I, II, III, IV, V, No Source Documentation, unknown",,,FALSE,Melanoma Tier 3,,,
Cutaneous Melanoma Surgical Margins,Text term to indicate presence of tumor at resection margins,"Positive, Negative, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,,
Melanoma Lesion Size,"Diameter of lesion determined on skin examination (pre-bx), in mm",,,,FALSE,Melanoma Tier 3,,,
History of Atypical Nevi,Patient has a history of atypical nevi,"Yes (more than 50), Yes (less than 50), No, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,,
Fitzpatrick Skin Tone,The Fitzpatrick classification of skin phototype,"I, II, III, IV, V, VI, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,,
History of Chronic UV Exposure,History of chronic UV exposure,"Outdoor occupational, Outdoor recreational, Therapeutic, None, Not Reported",,,FALSE,Melanoma Tier 3,,,
History of Blistering Sunburn,Patient has history of blistering sunburn,"Yes, No, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,,
History of Tanning Bed Use,History of tanning bed use of the patient,"Never, Less than 10 times, 10-50 times, 50-100 times, More than 100 times, Not Reported",,,FALSE,Melanoma Tier 3,,,
Immediate Family History Melanoma,Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.,"Before age 50, Not before age 50, unknown",,,FALSE,Melanoma Tier 3,,,
Melanoma Biopsy Resection Sites,Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2),"skin of scalp, skin of eye lid, skin of nose, skin of lip, skin of ear, skin of neck, skin of other parts of face, skin of chest, skin of back, skin of abdomen, skin of trunk-other, skin of breast, skin of upper limb and shoulder, skin of palm, skin of lower limb and hip, skin of sole, skin of penis, skin of scrotum, skin of vulva, skin other, skin NOS, Not Reported",,,FALSE,Melanoma Tier 3,,,
Cutaneous Melanoma Ulceration,Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.,"Absent, Present, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,,
Cutaneous Melanoma Additional Findings,Significant pathologic finding present in addition to the cutaneous melanoma.,"Actinic Keratosis, Nevus Remnant, Solar Elastosis, Fibrosing Regression, Nesting Melanoma, Pagetoid Spread, Vascular Proliferation, Other, unknown, Not Applicable",,,FALSE,Melanoma Tier 3,,,
HTAN RPPA Antibody Table ID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,,,,TRUE,HTAN RPPA Antibody Table,,,
Ab Name Reported on Dataset,The antibody name.,,,,TRUE,HTAN RPPA Antibody Table,,,
GENCODE Gene Symbol Target,The comma separated list of gene symbols targeted by the antibody.,,,,TRUE,HTAN RPPA Antibody Table,,,
UNIPROT Protein ID Target,The comma separated list of UNIPROT IDs targeted by the antibody.,,,,TRUE,HTAN RPPA Antibody Table,,,
Phosphoprotein Flag,A flag the denotes if an antibody targets a phosphoprotein.,"True, False",,,TRUE,HTAN RPPA Antibody Table,,,
Internal Ab ID,Internal lab ID for an antibody.,,,,TRUE,HTAN RPPA Antibody Table,,,
Species,Host animal.,"Mouse, Rabbit, Goat",,,TRUE,HTAN RPPA Antibody Table,,,
RPPA Dilution,The dilution ratio.,,,,FALSE,HTAN RPPA Antibody Table,,,
Phospho Site,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),,Phosphoprotein Flag,,FALSE,HTAN RPPA Antibody Table,,,
RPPA Validation Status,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),"Valid, Use with Caution, Under Evaluation, Used for QC",,,FALSE,HTAN RPPA Antibody Table,,,
Antibody Notes,Notes on antibodies replacements and antibody recognition observations.,,,,FALSE,HTAN RPPA Antibody Table,,,
Pre-processing Completed,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,"Illumination correction, Tile Stitching, Channel/Cycle Registration, TMA de-arraying, None, Other",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Pre-processing Required,Pre-processing steps required to convert level 1 raw data to a single level 2 image,"Illumination correction, Tile Stitching, Channel/Cycle Registration, TMA de-arraying, None, Other",,,TRUE,Imaging,,https://www.miti-consortium.org/,
Publication,An empty parent attribute for publications,,,,FALSE,,,,
Publication Manifest,Publication specific attributes.,,"Component,Publication-associated HTAN Parent Data File ID, HTAN Grant ID, HTAN Center ID, Publication Content Type, DOI, Title, Authors, Corresponding Author, Corresponding Author ORCID, Year of Publication, Location of Publication, Publication Abstract, License, PMID, Publication contains HTAN ID, Data Type, Tool, Supporting Link, Supporting Link Description",,FALSE,Publication,,,
Publication-associated HTAN Parent Data File ID,HTAN Data File Identifier(s) of the files associated with the content presented/published. Should be comma-separated lists.,,,,TRUE,Publication,,,list like
HTAN Grant ID,HTAN grant number(s) (i.e. CA------ format) associated with the content presented/published.,,,,TRUE,Publication,,,list like
HTAN Center ID,List of HTAN Center ID(s) associated with the content presented/published.,"HTA1, HTA2, HTA3, HTA4, HTA5, HTA6, HTA7, HTA8, HTA9, HTA10, HTA11, HTA12, HTA13, HTA14,HTA15,HTA16",,,TRUE,Publication,,,list like
Publication Content Type,The type of content presented or published.,"Preprint, Published manuscript, Conference proceedings",,,TRUE,Publication,,,
DOI,The digital object identifier (DOI) of the content in the form of https://www.doi.org/{doi} to comply with CrossRef DOI display guidelines.,,,,TRUE,Publication,,https://www.doi.org/,url
Corresponding Author,"The name(s) of the corresponding author(s) of the content presented/published. If more than one corresponding author, please list in the order they appear in the author list.",,,,TRUE,Publication,,,
Corresponding Author ORCID,"The ORCiD(s) of the corresponding author(s) of the content presented/published. Should be a valid ORCiD url starting with https://orcid.org/ followed by a 16 digit identifier in dash separated groups of 4 (for example https://orcid.org/0000-0002-1825-0097). If more than one corresponding author, please list ORCiDs in the order the authors appear in the author list.",,,,TRUE,Publication,,https://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier,
Title,The title of the content presented or published.,,,,TRUE,Publication,,,
Authors,"The names of the author(s) of the content presented/published, in the order they appear.",,,,TRUE,Publication,,,
Year of Publication,The year the content was presented or published (format YYYY).,,,,TRUE,Publication,,,regex search ^(19|20)\d{2}$
Location of Publication,"The name of the preprint server, journal, or conference where the content was presented/published.",,,,TRUE,Publication,,,
Publication Abstract,The abstract or short description of the content presented/published.,,,,TRUE,Publication,,,
License,The type of license applicable to the content.,"0BSD, AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement, Proprietary, Other, Not licensed, Freeware",,,FALSE,Publication,,,list like
PMID,The PubMed identifier associated with the publication (applicable to published manuscripts). Provide as a URL of the form https://pubmed.ncbi.nlm.nih.gov/{pmid},,,,FALSE,Publication,,,url
Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,,list like
Other Data Type Specified,Other types of data associated with the content.,,,,FALSE,Publication,,,list like
Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url warning
Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,,
Tool,Were any software or computational tools generated for this content,"Yes, No",,,TRUE,Publication,,,
Accessory Data Type,Accesory specific data type,,,,FALSE,,,,
Accessory,An empty parent attribute for accessory ,,,,FALSE,,,,
Accessory Manifest,Accessory specific attributes,,"Component,Dataset Name,Accessory Synapse ID,Accessory Description, Accessory Data Type,HTAN Center ID,HTAN Parent Biospecimen ID,Accessory-associated HTAN Parent Data File ID",,FALSE,Accessory,,,
Dataset Name,Name of a dataset (e.g. a Synapse folder),,,,TRUE,Accessory,,,
Accessory Synapse ID,Synapse ID of folder containing accessory files,,,,TRUE,Accessory,,,regex match syn\d+
Accessory Description,Free text field containing description of accessory file(s),,,,TRUE,Accessory,,,
Accessory-associated HTAN Parent Data File ID,HTAN Data File Identifier(s) of the files associated with the accessory content. Should be comma-separated lists.,,,,FALSE,Accessory,,,list like
MapQ30,Number of reads with Quality >= 30.,,,,FALSE,"scATAC-seq Level 1, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
scATAC-seq Object ID,Orig.Ident or scATAC-seq Object ID,,,,FALSE,scATAC-seq Level 3,,,
nCount Peaks,Total number of fragments in peaks,,,,FALSE,scATAC-seq Level 2,,,
nFeature Peaks,Number of peaks with at least one read,,,,FALSE,scATAC-seq Level 2,,,
Total Read-Pairs,Total read-pairs,,,,FALSE,scATAC-seq Level 2,,,
Duplicate Read-Pairs,Number of duplicate read-pairs,,,,FALSE,scATAC-seq Level 2,,,
Chimeric Read-Pairs,Number of chimerically mapped read-pairs,,,,FALSE,scATAC-seq Level 2,,,
Unmapped Read-Pairs,Number of read-pairs with at least one end not mapped,,,,FALSE,scATAC-seq Level 2,,,
LowMapQ,Number of read-pairs with <30 mapq on at least one end,,,,FALSE,scATAC-seq Level 2,,,
Mitochondrial Read-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,,,,FALSE,scATAC-seq Level 2,,,
Passed Filters,"Number of non-duplicate, usable read-pairs i.e. fragments",,,,FALSE,scATAC-seq Level 2,,,
TSS Fragments,Number of fragments overlapping with TSS regions,,,,FALSE,scATAC-seq Level 2,,,
DNase Sensitive Region Fragments,Number of fragments overlapping with DNase sensitive regions,,,,FALSE,scATAC-seq Level 2,,,
Enhancer Region Fragments,Number of fragments overlapping enhancer regions,,,,FALSE,scATAC-seq Level 2,,,
Promoter Region Fragments,Number of fragments overlapping promoter regions,,,,FALSE,scATAC-seq Level 2,,,
On Target Fragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",,,,FALSE,scATAC-seq Level 2,,,
Blacklist Region Fragments,Number of fragments overlapping blacklisted regions,,,,FALSE,scATAC-seq Level 2,,,
Peak Region Fragments,Number of fragments overlapping peaks,,,,FALSE,scATAC-seq Level 2,,,
Peak Region Cutsites,Number of ends of fragments in peak regions,,,,FALSE,scATAC-seq Level 2,,,
Nucleosome Signal,"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-seq Level 2,,,
Nucleosome Percentile,Percentile rank of nucleosome score,,,,FALSE,scATAC-seq Level 2,,,
TSS Enrichment,Transcription start site (TSS) enrichment score,,,,FALSE,scATAC-seq Level 2,,,
TSS Percentile,Percentile rank of TSS score,,,,FALSE,scATAC-seq Level 2,,,
Pct Reads in Peaks,Percentage of reads in peaks,,,,FALSE,scATAC-seq Level 2,,,
Blacklist Ratio,Ratio of reads in blacklist regions,,,,FALSE,scATAC-seq Level 2,,,
Seurat Clusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,,,,FALSE,scATAC-seq Level 2,,,
nCount RNA,Total number of fragments in genes,,,,FALSE,scATAC-seq Level 2,,,
nFeature RNA,Number of genes detected in cell,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Seqnames,Chromosome id,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Start,Genomic starting position in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 End,Genomic ending position in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Width,Width of the peak in bases in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Strand,DNA stand aligned with in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Name,Name of the peak in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Score,Peak score (proportional to q-value) in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Fold Change,Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Neg Log10 pvalue Summit,Negative log10 p-value for the peak summit in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Neg Log10 qvalue Summit,Negative log10 q-value for the peak summit in MACS2,,,,FALSE,scATAC-seq Level 2,,,
MACS2 Relative Summit Position,Position of the peak summit related to the start position in MACS2,,,,FALSE,scATAC-seq Level 2,,,
Is lowest level,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,"Yes - Is lowest level,No",,,FALSE,scRNA-seq Level 2,,,
Yes - Is lowest level,If manifest is lowest level require HTAN Parent Biospecimen ID,,HTAN Parent Biospecimen ID,,FALSE,scRNA-seq Level 2,,,
Normalization Method,Description of Normalization Process,,,,FALSE,RPPA Level 2,,,
Batch Correction Method,Method that was used to batch correct Level 3 data,,,,FALSE,RPPA Level 3,,,
MS Batch ID,Batch ID indicating a set of samples that were run together.,,,,TRUE,Mass Spectrometry Level 1,,,
MS-based Assay Type,Analytes are the target molecules being measured with the assay.,"LC-MS,MS,TMT,LC-MS/MS",,,TRUE,Mass Spectrometry Level 1,,,
MS-based Targeted,Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.,"Targeted,Untargeted",,,TRUE,Mass Spectrometry Level 1,,,
MS Instrument Vendor and Model,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,Mass Spectrometry Level 1,,,
MS Source,"The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)","MALDI, MALDI-2, DESI, SIMS, nESI, Other",,,TRUE,Mass Spectrometry Level 1,,,
Polarity,The polarity of the mass analysis (positive or negative ion modes),"positive,negative",,,TRUE,Mass Spectrometry Level 1,,,
Mass Range Low Value,The low value of the scanned mass range for MS1 in m/z.,,,,TRUE,Mass Spectrometry Level 1,,,
Mass Range High Value,The high value of the scanned mass range for MS1 in m/z.,,,,TRUE,Mass Spectrometry Level 1,,,
Data Collection Mode,Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.,"DDA,DIA,Other",,,TRUE,Mass Spectrometry Level 1,,,
MS Scan Mode,"Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)","MS, MS/MS, MS3, other",,,TRUE,Mass Spectrometry Level 1,,,
MS Labeling,"Indicates whether samples were labeled prior to MS analysis (e.g., TMT)",,,,TRUE,Mass Spectrometry Level 1,,,
LC Instrument Vendor and Model,The manufacturer of the instrument used for LC.,,,,TRUE,Mass Spectrometry Level 1,,,
LC Column Vendor and Model,"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,Mass Spectrometry Level 1,,,
LC Resin,"Details of the resin used for lc, including vendor, particle size, pore size",,,,TRUE,Mass Spectrometry Level 1,,,
LC Length Value,LC column length in cm.,,,,TRUE,Mass Spectrometry Level 1,,,
LC Temp Value,LC temperature in C.,,,,TRUE,Mass Spectrometry Level 1,,,
LC ID Value,LC column inner diameter in microns.,,,,TRUE,Mass Spectrometry Level 1,,,
LC Flow Rate,LC flow rate in nL/min.,,,,TRUE,Mass Spectrometry Level 1,,,
LC Gradient,The program dictates the mobile phase solvent composition over the course of the chromatographic run.,,,,TRUE,Mass Spectrometry Level 1,,,
LC Mobile Phase A,Composition of mobile phase A,,,,TRUE,Mass Spectrometry Level 1,,,
LC Mobile Phase B,Composition of mobile phase B,,,,TRUE,Mass Spectrometry Level 1,,,
MS Instrument Metadata File,Additional file containing instrument metadata details. Use either synapse_path or entity_Id,,,,FALSE,Mass Spectrometry Level 1,,,
Bisulfite Conversion,Name of the kit used in bisulfite conversion.,"Zimo EZ DNA Methylation Kit, Zimo EZ-96 DNA Methylation Shallow Kit, Zimo EZ-96 DNA Methylation Deep Kit, NEBNext Enzymatic Methyl-seq Kit, Agilent SureSelectXT Methyl-Seq",,,TRUE,Bulk Methylation-seq Level 1,,,
Replicate Type,A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.,"Technical replicate, Biological replicate, Not Applicable",,,TRUE,Sequencing,,,
Bulk Methylation Assay Type,Assay types normally determine genomic coverage,"Whole genome, Targeted Genome, Beadchip Array ","Targeted Genome, Beadchip Array",,TRUE,Bulk Methylation-seq Level 1,,,
Targeted Genome,Assay for analyzing specific mutations in a given sample,"MeDIP, RRBS",,,FALSE,Bulk Methylation Assay Type,,,
Beadchip Array,Assay that uses beads to target a specific locus on the genome.,"HM27K, HM450K",,,FALSE,Bulk Methylation Assay Type,,,
Total DNA Input,"Overall number of reads for a given sample in digits (microgram, nanogram).",,,,FALSE,Bulk Methylation Assay Type,,,
Trimmer,Software used for trimming,"FASTX toolkit, SolexaQA, Btrim, Cutadapt, Kraken, PRINSEQ, Adapter removal, Trim Galore!, ConDeTri, ERNE-FILTER, Trimmo-matic",,,TRUE,Bulk Methylation-seq Level 2,,,
Bulk Methylation Genomic Reference,The human genome reference used in the alignment of reads,"HG19, HG38, T2T CHM13",,,TRUE,Bulk Methylation-seq Level 2,,,
Duplicate Removal Software,Software used for remove duplicate reads,"Samtools sort, picard MarkDuplicates",,,TRUE,Bulk Methylation-seq Level 2,,,
Proportion of Minimum CpG Coverage 10X,"Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.",,,,FALSE,Bulk Methylation-seq Level 2,,,
DMC Calling Tool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),"MethylKit, BSmooth, BiSeq, MethylSig, DSS, MOABS, DSS-single, metilene, MACAU, MethylDackel",,,TRUE,Bulk Methylation-seq Level 3,,,
DMC Calling Workflow URL,Generic name for the workflow used to analyze a data set,,,,TRUE,Bulk Methylation-seq Level 3,,,url
DMR Calling Tool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),"MethylKit, BSmooth, BiSeq, MethylSig, DSS, MOABS, DSS-single, metilene, MACAU",,,TRUE,Bulk Methylation-seq Level 3,,,
DMR Calling Workflow URL,Generic name for the workflow used to analyze a data set,,,,TRUE,Bulk Methylation-seq Level 3,,,url
pUC19 methylation ratio,"Methylation ratio of mostly methylated pUC19 control, as a percentage",,,,TRUE,Bulk Methylation-seq Level 3,,,
Lambda methylation ratio,"Methylation ratio of mostly unmethylated lambda control, as a percentage",,,,TRUE,Bulk Methylation-seq Level 3,,,
DMC data file format,Format of the data files,"BED, bedGraph",,,TRUE,Bulk Methylation-seq Level 3,,,
DMR data file Format,Format of the data files.,"BED, bedGraph",,,TRUE,Bulk Methylation-seq Level 3,,,
MS Assay Category,Type of Mass Spectrometry performed.,,,,TRUE,Mass Spectrometry Level 2,,,
Publication contains HTAN ID,HTAN IDs are used in the publication.,"Yes, No",,,TRUE,Publication,,,
Electron Microscopy Level 1,Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montage,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, EM method, EM signal or contrast mech, EM instrument, Protocol Link, Software and Version, SizeX, SizeY, SizeC, SizeZ, PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ, EM dwell or exposure time,EM voltage, EM beam current, EM spot size, EM stage tilt, EM signal processing, EM contrast type",,FALSE,Assay,Biospecimen,,
Electron Microscopy Level 2,Processed electron microscopy data as one OME-TIFF image per plane or montage,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID,Tile overlap X, Tile overlap Y,EM contrast type",,FALSE,Assay,Electron Microscopy Level 1,,
Electron Microscopy Level 3,Segmented electron microscopy data as .am or .tiff formats,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Imaging Object Class",,FALSE,Assay,Electron Microscopy Level 2,,
Electron Microscopy Level 4,Movies or other derived files from electron microscopy data,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Comment",,FALSE,Assay,Electron Microscopy Level 3,,
EM instrument,Make and model of the EM instrument used,,,,TRUE,Electron Microscopy Level 1,,,str
EM method,Electron microscopy method used,"SEM, FIB-SEM, SBF-SEM, AT, TEM, ET, cryo ET, ssTEM",,,TRUE,Electron Microscopy Level 1,,,
EM signal or contrast mech,How the electron microscopy signal is generated from the sample,"BSE, SE, phase, bright-field, dark-field",,,TRUE,Electron Microscopy Level 1,,,
EM dwell or exposure time,Duration in microseconds (µs) of electron beam data collection per pixel or frame,,,,FALSE,Electron Microscopy Level 1,,,num
EM voltage,Accelerating voltage in kiloelectronvolts (keV),,,,FALSE,Electron Microscopy Level 1,,,num
EM beam current,Beam current in nanoamps (nA),,,,FALSE,Electron Microscopy Level 1,,,num 
EM spot size,Beam spot size in micrometers (µm),,,,FALSE,Electron Microscopy Level 1,,,num 
EM stage tilt,Physical stage tilt in degrees with respect to the electron beam,,,,FALSE,Electron Microscopy Level 1,,,num
EM signal processing,SNR improvement strategies used,"None, line integration, frame integration, frame averaging",,,FALSE,Electron Microscopy Level 1,,,
EM contrast type,Does the image use standard SEM contrast or TEM contrast,"SEM,TEM",,,FALSE,Electron Microscopy Level 1,,,
Tile overlap X,Percentage of image overlap to allow tile stitching in x direction,,,,TRUE,Electron Microscopy Level 1,,,num
Tile overlap Y,Percentage of image overlap to allow tile stitching in x direction,,,,TRUE,Electron Microscopy Level 1,,,num
Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophagus goblet cells.,"Yes, No",,,FALSE,Follow Up,,,
Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num
HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,,
Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,,
Associated mRNA Library Data File ID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,Multiplexed CITE-seq Level 1,,,
Single Cell Barcode Method Applied,The method by which cells are multiplex or labeled with cell surface markers or probes,"Cite-seq custom panel,Biolegend Total seq A Custom,Biolegend Total seq B Custom,Biolegend Total seq C Custom,Biolegend Total seq A Human,Universal cocktail V1.0,Biolegend Total seq B Human Universal cocktail V1.0,Biolegend Total seq C Human Universal cocktail V1.0,Cell,Hashtag- multiplex,Nuclear Hashtag- multiplex,Other",,,TRUE,Multiplexed CITE-seq Level 1,,,
Feature Barcode Library Type,The library construction methods for the feature barcode library,"10x ADT – citeseq/hashing,10x TCR,10x BCR",,,TRUE,Multiplexed CITE-seq Level 1,,,
Barcode Folder Synapse ID,Synapse ID of the folder containing the barcode lists,,,,TRUE,Multiplexed CITE-seq Level 1,,,
Barcode Folder File List,A comma separated list of filenames in the gzipped folder detailing what barcodes are specific to demultiplexing samples versus providing surface protein data,,,,TRUE,Multiplexed CITE-seq Level 1,,,
Microarray Platform ID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,,,,TRUE,Microarray Level 1,,,regex match GPL\d+
Microarray Molecule,Microarray is measuring this kind of molecule,"DNA, RNA",,,TRUE,Microarray Level 1,,,
Microarray Label,Microarray used this kind of label,,,,TRUE,Microarray Level 1,,,
Microarray Value Definition,What the provided value signifies,,,,TRUE,Microarray Level 1,,,
Microarray Protocol Auxiliary File,"Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).",,,,TRUE,Microarray Level 1,,,regex match syn\d+
Participant Vital Status Update,Updates to a participants vital status,,"Component, HTAN Participant ID, Vital Status",,FALSE,Patient,,,
Precancer Diagnosis,Diagnosis of a precancerous condition,,"Component, HTAN Participant ID, Precancer Case",,FALSE,Patient,,,
Alive,This indicates the participant is alive and defines further required metadata,,Days to Vital Status Reference,,FALSE,Patient,,,
Days to Vital Status Reference,Number of days between the date used for index and the reference date for designation of vital status,,,,TRUE,Patient,,,int
Precancer Case,Yes/No indicator to designate the participant for whom precancerous lesion(s) was identified (premalignancy only).,"Yes - Precancer Case, No, Not Reported, unknown",,,TRUE,Patient,,,
Yes - Precancer Case,Indicates that the participant is a precancer case,,"Precancerous Condition Type, Days to Precancer Case Designation, WHO Precursor Lesion Code",,FALSE,Patient,,,
Days to Precancer Case Designation,Number of days between the date used for index and the reference date for designation of precancer status.,,,,FALSE,Patient,,,int
WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$