From c1f779ec74b9b581dfa6eac05a008b846c187ed2 Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 23 Mar 2026 16:31:54 +0000 Subject: [PATCH 1/7] Edits ARC to pass test_skip_logic_presets In most cases, involves adding in housekeeping variables which were missing. --- ARC.csv | 54 ++++++++++++++++++++-------------------- tests/test_skip_logic.py | 54 ++++++++++++++++++++++++++++++++-------- 2 files changed, 71 insertions(+), 37 deletions(-) diff --git a/ARC.csv b/ARC.csv index e4a2e74..bba9b4c 100644 --- a/ARC.csv +++ b/ARC.csv @@ -42,8 +42,8 @@ presentation,DEMOGRAPHICS,demog_birthknow,radio,Is the date of birth known?,"1, presentation,DEMOGRAPHICS,demog_birthdate,date_dmy,Date of birth,,date_dmy,,today,,[demog_birthknow]='1',,This refers to the calendar date on which the patient was born.,Enter the participant's date of birth. (Use the format DD/MM/YYYY),SNOMED,"184099003, Date of birth (observable entity)","C0421451, Patient date of birth",1,risk_factor_demo,1,1,1,1,1,1,1,1,,,,, presentation,DEMOGRAPHICS,demog_age,number,Age,,number,0,150,,[demog_birthknow]='0',,This refers to the patient's age.,"For participants over the age of two years, please report age in years. For children under the age of two years, please report in months. For neonates below the age of one month, please report in days.",SNOMED,"424144002, Current chronological age (observable entity)",,,risk_factor_demo,1,1,1,1,1,1,1,1,,,,, presentation,DEMOGRAPHICS,demog_age_units,radio,Age units,"1, Years | 2, Months | 3, Days",,,,,[demog_birthknow]='0',,This refers to the patient's age at presentation to the health facility.,Select the most appropriate units for age.,SNOMED,"424144002, Current chronological age (observable entity)",,,risk_factor_demo,1,1,1,1,1,1,1,1,,,,, -presentation,DEMOGRAPHICS,demog_calcage_days,calc,Calculated Age (days),"if([demog_birthknow]='1',datediff([demog_birthdate],[pres_date],""d""),if([demog_age_units]='1',[demog_age]*365,if([demog_age_units]='2',round([demog_age]*365/12,0),if([demog_age_units]='3',[demog_age],''))))",,,,,,,This refers to the patient's age in days.,"Age is calculated, if the date of birth is known, as the difference between the date of birth and the most recent date of presentation or admission to the facility.",SNOMED,"424144002, Current chronological age (observable entity)",,,risk_factor_demo,1,1,1,1,1,1,,1,,,,, -presentation,DEMOGRAPHICS,demog_sex,radio,Sex at birth,"1, Male | 2, Female | 99, Not specified/Unknown | 88, Other",,,,,,,This refers to the physical sexual characteristics at birth.,Select the most appropriate option that represents the physical sexual characteristics at birth.,SNOMED,"281053000, Sex of baby at delivery (observable entity)",,,risk_factor_demo,1,1,1,1,1,1,1,,,,,, +presentation,DEMOGRAPHICS,demog_calcage_days,calc,Calculated Age (days),"if([demog_birthknow]='1',datediff([demog_birthdate],[pres_date],""d""),if([demog_age_units]='1',[demog_age]*365,if([demog_age_units]='2',round([demog_age]*365/12,0),if([demog_age_units]='3',[demog_age],''))))",,,,,,,This refers to the patient's age in days.,"Age is calculated, if the date of birth is known, as the difference between the date of birth and the most recent date of presentation or admission to the facility.",SNOMED,"424144002, Current chronological age (observable entity)",,,risk_factor_demo,1,1,1,1,1,1,1,1,,,1,1,1 +presentation,DEMOGRAPHICS,demog_sex,radio,Sex at birth,"1, Male | 2, Female | 99, Not specified/Unknown | 88, Other",,,,,,,This refers to the physical sexual characteristics at birth.,Select the most appropriate option that represents the physical sexual characteristics at birth.,SNOMED,"281053000, Sex of baby at delivery (observable entity)",,,risk_factor_demo,1,1,1,1,1,1,1,,,,,1,1 presentation,DEMOGRAPHICS,demog_sex_oth,text,Specify other sex at birth,,,,,,[demog_sex]='88',,This refers to the physical sexual characteristics at birth.,"If 'Other', specify the physical sexual characteristics at birth.",SNOMED,"281053000, Sex of baby at delivery (observable entity)",,,risk_factor_demo,1,1,,1,1,1,1,,,,,, presentation,DEMOGRAPHICS,demog_gender,radio,Gender,"1, Male | 2, Female | 3, Non-binary | 99, Unknown | 88, Other",,,,,[demog_calcage_days]>3650,,"This refers to a person's internally held sense of their gender, which may or may not correspond to the individual's genotypic or phenotypic sex.",Select the most appropriate option that represents the patient's gender identity.,SNOMED,"263495000, Gender (observable entity)","C0079399, Gender",,,1,1,1,1,1,1,1,,,,,, presentation,DEMOGRAPHICS,demog_gender_oth,text,Specify other gender,,,,,,[demog_gender]='88',,"This refers to a person's internally held sense of their gender, which may or may not correspond to the individual's genotypic or phenotypic sex.",If 'Other' specify patient's gender identity.,SNOMED,"263495000, Gender (observable entity)","C0079399, Gender",,,1,1,1,1,1,1,1,,,,,, @@ -68,7 +68,7 @@ presentation,DEMOGRAPHICS,demog_residence,radio,Patient's city of residence,"1, presentation,DEMOGRAPHICS,demog_residence_oth,text,"If different from health case facility, specify the patient's region of residence.",,,,,,[demog_residence]='2',,This refers to the city which a person dwells more than temporarily or lives permanently.,"If 'Different from health case facility', specify the patient's region of residence.",SNOMED,"433178008, City of residence (observable entity)","C2316883, City of residence",,risk_factor_socio,,,1,,,,1,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_travel,radio,Did the patient travel outside of their home region in the past 14 days?,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to travel to another city/town or region, another part of the country or abroad to another country within 14 days before symptoms relating to the current illness began.","Indicate 'Yes', if the patient travelled to another city/town or region, another part of the country or abroad to another country within 14 days before symptoms relating to the current illness began.",SNOMED,"129018004, Traveling (observable entity)","C0040802, travel",,,,,1,,,,1,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_travel_loc,notes,specify all city / cities or town(s) and region(s) of travel,,,,,,[expo14_travel] = '1',,"This refers to all city / cities or town(s) and region(s), which the patient travelled to within 14 days before symptoms relating to the current illness began.","If the patient has travelled away from their usual place of residence within 14 days of symptom onset, enter the location(s) that were visited.",,,,,,,,1,,,,1,,,,,, -presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_yn,radio,History of contact with suspected or confirmed human case of same pathogen?,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to the patient having a history of contact with anyone presenting with similar symptoms or with known confirmed case, or with contaminated material from a suspected or confirmed case (e.g. body fluids, objects, bedding etc.).","Indicate 'Yes', if the patient has a history of contact with anyone presenting with similar symptoms or with known confirmed case, or with contaminated material from a suspected or confirmed case (e.g. body fluids, objects, bedding etc.).",,,,,,,1,,1,1,1,1,,,,,, +presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_yn,radio,History of contact with suspected or confirmed human case of same pathogen?,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to the patient having a history of contact with anyone presenting with similar symptoms or with known confirmed case, or with contaminated material from a suspected or confirmed case (e.g. body fluids, objects, bedding etc.).","Indicate 'Yes', if the patient has a history of contact with anyone presenting with similar symptoms or with known confirmed case, or with contaminated material from a suspected or confirmed case (e.g. body fluids, objects, bedding etc.).",,,,,,,1,,1,1,1,1,,,,,1, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_typecomm,radio,Community contact,"1, Yes | 0, No | 99, Unknown",,,,,[expo14_yn]='1',,This refers to the mode of exposure to a suspected or confirmed case. Community contact refers to exposure event outside of healthcare setting.,Indicate 'Yes' if the patient experienced this mode of exposure to a suspected or confirmed human case.,SNOMED,"277057000, Community acquired (qualifier value) | 1290740005, Vertical transmission (qualifier value) | 8098009, Sexually transmitted infectious disease (disorder)","C5392207, Community Transmission | C0242648, Vertical Disease Transmission | C0036916, Sexually Transmitted Diseases",,,,,,1,1,,,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_typevert,radio,Vertical transmission,"1, Yes | 0, No | 99, Unknown",,,,,[expo14_yn]='1' and [demog_calcage_days]<365,,This refers to the mode of exposure to a suspected or confirmed case. Vertical transmission refers to transmission from mother-to-child.,Indicate 'Yes' if the patient experienced this mode of exposure to a suspected or confirmed human case.,SNOMED,"277057000, Community acquired (qualifier value) | 1290740005, Vertical transmission (qualifier value) | 8098009, Sexually transmitted infectious disease (disorder)","C5392207, Community Transmission | C0242648, Vertical Disease Transmission | C0036916, Sexually Transmitted Diseases",,,,,,1,1,,,,,,,1, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_typehcw,radio,Healthcare worker exposure,"1, Yes | 0, No | 99, Unknown",,,,,[expo14_yn]='1' and [demog_calcage_days]>5840,,This refers to the mode of exposure to a suspected or confirmed case. Healthcare worker exposure refers to an exposure event in a healthcare setting.,Indicate 'Yes' if the patient experienced this mode of exposure to a suspected or confirmed human case.,SNOMED,"277057000, Community acquired (qualifier value) | 1290740005, Vertical transmission (qualifier value) | 8098009, Sexually transmitted infectious disease (disorder)","C5392207, Community Transmission | C0242648, Vertical Disease Transmission | C0036916, Sexually Transmitted Diseases",,,,,,1,1,,,,,,,, @@ -80,7 +80,7 @@ presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_typeoth_spec,text,Speci presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_date,date_dmy,Date of contact with suspected or confirmed case,,date_dmy,,today,,[expo14_yn]='1',,"This refers to the date of contact with anyone presenting with similar symptoms or with known confirmed case, or with contaminated material from a suspected or confirmed case (e.g. body fluids, objects, bedding etc.).",Enter the date of contact with suspected or confirmed human case. (Use the format DD/MM/YYYY),,,,,,,1,,1,1,1,,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_setting,radio,Contact setting,"1, Household | 2, Occupational | 4, Healthcare facility | 99, Unknown | 88, Other",,,,,,,This refers to the environment within which the person may have come into contact with a suspected or confirmed case.,Select the most appropriate option that represents the contact setting with a confirmed or suspected human case.,,,,,,,1,,,,1,,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_setting_oth,text,Specify other contact setting,,,,,,[expo14_setting]='88',,This refers to the environment within which the person may have come into contact with a suspected or confirmed case.,"If 'Other', specify the contact setting with a confirmed or suspected case.",,,,,,,1,,,,1,,,,,,, -presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_ancon,radio,"Any contact with animals, animal homes, meats or other animal products in the last 14 days?","1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to contact with animals, animal homes, meats or other animal products which occurred in the last 14 days.","Indicate 'Yes' if the patient was in contact with animals, animal homes, meats or other animal products which occurred in the last 14 days.",,,,,,,1,,,1,1,1,,,,,, +presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_ancon,radio,"Any contact with animals, animal homes, meats or other animal products in the last 14 days?","1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to contact with animals, animal homes, meats or other animal products which occurred in the last 14 days.","Indicate 'Yes' if the patient was in contact with animals, animal homes, meats or other animal products which occurred in the last 14 days.",,,,,,,1,,1,1,1,1,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_ancon_date,date_dmy,Date of contact with suspected or confirmed animal source,,date_dmy,,today,,[expo14_ancon]='1',,"This refers to the date of contact with animals, animal homes, meats or other animal products which occurred in the last 14 days.","Enter the date of contact with animals, animal homes, meats or other animal products which occurred in the last 14 days. (Use the format DD/MM/YYYY)",,,,,,,1,,,,1,1,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_ancon_lstock,radio,Contact with livestock,"1, Yes | 0, No | 99, Unknown",,,,,[expo14_ancon]='1',,"This refers to contact with live bird (e.g. chickens, turkeys, ducks) which occurred in the last 14 days.",Indicate 'Yes' if the patient experienced this in the last 14 days.,,,,,,,1,,,,1,,,,,,, presentation,EXPOSURE HISTORY IN PREVIOUS 14 DAYS,expo14_ancon_lstock_bird,radio,"Contact with poultry or other birds(e.g. chickens, turkeys, ducks, exotic birds)","1, Yes | 0, No | 99, Unknown",,,,,[expo14_ancon_lstock] = '1',,"This refers to contact with live bird (e.g. chickens, turkeys, ducks) which occurred in the last 14 days.",Indicate 'Yes' if the patient experienced this in the last 14 days.,,,,,,,1,,,,1,,,,,,, @@ -366,7 +366,7 @@ presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from ons presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_abdpain,radio,Abdominal pain,"1, Yes | 0, No | 99, Unknown",,,,,[demog_calcage_days]>=365,Gastrointestinal,"Defined as an unpleasant sensation of discomfort, distress or agony in the abdominal region.","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"21522001, Abdominal pain","C3553274, Abdominal pain",,clinical_features,1,1,1,1,1,1,1,,,,1,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_diarrhoea,radio,Diarrhoea,"1, Yes | 0, No | 99, Unknown",,,,,,Gastrointestinal,Defined as abnormally increased frequency (usually defined as three or more) loose or liquid bowel movement per day (or more frequent passage than is normal for the individual).,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"62315008, Diarrhea","C3554472, Diarrhea",,clinical_features,1,1,1,1,1,1,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_consti,radio,Constipation,"1, Yes | 0, No | 99, Unknown",,,,,,Gastrointestinal,Defined as irregular and infrequent or difficult evacuation of the bowels.,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"14760008, Constipation","C3551741, Constipation",,clinical_features,,,,1,1,,,,,,,, -presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_vomit,radio,Vomiting,"1, Yes | 0, No | 99, Unknown",,,,,,Gastrointestinal,Defined as the expulsion of the stomach or small intestines through the mouth.,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"422400008, Vomiting","C4230730, Vomiting",,clinical_features,1,1,1,1,1,1,1,,,,,, +presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_vomit,radio,Vomiting,"1, Yes | 0, No | 99, Unknown",,,,,,Gastrointestinal,Defined as the expulsion of the stomach or small intestines through the mouth.,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"422400008, Vomiting","C4230730, Vomiting",,clinical_features,1,1,1,1,1,1,1,,,,1,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_vomit2d,radio,Persistent vomiting? (>=2/day),"1, Yes | 0, No | 99, Unknown",,,,,[adsym_vomit]='1',Gastrointestinal,"This refers to persistent vomiting, defined here as vomiting two times or more per day.","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"196746003, Persistent vomiting","C0152165, Persistent vomiting",,clinical_features,1,1,1,1,1,1,1,,,,1,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_vomitbld,radio,Vomiting blood (haematemesis),"1, Yes | 0, No | 99, Unknown",,,,,[adsym_vomit]='1',Gastrointestinal,This refers to vomiting of blood.,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"8765009, Haematemesis","C0018926, Haematemesis",,clinical_features,,,,,1,,,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_nausea,radio,Nausea,"1, Yes | 0, No | 99, Unknown",,,,,[demog_calcage_days]>=1095,Gastrointestinal,Defined as the the unpleasant painless subjective feeling that one will imminently vomit.,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"422587007, Nausea","C3554470, Nausea",,clinical_features,1,1,,1,1,1,1,,,,,, @@ -488,8 +488,8 @@ presentation,SIGNS ON ADMISSION: Indicate if experienced at any time from onset presentation,SIGNS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsign_bulgefont,radio,Bulging fontanelle,"1, Yes | 0, No | 99, Unknown",,,,,[demog_calcage_days]<=28,Paediatric,,,,,,,,,,,,,,,,,,,1, presentation,SIGNS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsign_otherdesc,descriptive,Other signs,,,,,,,Other,,,,,,,,,,,,,,,,,,,, presentation,SIGNS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsign_unlisted,list,Other sign(s),"1, Yes | 0, No | 99, Unknown",,,,conditions_Symptoms,,Other,"This refers to other signs and symptoms, not specified above.","Indicate other signs and symptoms, not specified above, the patient has exeprienced at any time from onset of this illness to presentation.",,,,,clinical_features,,,,,,,,,,,,, -presentation,PREGNANCY PRESENTATION,preg_pregnant,radio,Pregnant,"1, Yes | 0, No | 99, Unknown",,,,,[demog_sex]='2' and [demog_calcage_days]>=4380,,This refers to women who reports to be pregnant at presentation and/or have had a positive pregnancy test in recent days prior to presentation.,"Indicate 'Yes', if the patient is pregnant at presentation. If the patient is of fertile age with no negative pregnancy test select 'Unknown'.",SNOMED,"77386006, Pregnant (finding)","C0549206, Pregnant",,risk_factor_demo,1,1,1,1,1,1,1,,,,,,1 -presentation,PREGNANCY PRESENTATION,preg_postpartum,radio,Post-partum (within 6 weeks of delivery),"1, Yes | 0, No | 99, Unknown",,,,,[demog_sex]='2' and [preg_pregnant]='0' and [demog_calcage_days]>=4380,,This refers to the temporal period relating to mother from completion of labour until six weeks post-delivery.,"Indicate 'Yes', if the patient is in post-partum period (within 6 weeks of delivery).",SNOMED,"86569001, Postpartum state (finding)","C0086839, Postpartum Period",,risk_factor_demo,1,1,1,1,1,1,1,,,,,,1 +presentation,PREGNANCY PRESENTATION,preg_pregnant,radio,Pregnant,"1, Yes | 0, No | 99, Unknown",,,,,[demog_sex]='2' and [demog_calcage_days]>=4380,,This refers to women who reports to be pregnant at presentation and/or have had a positive pregnancy test in recent days prior to presentation.,"Indicate 'Yes', if the patient is pregnant at presentation. If the patient is of fertile age with no negative pregnancy test select 'Unknown'.",SNOMED,"77386006, Pregnant (finding)","C0549206, Pregnant",,risk_factor_demo,1,1,1,1,1,1,1,,,,,1,1 +presentation,PREGNANCY PRESENTATION,preg_postpartum,radio,Post-partum (within 6 weeks of delivery),"1, Yes | 0, No | 99, Unknown",,,,,[demog_sex]='2' and [preg_pregnant]='0' and [demog_calcage_days]>=4380,,This refers to the temporal period relating to mother from completion of labour until six weeks post-delivery.,"Indicate 'Yes', if the patient is in post-partum period (within 6 weeks of delivery).",SNOMED,"86569001, Postpartum state (finding)","C0086839, Postpartum Period",,risk_factor_demo,1,1,1,1,1,1,1,,,,,1,1 presentation,PREGNANCY PRESENTATION,preg_formdesc,descriptive,Please complete the Pregnancy Form with information from the most recent pregnancy.,,,,,,[preg_postpartum]=1,,,,,,,,,,,,,1,,,,,,,,1 presentation,PREGNANCY PRESENTATION,preg_geswek,number,Gestational weeks at presentation,,number,0,45,,[preg_pregnant] = '1',,This refers to the gestational age of the foetus (written in weeks). It can be calculated from the woman's last menstrual period (LMP) or calculated using the best obstetrical estimated due date (EDD) based on the following formula: Gestational Age = (280 - (EDD - Reference Date)). The reference date is the date in which you are trying to determine the gestational age.,Indicate the estimated gestational age of the foetus (in weeks).,SNOMED,57036006 |Fetal gestational age (observable entity)|,"CL1385889, Gestational weeks",,,1,1,1,1,1,1,1,,,,,,1 presentation,PREGNANCY PRESENTATION,preg_recent1,radio,Was patient pregnant either within <=21 days of symptoms onset or within 22-42 days from admission,"1, Yes | 0, No | 99, Unknown",,,,,[preg_postpartum] = '1',,"If non-pregnant currently, this refers to whether the patient was pregnant within 21 days of onset of symptoms.","Indicate 'Yes, if the patient was pregnant within 21 days of onset of symptoms.",,,,,,,,,,1,,,,,,,,1 @@ -511,7 +511,7 @@ presentation,INFANT: LESS THAN 12 MONTHS OLD,infa_brefedduration,number,How long presentation,INFANT: LESS THAN 12 MONTHS OLD,infa_aprvac,radio,Vaccinations appropriate for age/country,"1, Yes | 0, No | 99, Unknown",,,,,[demog_calcage_days]<=730,,This refers to the vaccination status according to the age of the infant and country-specific recommendations.,"Indicate 'Yes', if the infant is appropriately vaccinated for age with respect to country-specific recommendations.",SNOMED,"713404003, Vaccination given (situation)","C0042196, Vaccination",,,1,1,,,,1,,,,,,1, daily,DAILY ASSESSMENT,daily_date,date_dmy,DATE OF ASSESSMENT,,date_dmy,,today,,,,This indicates the day of data collection and sampling (may not be the date of completion). This may be retrospective information at the time of discharge (transfer to other hospital or dead in hospital).,Enter the date of assessment. (Use the format DD/MM/YYYY),,,,,,1,1,1,1,1,1,1,,,,,, daily,DAILY ASSESSMENT,asses_lvlcare,radio,Current level of care,"1, Outpatient | 2, Admitted to normal ward for isolation only | 3, Admitted to normal ward for clinical care | 4, High dependency | 5, Intensive care admission",,,,,,,Refers to the level of care on date of assessment.,Select the highest level of care on the date of assessment.,SNOMED,SNOMED,"C4545175, Outpatient care management | C0583229, Admission to ward | C1301858, Admission to high dependency unit | C0583239, Admission to intensive care unit",,,1,1,1,1,1,1,1,,,,,, -daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_dailydata,radio,Enter Vital Signs data for this date?,"1, Yes | 0, No",,,,,,,This refers to vital signs data recorded for this date.,"Indicate 'Yes', if you want to record vital sign data for this day of assessment. If 'Yes', for the following questions unless otherwise specified, Record the value furthest from the normal physiological range recorded between 00:00 and 24:00 hours on day of assessment. Results that were rejected by the clinical team should not be included.",SNOMED,SNOMED,"C0150404, Taking vital signs",,,1,1,1,1,1,1,1,,,,,, +daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_dailydata,radio,Enter Vital Signs data for this date?,"1, Yes | 0, No",,,,,,,This refers to vital signs data recorded for this date.,"Indicate 'Yes', if you want to record vital sign data for this day of assessment. If 'Yes', for the following questions unless otherwise specified, Record the value furthest from the normal physiological range recorded between 00:00 and 24:00 hours on day of assessment. Results that were rejected by the clinical team should not be included.",SNOMED,SNOMED,"C0150404, Taking vital signs",,,1,1,1,1,1,1,1,,1,1,1,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_highesttem,number,Highest temperature (select units),,number,32,106.7,,[vital_dailydata]='1',,Refers to the highest peripheral body temperature (rectal if <3 months) between 00:00 and 24:00 on day of assessment.,Enter the highest peripheral body temperature recorded between 00:00 and 24:00 on day of assessment.,,,,,clinical_features,1,1,1,1,1,1,1,,,,,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_highesttem_units,radio,Highest temperature (select units),"1, °C | 2, °F",units,,,,[vital_dailydata]='1',,,,,,,,clinical_features,1,1,1,1,1,1,,,,,,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_highesttem_c,number,Highest temperature (°C),,number,32,41.5,,[vital_dailydata]='1',,Refers to the highest peripheral body temperature (rectal if <3 months) between 00:00 and 24:00 on day of assessment.,Enter the highest peripheral body temperature (°C) recorded between 00:00 and 24:00 on day of assessment.,SNOMED,SNOMED,,,clinical_features,1,1,1,1,1,1,1,,,,,, @@ -523,7 +523,7 @@ daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range bet daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_meanbp,number,Mean arterial blood pressure (mmHg),,number,0,200,,[vital_dailydata]='1',,"Mean arterial blood pressure (MAP) may be directly measured (via intra-arterial catheter) or be approximated without an invasive procedure using the following formula: diastolic pressure plus 1/3 of the pulse pressure, where pulse pressure is systolic pressure - diastolic pressure.",Enter the lowest recorded MAP that occurred between 00:00 to 24:00 on day of assessment.,SNOMED,SNOMED,,,clinical_features,1,1,1,,,1,,,1,1,1,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_spo2room,number,Oxygen saturation at room air (no oxygen support) (%),,number,0,100,,[vital_dailydata]='1',,"This refers to the measurement of the ratio of oxygenated hemoglobin to total hemoglobin in the blood, measured at room air with no oxygen support.",Indicate the measurement of oxygen saturation at room air with no oxygen support.,,,,,clinical_features,1,1,1,1,1,1,1,,,,,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_spo2roomhow,radio,How was oxygen saturation at room air measured?,"1, Pulse Oximetry | 2, Arterial blood gas measurement | 88, Other | 99, Unknown",,,,,[vital_dailydata]='1',,This refers to the method of measurement of oxygen saturation.,Select the most appropriate option which represents the method of measurement of oxygen saturation.,,,,,clinical_features,,,,,,1,1,,,,,, -daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_o2supp,radio,Supplemental oxygen?,"1, Yes | 0, No | 99, Unknown",,,,,[vital_dailydata]='1',,"This refers to the delivery of supplemental oxygen at the time of the above, lowest SpO2 (%), recording.","Indicate 'Yes', if the FiO2 was measured along-side the lowest oxygen saturation (SpO2) reported above.",SNOMED,SNOMED,,,clinical_features,1,1,1,1,1,1,1,,,,,, +daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_o2supp,radio,Supplemental oxygen?,"1, Yes | 0, No | 99, Unknown",,,,,[vital_dailydata]='1',,"This refers to the delivery of supplemental oxygen at the time of the above, lowest SpO2 (%), recording.","Indicate 'Yes', if the FiO2 was measured along-side the lowest oxygen saturation (SpO2) reported above.",SNOMED,SNOMED,,,clinical_features,1,1,1,1,1,1,1,,1,1,1,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_o2supp_type,radio,Type of supplemental oxygen?,"1, Nasal Prongs | 2, Face mask | 3, High flow nasal oxygen | 4, Non-invasive ventilation | 5, Invasive ventilation | 6, ECMO / ECLS | 99, Unknown",,,,,[vital_o2supp]='1',,"This refers to the type / mode of delivery for supplemental oxygen at the time of the above, lowest SpO2 (%), recording.","Select the most approproate option which represents the type / mode of delivery for supplemental oxygen at the time of the above, lowest SpO2 (%), recording.",SNOMED,SNOMED,"C0445087, Nasal prongs | C1299377, Oxygen administration by mask | C4761117, High-flow nasal cannula oxygen therapy | C1997883, Noninvasive Ventilation | C0015357, Extracorporeal Membrane Oxygenation",,clinical_features,1,1,1,1,1,1,1,,,,,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_o2supp_spo2,number,Oxygen saturation with supplemental oxygen (%),,number,0,100,,[vital_o2supp]='1',,"This refers to the oxygen saturation, that may be measured by pulse oximetry or by arterial blood gas analysis. It is irrespective of ventilation or supplemental oxygen requirement.",Enter the percentage oxygen saturation. Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,SNOMED,SNOMED,,,clinical_features,1,1,1,1,1,1,1,,1,1,1,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_o2supp_spo2how,radio,How was oxygen saturation with supplemental oxygen measured?,"1, Pulse Oximetry | 2, Arterial blood gas measurement | 88, Other | 99, Unknown",,,,,[vital_o2supp]='1',,This refers to the method of measurement of oxygen saturation.,Select the most appropriate option which represents the method of measurement of oxygen saturation.,,,,,,,,,,,1,1,,,,,, @@ -537,7 +537,7 @@ daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range bet daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_gcs,number,Glasgow Coma Score (GCS / 15),,number,3,15,,[vital_dailydata]='1',,The Glasgow Coma Scale is a scoring system for consciousness. It is scored out of 15 and requires an assessment of responsiveness to stimulus. Glasgow Coma Score: https://www.glasgowcomascale.org/downloads/GCS-Assessment-Aid-English.pdf?v=3,"Enter the lowest GCS recorded between 00:00 to 24:00 on day of assessment. For intubated patients and patients with a non-fenestrated tracheostomy, give 1 point for the voice component and calculate the total as usual. Suffixes such as 't' for tracheostomy cannot be entered on to the database. If the patient is sedated on the day of assessment these parameters should correspond to the values observed before sedation.",SNOMED,SNOMED,,,clinical_features,1,1,1,1,1,1,1,,1,1,1,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_rass,number,Richmond Agitation-Sedation Scale (RASS),,number,-5,4,,[vital_dailydata]='1',,"Richmond Agitation-Sedation Scale (RASS) is a medical scale used to measure the agitation or sedation level of a person. It ranges from -5 to +4, where 0 refers to an 'Alert and calm' patient that spontaneously pays attention.","If performed, enter the lowest value (between -5 and +4) between 00:00 to 24:00 hours on day of assessment.",,,"C4720839, Richmond Agitation-Sedation Scale",,clinical_features,1,,,,,1,,,,,,, daily,VITAL SIGNS & ASSESSMENTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,vital_urineflow,number,Urine output (mL/day),,number,0,20000,,[vital_dailydata]='1',,"This refers to the amount of urine the patient has produced over a 24-hour period, specifically the date of assessment. This may be measured e.g. via use of a urinary catheter or estimated.",Record the patient's urine output (in ml/24hours) over the day of assessment,SNOMED,SNOMED,,,clinical_features,1,,1,,,1,1,,,1,1,, -daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_dailydata,radio,Enter patient reported symptoms data for this date?,"1, Yes | 0, No",,,,,,,This refers to signs and symptoms recorded o this date.,"Indicate 'Yes', if you want to record signs and symptoms data for this day of assessment.",SNOMED,SNOMED,"C0037088, Signs and Symptoms",,,,1,1,1,1,,,,,,,, +daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_dailydata,radio,Enter patient reported symptoms data for this date?,"1, Yes | 0, No",,,,,,,This refers to signs and symptoms recorded on this date.,"Indicate 'Yes', if you want to record signs and symptoms data for this day of assessment.",SNOMED,SNOMED,"C0037088, Signs and Symptoms",,,1,1,1,1,1,,1,,,,1,1, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_sys,descriptive,Systemic / general symptoms,,,,,,[sympt_dailydata]='1',Systemic/General,This refers to systemic / general / non-specific signs and symptoms,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,,1,,1,1,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_fever,radio,Fever,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,"Defined as the sensation of elevated body temperature without formal measurement, or a measured body temperature greater or equal to 38-degrees Celsius (38°C) or 100.4-Fahrenheit (100.4°F).","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C0015967, Fever",,clinical_features,,1,,1,1,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_rigchill,radio,Chills or rigors,"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata]='1' and [initial_assessment_arm_1][demog_calcage_days]>=28,Systemic/General,Defined as severe chills with violent shivering. A rigor is an episode of shaking or exaggerated shivering which can occur with a high fever.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,,,,1,1,,,,,,,, @@ -589,7 +589,7 @@ daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessm daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_abdpain,radio,Abdominal pain,"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata]='1' and [initial_assessment_arm_1][demog_calcage_days]>=365,Gastrointestinal,"Defined as an unpleasant sensation of discomfort, distress or agony in the abdominal region.","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C3553274, Abdominal pain",,clinical_features,,1,1,1,1,,1,,,,1,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_diarrhoea,radio,Diarrhoea,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Gastrointestinal,Defined as three or more loose or liquid bowel movement per day (or more frequent passage than is normal for the individual).,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C3554472, Diarrhea",,clinical_features,,1,,1,1,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_consti,radio,Constipation,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Gastrointestinal,This refers to irregular and infrequent or difficult evacuation of the bowels.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C3551741, Constipation",,clinical_features,,,,1,1,,,,,,,, -daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_vomit,radio,Vomiting,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Gastrointestinal,Defined as the expulsion of the stomach or small intestines through the mouth.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C4230730, Vomiting",,clinical_features,,1,,1,1,,1,,,,,, +daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_vomit,radio,Vomiting,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Gastrointestinal,Defined as the expulsion of the stomach or small intestines through the mouth.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C4230730, Vomiting",,clinical_features,,1,1,1,1,,1,,,,1,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_vomit2d,radio,Persistent vomiting? (>=2/day),"1, Yes | 0, No | 99, Unknown",,,,,[sympt_vomit]='1',Gastrointestinal,Persistent vomiting is defined here as vomiting two times or more per day.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C0152165, Persistent vomiting",,clinical_features,,1,1,1,1,,1,,,,1,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_vomitbld,radio,Vomiting blood (haematemesis),"1, Yes | 0, No | 99, Unknown",,,,,[sympt_vomit]='1',Gastrointestinal,This refers to vomiting of blood.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,,,,,1,,,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_nausea,radio,Nausea,"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata]='1' and [initial_assessment_arm_1][demog_calcage_days]>=1095,Gastrointestinal,Defined as the the unpleasant painless subjective feeling that one will imminently vomit.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C3554470, Nausea",,clinical_features,,1,,1,1,,1,,,,,, @@ -638,7 +638,7 @@ daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessm daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_feedingdiff,radio,Feeding difficulty,"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata] = '1' and [initial_assessment_arm_1][demog_calcage_days]<=365,,,,,,,,,,,,,1,,,,,,,1, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_otherdesc,descriptive,Other symptoms,,,,,,[sympt_dailydata]='1',Other,,,,,,,,,1,,1,1,,,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_unlisted,list,Other symptom(s),"1, Yes | 0, No | 99, Unknown",,,,conditions_Symptoms,[sympt_dailydata]='1',Other,This refers the presence of an alternative sign(s) or symptom(s) not listed above.,"Indicate 'Yes', if the patient has experienced another sign or symptom not listed above between 00:00 to 24:00 on day of assessment.",,,,,clinical_features,,1,,1,1,,,,,,,, -daily,SIGNS: Record the clinical findings observed between 00:00 and 24:00 on the day of assessment,sign_dailydata,radio,Enter clinical signs data for this date?,"1, Yes | 0, No",,,,,,,This refers to signs and symptoms recorded o this date.,"Indicate 'Yes', if you want to record signs and symptoms data for this day of assessment.",SNOMED,SNOMED,"C0037088, signs",,,1,1,,1,1,1,1,,,,,, +daily,SIGNS: Record the clinical findings observed between 00:00 and 24:00 on the day of assessment,sign_dailydata,radio,Enter clinical signs data for this date?,"1, Yes | 0, No",,,,,,,This refers to signs and symptoms recorded o this date.,"Indicate 'Yes', if you want to record signs and symptoms data for this day of assessment.",SNOMED,SNOMED,"C0037088, signs",,,1,1,1,1,1,1,1,,1,,1,1, daily,SIGNS: Record the clinical findings observed between 00:00 and 24:00 on the day of assessment,sign_sys,descriptive,Systemic / general signs,,,,,,[sign_dailydata]='1',Systemic/General,This refers to systemic / general / non-specific signs and symptoms,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,1,1,,1,1,1,1,,,,,, daily,SIGNS: Record the clinical findings observed between 00:00 and 24:00 on the day of assessment,sign_hypotherm,radio,Hypothermia,"1, Yes | 0, No | 99, Unknown",,,,,[sign_dailydata]='1',Systemic/General,This refers to abnormally reduced body temperature due to failed thermoregulation.,"Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,,,,,1,,,,,,,, daily,SIGNS: Record the clinical findings observed between 00:00 and 24:00 on the day of assessment,sign_coldperiph,radio,Cold / clammy peripheries,"1, Yes | 0, No | 99, Unknown",,,,,[sign_dailydata]='1',Systemic/General,"This refers to skin that feels cool and moist to the touch, often associated with circulatory failure and symptoms like restlessness and hypotension.","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,,"C2106366, cold and clammy extremities",,,1,,1,,,,,,,,1,, @@ -780,7 +780,7 @@ daily,SKIN & MUCOSA ASSESSMENT: Record the information furthest from normal betw daily,SKIN & MUCOSA ASSESSMENT: Record the information furthest from normal between 00:00 to 24:00 on day of assessment.,lesion_mlpain,radio,Pain at any mucosal lesion site(s),"1, Yes | 0, No | 99, Unknown",,,,,[lesion_dailydata]='1',,"This refers to an unpleasant, uncomfortable or painful sensation at the site(s) of the mucosal lesion.","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,,,,1,1,,,,,,,, daily,SKIN & MUCOSA ASSESSMENT: Record the information furthest from normal between 00:00 to 24:00 on day of assessment.,lesion_mlpain_score,number,"Maximal pain score, where 0 means ""no pain"", and 10 means ""the worst possible pain.""",,number,0,10,,[lesion_mlpain]='1',,"This refers to the patient's objective rating of the severity of pain at the site(s) of the lesion, on a scale of 0 to 10. Where 0 represents ""no pain"" and 10 represents the ""worst imaginable pain"".",Indicate the patient's rating of the severity of the pain at the site(s) of lesion.,,,,,,,,,1,1,,,,,,,, daily,SKIN & MUCOSA ASSESSMENT: Record the information furthest from normal between 00:00 to 24:00 on day of assessment.,lesion_desc,text,Describe any other lesion complication(s),,,,,,[lesion_dailydata]='1',,This refers to other lesion complication(s) which have not been specified above.,"Describe other lesion complication(s) that occurred or were first identified between 00:00 to 24:00 on day of assessment, that have not been specified above.",,,,,,,,,1,1,,,,,,,, -daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_dailydata,radio,Enter Treatments & Interventions data for this date?,"1, Yes | 0, No",,,,,,,This section refers to treatments or interventions that are typically conducted and recorded in the emergency room and/or the ward or acute medical unit to which the patient was admitted between 00:00 and 24:00 hours on day of assessment.,"Indicate 'Yes', if treatments or interventions were conducted and recorded between 00:00 and 24:00 hours on day of assessment.",,,,,,,,1,,,1,1,,,,,, +daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_dailydata,radio,Enter Treatments & Interventions data for this date?,"1, Yes | 0, No",,,,,,,This section refers to treatments or interventions that are typically conducted and recorded in the emergency room and/or the ward or acute medical unit to which the patient was admitted between 00:00 and 24:00 hours on day of assessment.,"Indicate 'Yes', if treatments or interventions were conducted and recorded between 00:00 and 24:00 hours on day of assessment.",,,,,,1,,1,,,1,1,,,,1,, daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_fluid,radio,Any fluids prescribed,"1, Yes | 0, No | 99, Unknown",,,,,[treat_dailydata]='1',,"This refers to any prescribed fluids (oral or intravenous), excluding those the patient consumes in a non-prescribed dietary manner.","Indicate 'Yes', if the patient was received oral rehydration fluids between 00:00 and 24:00 hours on day of assessment.",,,"C44192, Administration of fluid therapy",,,,,1,,,,1,,,,,, daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_fluid_oral,radio,Oral rehydration,"1, Yes | 0, No | 99, Unknown",,,,,[treat_dailydata]='1',,"This refers to oral (enteral) rehydration fluids, excluding those the patient consumes in a non-prescribed dietary manner.","Indicate 'Yes', if the patient received oral rehydration fluids between 00:00 and 24:00 hours on day of assessment.",SNOMED,"243222002, Oral rehydration therapy (procedure)","C0029168, Oral Rehydration Therapy",,,,,1,,,,1,,,,,, daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_fluid_oralvol,text,Oral rehydration volume (mL/24 hours),,,,,,[treat_fluid_oral] = '1',,"This refers to oral (enteral) rehydration fluids, excluding those the patient consumes in a non-prescribed dietary manner.","If 'Yes', record the amount of oral rehydration fluids given between 00:00 and 24:00 on day of assessment in millilitres (mL).",SNOMED,"243222002, Oral rehydration therapy (procedure)","C0029168, Oral Rehydration Therapy",,,,,1,,,,1,,,,,, @@ -800,9 +800,9 @@ daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 t daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_plasmapher,radio,Plasmapheresis / plasma exchange,"1, Yes | 0, No | 99, Unknown",,,,,[treat_dailydata]='1',,Plasmapheresis (plasma exchange) refers to a procedure that separate and extracts plasma from the peripheral blood while returning the rest of the blood components to the donor.,"Indicate 'Yes', if the patient received plasmapheresis between 00:00 and 24:00 hours on the day of assessment.",SNOMED,"20720000, Plasmapheresis (procedure)","C32134, Plasmapheresis",,,,,1,,,,1,,,,,, daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_antibiotic,radio,Antibiotics,"1, Yes | 0, No | 99, Unknown",,,,,[treat_dailydata]='1',,Antibiotic refers to any agent(s) that selectively target bacteria. Topical preparations should not be recorded.,"Indicate 'Yes', if the patient received antibiotics between 00:00 and 24:00 hours on day of assessment",SNOMED,"281789004, Antibiotic therapy (procedure)","C279516, Antibacterial",,,,,,,,,1,,,,,, daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_steroids,radio,Corticosteroids,"1, Yes | 0, No | 99, Unknown",,,,,[treat_dailydata]='1',,"Corticosteroids (commonly referred to as 'steroids') refers to all types of therapeutic corticosteroid, made in the adrenal cortex (the outer part of the adrenal gland). They are also made in the laboratory. Examples include: prednisolone, prednisone, methyl-prednisolone, dexamethasone, hydrocortisone, fluticasone, betametasone. Topical preparations are not included, but inhaled preparations are included.","Indicate 'Yes', if the patient received 'steroids' between 00:00 and 24:00 hours on day of assessment.",SNOMED,"1290388005, Systemic corticosteroid therapy (procedure)","CL55461, Therapeutic corticosteroid",,,,,,,,,1,,,,,, -daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_other,radio,Other intervention(s) or procedure(s),"1, Yes | 0, No | 99, Unknown",,,,,[treat_dailydata]='1',,"Refers to treatment with corticosteroids via a delivery method that will affect the entire body (oral, intramuscular, intravenous or inhaled). Examples: prednisolone, prednisone, methyl-prednisolone, dexamethasone, hydrocortisone, fluticasone, betametasone. Topical preparations are not included.","Indicate 'Yes', if the patient received systemic corticosteroid therapy between 00:00 and 24:00 hours on day of assessment.",SNOMED,"1290388005, Systemic corticosteroid therapy (procedure)","CL55461, Therapeutic corticosteroid",,,,,1,,,,1,,,,,, +daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_other,radio,Other intervention(s) or procedure(s),"1, Yes | 0, No | 99, Unknown",,,,,[treat_dailydata]='1',,"Refers to treatment with corticosteroids via a delivery method that will affect the entire body (oral, intramuscular, intravenous or inhaled). Examples: prednisolone, prednisone, methyl-prednisolone, dexamethasone, hydrocortisone, fluticasone, betametasone. Topical preparations are not included.","Indicate 'Yes', if the patient received systemic corticosteroid therapy between 00:00 and 24:00 hours on day of assessment.",SNOMED,"1290388005, Systemic corticosteroid therapy (procedure)","CL55461, Therapeutic corticosteroid",,,,,1,,,1,1,,,,,, daily,TREATMENTS & INTERVENTIONS: Record all interventions given between 00:00 to 24:00 on day of assessment.,treat_other_spec,text,Please specify other intervention(s) or procedure(s),,,,,,[treat_other] = '1',,This refers to any other specific therapeutic intervention(s) or procedure(s) not otherwise characterised that you believe may be relevant.,Indicate 'Yes' if other intervention(s) or procedure(s) were used between 00:00 and 24:00 hours on day of assessment.,SNOMED,,"C184661, Interventional procedure",,,,,1,,,1,1,,,,,, -daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_o2supp,radio,Supplemental oxygen,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to any method of oxygen therapy that may be delivered via nose cannula, mask or non-invasive or invasive ventilation.","Indicate 'Yes', if the patient received supplemental oxygen between 00:00 and 24:00 hours on day of assessment.",SNOMED,"57485005, Oxygen therapy (procedure)","C428648, Inspired oxygen concentration",,,1,1,1,1,1,1,,,,,,, +daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_o2supp,radio,Supplemental oxygen,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to any method of oxygen therapy that may be delivered via nose cannula, mask or non-invasive or invasive ventilation.","Indicate 'Yes', if the patient received supplemental oxygen between 00:00 and 24:00 hours on day of assessment.",SNOMED,"57485005, Oxygen therapy (procedure)","C428648, Inspired oxygen concentration",,,1,1,1,1,1,1,,,,,1,, daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_nasalprongs,radio,Nasal prongs,"1, Yes | 0, No | 99, Unknown",,,,,[treat_o2supp] = '1',,This refers to nasal prongs or nasal cannluae which deliver oxygen through two small prongs or cannulae insterted into the nostrils.,"Indicate 'Yes', if this mode of respiratory support was used to deliver supplemental oxygen to the patient between 00:00 and 24:00 hours on day of assessment.",SNOMED,"261974006, Nasal prongs (physical object)","C44587, Nasal prongs",,,1,1,1,1,1,1,,,,,,, daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_facemask,radio,Face mask,"1, Yes | 0, No | 99, Unknown",,,,,[treat_o2supp] = '1',,"This refers to a simple oxygen face mask which is a device placed over a patient's nose, mouth, or tracheostomy to administer oxygen to the airway.","Indicate 'Yes', if this mode of respiratory support was used to deliver supplemental oxygen to the patient between 00:00 and 24:00 hours on day of assessment.",SNOMED,"261352009, Face mask (physical object)","C1299377, Oxygen administration by mask",,,1,1,1,1,1,1,,,,,,, daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_hfno,radio,High flow nasal oxygen,"1, Yes | 0, No | 99, Unknown",,,,,[treat_o2supp] = '1',,"This refers to high -flow nasal oxygen therapy which is a non-invasive respiratory support that delivers warmed, humidified, oxygen-enriched air to patients at flow rates greater than those typically delivered by standard-flow oxygen devices.","Indicate 'Yes', if this mode of respiratory support was used to deliver supplemental oxygen to the patient between 00:00 and 24:00 hours on day of assessment.",SNOMED,,"C4761117, High-flow nasal cannula oxygen therapy",,,1,1,1,1,1,1,,,,,1,, @@ -825,7 +825,7 @@ daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00 daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_highfio_pcnt,number,"FiO2 at time of PaO2 (%, 21-100)",,number,21,100,,[treat_pao2yn] = '1' or [treat_pao2yn] = '2' or [treat_pao2yn] = '3',,This refers to the measured fraction of inspired oxygen (FiO2) delivered at the time of the lowest PaO2 (partial pressure of oxygen in blood).,"Write the FiO2 at time of the lowest PaO2 (recorded above), expressed as a percentage, that occurred any time between 00:00 and 24:00 on day of assessment.",SNOMED,"250774007, Inspired oxygen concentration (observable entity)","C428648, Inspired oxygen concentration",,,1,1,1,1,,1,,,,,,, daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_o2supp_oth,radio,Other respiratory support intervention(s) or procedure(s),"1, Yes | 0, No | 99, Unknown",,,,,,,This refers to any other specific respiratory support intervention(s) or procedure(s) not otherwise characterised that you believe may be relevant.,Indicate 'Yes' if other respiratory support intervention(s) or procedure(s) were used between 00:00 and 24:00 hours on day of assessment.,SNOMED,,"C184661, Interventional procedure",,,1,,1,1,1,1,,,,,,, daily,RESPIRATORY SUPPORT: Record all respiratory interventions given between 00:00 to 24:00 on day of assessment.,treat_o2supp_oth_spec,text,Please specify other respiratory support intervention(s) or procedure(s),,,,,,[treat_o2supp_oth] = '1',,This refers to any other specific respiratory support intervention(s) or procedure(s) not otherwise characterised that you believe may be relevant.,"If 'Yes', please specify the respiratory support intervention(s) or procedure(s) not otherwise characterised that you believe may be relevant.",SNOMED,,"C184661, Interventional procedure",,,1,,1,1,1,1,,,,,,, -daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_critcare,radio,Were advanced care (including acute organ support and critical care) therapeutic interventions administered on this date?,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to any advanced care (including acute organ support and critical care) therapeutic intervention(s) that were administered between 00:00 and 24:00 hours on day of assessment. This section does not include any respiratory organ support intervention(s), which are recorded seperately.","Indicate 'Yes', if any advanced care (including acute organ support and critical care) therapeutic intervention(s) or procedure(s) were administered between 00:00 and 24:00 hours on day of assessment.",,,,,,1,1,1,1,1,1,,,,,,, +daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_critcare,radio,Were advanced care (including acute organ support and critical care) therapeutic interventions administered on this date?,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to any advanced care (including acute organ support and critical care) therapeutic intervention(s) that were administered between 00:00 and 24:00 hours on day of assessment. This section does not include any respiratory organ support intervention(s), which are recorded seperately.","Indicate 'Yes', if any advanced care (including acute organ support and critical care) therapeutic intervention(s) or procedure(s) were administered between 00:00 and 24:00 hours on day of assessment.",,,,,,1,1,1,1,1,1,,,1,,1,, daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_icu,radio,ICU / ITU / HDU / Intermediate Care Unit admission,"1, Yes | 0, No | 99, Unknown",,,,,[critd_critcare]='1',,"This refers to admission of the patient to intensive care units (ICU), intensive therapy/treatment units (ITU), critical care units, high dependency units (HDU) or unit of similar level between 00:00 and 24:00 hours on day of assessment.","Indicate 'Yes', if the patient was admitted to ICU (or unit of similar level) between 00:00 and 24:00 hours on day of assessment.",SNOMED,"305351004, Admission to intensive care unit (procedure)",,,,1,1,1,1,1,1,,,,,,, daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_neuromusc,radio,Neuromuscular blocking agents,"1, Yes | 0, No | 99, Unknown",,,,,[critd_critcare]='1',,"This refers to the use of neuromuscular blockers between 00:00 and 24:00 hours on day of assessment.. Examples include Atracurium, Cisatracurium, Nimbex etc.","Indicate 'Yes', if neuromuscular blockers were used between 00:00 and 24:00 hours on day of assessment.",SNOMED,"373295003, Neuromuscular blocking agent (substance)","C27866, Neuromuscular Blocking Agents",,,1,1,1,1,1,1,,,,,,, daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_nitricoxide,radio,Inhaled nitric oxide,"1, Yes | 0, No | 99, Unknown",,,,,[critd_critcare]='1',,"This refers to nitric oxide adminstered as in inhalant, typically used to manage hypoxic respiratory failure in patients.",Indicate 'Yes' if inhaled nitric oxide was used any time between 00:00 and 24:00 hours on day of assessment.,SNOMED,"1255879001, Administration of nitric oxide (procedure)","C1135443, Administration of inhaled nitric oxide",,,1,1,1,1,1,1,,,,,,, @@ -841,7 +841,7 @@ daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_vasopress_type,checkbox,Vasopressor / Inotropic support type,"1, Dopamine (<5ug/kg/min) | 2, Dopamine (5-15ug/kg/min) | 3, Dopamine (>15ug/kg/min) | 4, Norepinephrine (noradrenaline) < 0.1ug/kg/min | 5, Norepinephrine (noradrenaline) > 0.1ug/kg/min |6, Epinephrine (adrenaline) | 7, Dobutamine | 8, Milrinone | 9, Levosimendan | 10, Vasopressin|11,Phenylephrine| 12,Terlipressin |13,Angiotensin-II",,,,,[critd_vasopress] = '1',,This refers to the type of vasopressors used.,Select the most appropriate option(s) if these agent(s) were used for at least one hour between 00:00 and 24:00 hours on day of assessment.,,,,,,1,1,1,1,,1,,,,,1,, daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_critcareunlst,radio,Other advanced care intervention(s) or procedure(s),"1, Yes | 0, No | 99, Unknown",,,,,[critd_critcare]='1',,This refers to any other specific advanced care (including acute organ support and critical care) therapeutic intervention(s) or procedure(s) not otherwise characterised that you believe may be relevant.,Indicate 'Yes' if other advanced care intervention(s) or procedure(s) were used between 00:00 and 24:00 hours on day of assessment.,,,,,,,1,,,,1,,,,,,, daily,ADVANCED CARE INTERVENTIONS: Record all advanced care interventions given between 00:00 to 24:00 on day of assessment.,critd_critcareunlst_oth,text,Please specify other advanced care intervention(s) or procedure(s),,,,,,[critd_critcareunlst] = '1',,This refers to any other advanced care (including acute organ support and critical care) therapeutic intervention(s) or procedure(s) not otherwise characterised that you believe may be relevant.,"If 'Yes', please specify the advanced care therapeutic intervention(s) or procedure(s)not otherwise characterised that you believe may be relevant.",,,,,,,1,,,,1,,,,,,, -daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_dailydata,radio,Enter Laboratory Results data for this date?,"1, Yes | 0, No",,,,,,,"This section refers only to laboratory tests performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment. In general, results that were rejected by the clinical team (e.g. haemolysed blood samples, contaminated microbiology results) should not be reported.","Indicate 'Yes', if laboratory samples were taken on the date of assessment. If no laboratory samples were taken on the date of assessment indicate 'No' and skip to the next section. In general, do not report results that have been rejected by the clinical team (e.g. haemolysed sample). Unless otherwise specified, if there are multiple measurements, please report the measure furthest from the normal physiological or laboratory range between 00:00 and 24:00 hours on day of assessment.",,,,,,1,1,1,1,1,1,1,,,,,, +daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_dailydata,radio,Enter Laboratory Results data for this date?,"1, Yes | 0, No",,,,,,,"This section refers only to laboratory tests performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment. In general, results that were rejected by the clinical team (e.g. haemolysed blood samples, contaminated microbiology results) should not be reported.","Indicate 'Yes', if laboratory samples were taken on the date of assessment. If no laboratory samples were taken on the date of assessment indicate 'No' and skip to the next section. In general, do not report results that have been rejected by the clinical team (e.g. haemolysed sample). Unless otherwise specified, if there are multiple measurements, please report the measure furthest from the normal physiological or laboratory range between 00:00 and 24:00 hours on day of assessment.",,,,,,1,1,1,1,1,1,1,,1,1,1,, daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_fbc,descriptive,Full blood count,,,,,,[labs_dailydata]='1',,This refers to results from full blood count.,Indicate 'Yes' to enter full blood count results.,,,,,,1,1,1,1,1,1,1,,,,,, daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_haemo,number,Haemoglobin (select units),,number,0,2000,,[labs_dailydata]='1',Full Blood Count,Refers to the haemoglobin concentration in blood.,"Write haemoglobin concentration level. If there are multiple, report the measure furthest from the normal physiological or laboratory range between 00:00 and 24:00 hours on day of assessment.",,,,,clinical_features,1,1,1,1,1,1,1,,,,1,, daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_haemo_units,radio,Haemoglobin (select units),"1, g/dL | 2, g/L",units,,,,[labs_dailydata]='1',Full Blood Count,,,,,,,clinical_features,1,1,1,1,1,1,,,,,1,, @@ -987,17 +987,17 @@ daily,LABORATORY RESULTS: Record the value furthest from normal range between 00 daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_csf_culres,user_list,Specify the CSF culture result,,,,,pathogens_All,[labs_dailydata]='1',CSF,Refers to the organism(s) grown on CSF culture.,Indicate the organism(s) detected on CSF culture.,,"104174003, Microbial culture of cerebrospinal fluid (procedure)","C0430403, Cerebrospinal fluid culture (procedure)",,clinical_features,,,,,,,,,,,,, daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_csf_other,radio,Other CSF findings,"1, Yes | 0, No",,,,,[labs_dailydata]='1',CSF,"Refers to other CSF findings, not listed above.",Indicate 'Yes' if there are other CSF findings not listed above.,,"104174003, Microbial culture of cerebrospinal fluid (procedure)","C0430403, Cerebrospinal fluid culture (procedure)",,clinical_features,,,,,,,,,,,,, daily,LABORATORY RESULTS: Record the value furthest from normal range between 00:00 to 24:00 on day of assessment.,labs_csf_other_spec,text,Please specify other CSF findings,,,,,,[labs_csf_other]='1',CSF,"Refers to other CSF findings, not listed above.","If 'Yes', specify the CSF findings not listed above.",,"104174003, Microbial culture of cerebrospinal fluid (procedure)","C0430403, Cerebrospinal fluid culture (procedure)",,clinical_features,,,,,,,,,,,,, -daily,IMAGING,imagi_dailydata,radio,Enter Imaging data for this date?,"1, Yes | 0, No",,,,,,,This refers only to those imaging or radiological test(s) that were performed at the time that the patient stayed in the clinical facility (hospital) and collected on the date of assessment.,"Indicate 'Yes', if imaging or radiological test(s) were performed at the time that the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",,,,,,,1,1,1,1,1,1,,,,,, -daily,IMAGING,imagi_xray,radio,Chest X-ray performed,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_dailydata]='1',,"This refers to any chest x-ray that was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment. Chest x-ray refers to radiological visualization of the chest and organs of the thoracic cavity; not restricted to visualization of the lungs, using x-rays.","Indicate 'Yes', if any chest x-ray was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",SNOMED,SNOMED,"C0039985, Plain chest X-ray",,,1,1,1,1,1,1,1,,,,,, +daily,IMAGING,imagi_dailydata,radio,Enter Imaging data for this date?,"1, Yes | 0, No",,,,,,,This refers only to those imaging or radiological test(s) that were performed at the time that the patient stayed in the clinical facility (hospital) and collected on the date of assessment.,"Indicate 'Yes', if imaging or radiological test(s) were performed at the time that the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",,,,,,1,1,1,1,1,1,1,,,,1,, +daily,IMAGING,imagi_xray,radio,Chest X-ray performed,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_dailydata]='1',,"This refers to any chest x-ray that was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment. Chest x-ray refers to radiological visualization of the chest and organs of the thoracic cavity; not restricted to visualization of the lungs, using x-rays.","Indicate 'Yes', if any chest x-ray was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",SNOMED,SNOMED,"C0039985, Plain chest X-ray",,,1,1,1,1,1,1,1,,,,1,, daily,IMAGING,imagi_xray_date,date_dmy,Chest X-ray date,,date_dmy,,today,,[imagi_xray] = '1',,This refers to the date when the chest x-ray was performed.,Enter the date when the chest x-ray was performed (use the format DD/MM/YYYY).,,,,,,,,,,,,1,,,,,, -daily,IMAGING,imagi_xray_result,radio,Chest X-ray findings associated with this illness.,"1, Normal or no acute change | 5, Abnormal or acute change | 99, Unknown",,,,,[imagi_xray] = '1',,This refers to chest X-ray findings associated with this illness.,Select the single most appropriate option corresponding to the chest X-ray findings associated with this illness.,SNOMED,SNOMED,"C0239026, Standard chest X-ray normal | C0436503, Standard chest X-ray abnormal",,,1,1,1,1,1,1,1,,,,,, +daily,IMAGING,imagi_xray_result,radio,Chest X-ray findings associated with this illness.,"1, Normal or no acute change | 5, Abnormal or acute change | 99, Unknown",,,,,[imagi_xray] = '1',,This refers to chest X-ray findings associated with this illness.,Select the single most appropriate option corresponding to the chest X-ray findings associated with this illness.,SNOMED,SNOMED,"C0239026, Standard chest X-ray normal | C0436503, Standard chest X-ray abnormal",,,1,1,1,1,1,1,1,,,,1,, daily,IMAGING,imagi_xray_newinfilt,radio,New infiltrates present on X-ray,"1, Yes, bilateral | 2, Yes, unilateral | 0, No | 99, Unknown",,,,,[imagi_xray_result]='5',,"This refers to new pulmonary infiltrates present on the current chest x-ray, not visualised on previous chest radiographs of the patient. Pulmonary infiltrates result when a substance denser than air (e.g., pus, oedema, blood, surfactant, protein, or cells) is present within the lung parenchyma. Bilateral pulmonary infiltrates are present in both lungs. Unilateral pulmonary infiltrates are present in one lung only.","Select the single most appropriate option corresponding to the new pulmonary infiltrates present on the current chest x-ray, not visualised on previous chest radiographs of the patient.",,,,,,1,1,1,1,1,1,1,,,,,, daily,IMAGING,imagi_xray_infiltyp,checkbox,Infiltrates on X-ray consistent with,"1, Viral pneumonitis | 2, Bacterial pneumonia |3, Pulmonary oedema| 99, Unknown",,,,,[imagi_xray_newinfilt] = '1' or [imagi_xray_newinfilt]='2',,"This refers to the pathological condition with which the pulmonary infiltrates on chest x-ray may be consistent with. Viral pneumonitis characteristically produces bilateral perihilar peribronchial thickening and interstitial infiltrates which, particularly in children, due to their small-calibre airways, can result in areas of atelectasis or air trapping. Bacterial pneumonia characteristically produces focal segmental (i.e. bronchopneumonia) or lobar pulmonary opacities (i.e. lobar pneumonia). Pulmonary oedema may be characterised by cephalisation of upper lobe vessels, interstitial opacities, peribronchovascular cuffing, septal lines (Kerley B lines), airspace opacification (filling of the alveoli with fluid) which can have a perihilar or 'batwing' distribution when severe and acute; and pleural effusion.",Select all that apply.,SNOMED,SNOMED,"C0032310, Pneumonia, Viral | C0004626, Pneumonia, Bacterial | C0034063, Pulmonary Oedema",,,1,1,1,1,1,1,1,,,,,, daily,IMAGING,imagi_xray_pleueff,radio,Pleural effusion on X-ray,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_xray_result]='5',,This refers to presence of fluid in the pleural cavity resulting from excessive transudation or exudation from the pleural surfaces.,"Indicate 'Yes', if pleural effusion was visualised on chest x-ray.",SNOMED,SNOMED,"C0032227, Pleural effusion (disorder)",,,1,1,1,1,1,1,1,,,,1,, daily,IMAGING,imagi_xray_resultpleu,radio,Pleural effusion on X-ray details,"1, Unilateral | 2, Bilateral",,,,,[imagi_xray_pleueff]='1',,This refers to the location of the pleural effusion.,Indicate the location of the pleural effusion.,,,,,,1,1,1,1,1,1,1,,,,,, daily,IMAGING,imagi_xray_resultpleusite,checkbox,Side(s) where pleural effusion identified,"1, Right | 2, Left",,,,,[imagi_xray_pleueff]='1',,This refers to the side where the unilateral pleural effusion is located.,Indicate the side of the pleural effusion.,,,,,,,,1,,,,1,,,,,, -daily,IMAGING,imagi_ctchest,radio,CT chest performed,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_dailydata]='1',,This refers to computed tomography imaging of the chest.,"Indicate 'Yes', if any CT chest was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",,,,,,1,1,1,,,1,,,,,,, -daily,IMAGING,imagi_ctchest_result,radio,CT chest findings associated with this illness,"1, Normal or no acute change | 5, Abnormal or acute change | 99, Unknown",,,,,[imagi_ctchest] = '1',,"Refers to the findings identified on the CT chest. Pulmonary infiltrates refers to the presence of pulmonary or lung infiltrates and can include alveolar, air space, interstitial, or nodular infiltrates and typically refers to a substance or type of cell that is foreign to the lung, or accumulates in greater than normal quantity within it.",Select the single most appropriate option corresponding to the chest CT findings associated with this illness.,,,,,,1,1,,,,1,,,,,,, +daily,IMAGING,imagi_ctchest,radio,CT chest performed,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_dailydata]='1',,This refers to computed tomography imaging of the chest.,"Indicate 'Yes', if any CT chest was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",,,,,,1,1,1,,,1,,,,,1,, +daily,IMAGING,imagi_ctchest_result,radio,CT chest findings associated with this illness,"1, Normal or no acute change | 5, Abnormal or acute change | 99, Unknown",,,,,[imagi_ctchest] = '1',,"Refers to the findings identified on the CT chest. Pulmonary infiltrates refers to the presence of pulmonary or lung infiltrates and can include alveolar, air space, interstitial, or nodular infiltrates and typically refers to a substance or type of cell that is foreign to the lung, or accumulates in greater than normal quantity within it.",Select the single most appropriate option corresponding to the chest CT findings associated with this illness.,,,,,,1,1,1,,,1,,,,,1,, daily,IMAGING,imagi_ctchest_infiltra,radio,New infiltrates present on CT,"1, Yes, bilateral | 2, Yes, unilateral | 0, No | 99, Unknown",,,,,[imagi_ctchest_result]='5',,"This refers to new pulmonary infiltrates present on the current chest CT scan, not visualised on previous chest radiographs of the patient. Pulmonary infiltrates result when a substance denser than air (e.g., pus, oedema, blood, surfactant, protein, or cells) is present within the lung parenchyma. Bilateral pulmonary infiltrates are present in both lungs. Unilateral pulmonary infiltrates are present in one lung only.","Select the single most appropriate option corresponding to the new pulmonary infiltrates present on the current chest CT scan, not visualised on previous chest radiographs of the patient.",,,,,,1,1,,,,1,,,,,,, daily,IMAGING,imagi_ctchest_infiltyp,checkbox,Infiltrates on CT chest consistent with,"1, Viral pneumonitis | 2, Bacterial pneumonia |3, Pulmonary oedema| 99, Unknown",,,,,[imagi_ctchest_infiltra] = '1' or [imagi_ctchest_infiltra]='2',,"This refers to the pathological condition with which the pulmonary infiltrates on chest x-ray may be consistent with. Viral pneumonitis characteristically produces bilateral perihilar peribronchial thickening and interstitial infiltrates which, particularly in children, due to their small-calibre airways, can result in areas of atelectasis or air trapping. Bacterial pneumonia characteristically produces focal segmental (i.e. bronchopneumonia) or lobar pulmonary opacities (i.e. lobar pneumonia). Pulmonary oedema may be characterised by cephalisation of upper lobe vessels, interstitial opacities, peribronchovascular cuffing, septal lines (Kerley B lines), airspace opacification (filling of the alveoli with fluid) which can have a perihilar or 'batwing' distribution when severe and acute; and pleural effusion.",Select all that apply.,SNOMED,SNOMED,"C0032310, Pneumonia, Viral | C0004626, Pneumonia, Bacterial | C0034063, Pulmonary Oedema",,,1,1,,,,1,,,,,,, daily,IMAGING,imagi_ctchest_pleueff,radio,Pleural effusion on CT chest,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_ctchest_result]='5',,This refers to presence of fluid in the pleural cavity resulting from excessive transudation or exudation from the pleural surfaces.,"Indicate 'Yes', if pleural effusion was visualised on chest CT scan.",SNOMED,SNOMED,"C0032227, Pleural effusion (disorder)",,,1,1,1,,,1,,,,,1,, @@ -1008,10 +1008,10 @@ daily,IMAGING,imagi_ctbrain_findings,text,CT brain findings,,,,,,[imagi_ctbrain] daily,IMAGING,imagi_mrib,radio,MRI brain performed,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_dailydata]='1',,This refers to magnetic resonance imaging (MRI) of the brain.,"Indicate 'Yes', if any Brain MRI scan was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",,,,,,,1,,,,1,,,,,,, daily,IMAGING,imagi_mrib_date,date_dmy,MRI brain date,,date_dmy,,today,,[imagi_mrib] = '1',,This refers to the date of the brain MRI scan.,Enter the date when the MRI was performed. (Use the format DD/MM/YYYY),,,,,,,,,,,,,,,,,, daily,IMAGING,imagi_mrib_findings,text,MRI brain findings,,,,,,[imagi_mrib] = '1',,This refers to the key findings of the brain MRI scan.,Write the key findings of the Brain MRI scan.,,,,,,,1,,,,1,,,,,,, -daily,IMAGING,imagi_ultrasound,radio,Ultrasound performed,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_dailydata]='1',,This refers to any ultrasound imaging that was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.,"Indicate 'Yes', if ultrasound imaging was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",SNOMED,SNOMED,"C0041618, Ultrasonography",,,,1,1,,,1,1,,,,,, +daily,IMAGING,imagi_ultrasound,radio,Ultrasound performed,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_dailydata]='1',,This refers to any ultrasound imaging that was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.,"Indicate 'Yes', if ultrasound imaging was performed at the time the patient stayed in the clinical facility (hospital) and collected on the date of assessment.",SNOMED,SNOMED,"C0041618, Ultrasonography",,,1,1,1,,,1,1,,,,1,, daily,IMAGING,imagi_ultrasound_date,date_dmy,Ultrasound date,,date_dmy,,today,,[imagi_ultrasound] = '1',,This refers to the date when the ultrasound imaging was performed.,Enter the date when the ultrasound was performed. (Use the format DD/MM/YYYY),,,,,,,,,,,,1,,,,,, daily,IMAGING,imagi_ultrasound_site,radio,Ultrasound region,"1, Chest only | 2, Abdomen only | 3, Chest and abdomen | 4, Cranial | 99, Unknown",,,,,[imagi_ultrasound]='1',,This refers to the region of the body which was assessed using ultrasound imaging.,Indicate the region of the body which was assessed using ultrasound imaging.,SNOMED,SNOMED,"C0883613, Ultrasound chest | C0203464, Ultrasonography of abdomen | C4750624, Ultrasonography of chest and abdomen",,,,1,1,,,1,1,,,,,, -daily,IMAGING,imagi_ultrasound_findi,radio,Ultrasound findings associated with this illness,"1, Normal or no acute change | 5, Abnormal or acute change | 99, Unknown",,,,,[imagi_ultrasound]='1',,This refers to ultrasound imaging findings associated with this illness.,Select the single most appropriate option corresponding to the ultrasound imaging findings associated with this illness.,SNOMED,SNOMED,"C0581117, Ultrasound scan normal | C0581118, Ultrasound scan abnormal",,,,1,1,,,1,1,,,,,, +daily,IMAGING,imagi_ultrasound_findi,radio,Ultrasound findings associated with this illness,"1, Normal or no acute change | 5, Abnormal or acute change | 99, Unknown",,,,,[imagi_ultrasound]='1',,This refers to ultrasound imaging findings associated with this illness.,Select the single most appropriate option corresponding to the ultrasound imaging findings associated with this illness.,SNOMED,SNOMED,"C0581117, Ultrasound scan normal | C0581118, Ultrasound scan abnormal",,,1,1,1,,,1,1,,,,1,, daily,IMAGING,imagi_ultrasound_asc,radio,Ascites,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_ultrasound_findi]='5',,Ascites refers to a pathological increase of fluid in the peritoneal cavity.,Indicate 'Yes' If ascites were identified on ultrasound on date of assessment. Indicate 'No' if there was no ascites on ultrasound on date of assessment. If the peritoneal cavity was not examined by ultrasound for ascites on date of assessment indicate 'Unknown'.,SNOMED,SNOMED,"C0003962, Ascites",,,1,,1,,,,1,,,,1,, daily,IMAGING,imagi_ultrasound_ascsit,radio,Ascites grading,"1, Small | 2, Moderate | 3, Severe",,,,,[imagi_ultrasound_asc] = '1',,"Mild/small ascites (grade 1) is detectable only by ultrasonography and typically requires approximately 100mL of fluid (where normal volume is approximately 25-50mL); Moderate ascites (grade 2) implying at least 500-1000mL of peritoneal fluid and detected with physical examination; Severe ascites (grade 3) refers to the manifestation of grossly distended abdomen, may be described as tense ascites.",Select the single most appropriate option corresponding to the grade of ascites detected on ultrasound imaging.,,,,,,,,1,,,,1,,,,,, daily,IMAGING,imagi_ultrasound_consoli,radio,Consolidation,"1, Yes | 0, No | 99, Unknown",,,,,[imagi_ultrasound_findi]='5',,This refers to the presence of a radio-opaque area in the lung. The opacification is caused by fluid or solid material within the airways or lung parenchyma.,Indicate 'Yes' if consolidation was identified on ultrasound on date of assessment. Indicate 'No' if there was no pleural effusion(s) on ultrasound on date of assessment. Indicate 'Unknown' if the pleural space was not examined by ultrasound for pleural effusion(s) on date of assessment.,SNOMED,SNOMED,,,,,1,1,,,1,1,,,,,, @@ -1028,7 +1028,7 @@ daily,IMAGING,imagi_ecg,radio,Electrocardiogram (ECG),"1, Yes-normal | 2, Yes-ab daily,IMAGING,imagi_ecg_spec,text,ECG summary,,,,,,[imagi_ecg]='2',,Refers to a summary of the key ECG findings,If 'Yes-abnormal' give a summary of the key ECG findings.,,,,,,,,,,,,,,,,,, daily,IMAGING,imagi_ecg_date,date_dmy,ECG date,,date_dmy,,today,,[imagi_ecg]='1' or [imagi_ecg]='2',,Refers to the date of the ECG,Enter the date when the ECG was performed.. (Use the format DD/MM/YYYY),,,,,,,,,,,,,,,,,, medication,MEDICATION: Record medications administered or prescribed from day of presentation to day of discharge / outcome (one form per medication).,medi_medtype,user_list,Select agents administered while hospitalised or at discharge (one form per medication),,,,,drugs_Type,,,"This refers to all medications administered any time during the patient's admission in the clinical facility (hospital), including in the emergency department, and prescribed on discharge.","Indicate the type of agent, for all medications administered any time during the patient's admission in the clinical facility (hospital), including in the emergency department, and prescribed on discharge.",,,,,,1,1,1,1,1,1,1,,,,,, -medication,MEDICATION: Record medications administered or prescribed from day of presentation to day of discharge / outcome (one form per medication).,medi_treat,radio,Is this medication treating the disease?,"1, Yes | 0, No",,,,,,,This refers to whether the medication is being used to treat the disease caused by the pathogen of interest.,Indicate 'Yes' if this medication is being used to treat the disease caused by the pathogen of interest.,,,,,,1,,1,1,1,1,1,,,,,, +medication,MEDICATION: Record medications administered or prescribed from day of presentation to day of discharge / outcome (one form per medication).,medi_treat,radio,Is this medication treating the disease?,"1, Yes | 0, No",,,,,,,This refers to whether the medication is being used to treat the disease caused by the pathogen of interest.,Indicate 'Yes' if this medication is being used to treat the disease caused by the pathogen of interest.,,,,,,1,1,1,1,1,1,1,,,,,, medication,MEDICATION: Record medications administered or prescribed from day of presentation to day of discharge / outcome (one form per medication).,medi_antiviralagent,user_list,Antiviral,,,,,drugs_Antiviral,[medi_medtype] = '8',,"Refers to any agent(s) prescribed specifically to treat a suspected or confirmed viral infection. Examples of neuraminidase inhibitors include oseltamivir, ribavirin, acyclovir and lopinavir/ritonavir. Topical preparations are not included.","Select the antiviral agent(s) administered any time during the patient's admission in the clinical facility (hospital), including in the emergency department, and prescribed on discharge.",,,,,"clinical_features, treatment",1,1,,1,1,1,1,,,,,, medication,MEDICATION: Record medications administered or prescribed from day of presentation to day of discharge / outcome (one form per medication).,medi_antibioagent,user_list,Antibiotic,,,,,drugs_Antibiotics,[medi_medtype]='2',,Antibiotics refers to any agent(s) that selectively target bacteria.,"Select the antibiotic agent(s) administered any time during the patient's admission in the clinical facility (hospital), including in the emergency department, and prescribed on discharge.",SNOMED,346325008 |Medicinal product acting as antibacterial agent (product)|,"C0279516, Antibacterial",,"clinical_features, treatment",1,1,1,1,1,1,1,,,,,, medication,MEDICATION: Record medications administered or prescribed from day of presentation to day of discharge / outcome (one form per medication).,medi_topicantibiotgent,radio,Topical antibiotic,"1, Penicillins | 2, Cephalosporins | 3, Tetracyclines | 4, Aminoglycosides | 5, Macrolides | 6, Sulfonamides and trimethoprim | 7, Quinolones | 99, Unknown | 88, Other",,,,,[medi_medtype]='16',,Refers to the antibiotic class of topical antibiotic(s) administered during admission and/or prescribed on discharge.,Indicate the class of topical antibiotic(s) administered during admission and/or prescribed on discharge,,,,,,,,,1,1,,,,,,,, @@ -1060,7 +1060,7 @@ medication,MEDICATION: Record medications administered or prescribed from day of pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_collectiondate,date_dmy,Collection date,,date_dmy,,today,,,,This refers to the date of collection of a clinical specimen for pathogen testing.,Enter the date when the samples were collected. This may be different to the day in which the results are reported. (Use the format DD/MM/YYYY),,,,,,1,1,1,1,1,1,1,,,,,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_biospecimentype,user_list,Biospecimen type,,,,,pathogens_SampleType,,,This refers to the type of a clinical specimen collected for pathogen testing. Nasal / Nasopharyngeal (NP) swab refers to collection biological material from within the nasal passages/nasopharynx. Throat swab refers to collection biological material from within the throat/oropharynx. Combined nasal/NP + throat swab refers to collection using both nasal / nasopharyngeal (NP) swab and throat swab. Sputum refers to material coughed up from the lungs and expectorated via the mouth. Bronchoalveolar Lavage (BAL) refers to washing out of the lungs with saline or mucolytic agents for diagnostic or therapeutic purposes. Endotracheal aspirate (ETA) refers to collection of specimen from endotracheal tube. Eye swab refers to collection of biological sample from the surface of the eye. Lesion swab refers to collection of biological sample from a lesion on the skin or mucous membrane. Semen refers to the secretion of male reproductive organs discharged upon ejaculation. Faeces / rectal swab refers to biological sample collected from faecal matter or from the rectum by swabbing.,Select the single most appropriate option that represents the type of clinical specimen collected for pathogen testing.,,,,,,1,1,1,1,1,1,1,,,,,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_pathtested,user_list,Pathogen tested / detected,,,,,pathogens_All,,,This refers to the pathogen(s) tested for using the biological sample.,Indicate the pathogen(s) which were tested for using the biological sample.,,,,,,1,1,1,1,1,1,1,,,,1,, -pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_labtestmethod,radio,Lab test method,"1, PCR (NAAT) | 3, Culture | 6, RDT | 7, ELISA | 8,Other NAAT | 99, Unknown",,,,,,,This refers to the laboratory method used to test for the pathogen.,Select the single most appropriate option that represents the laboratory method used to test for the pathogen.,,,,,,1,1,1,1,1,1,1,,,,,, +pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_labtestmethod,radio,Lab test method,"1, PCR (NAAT) | 3, Culture | 6, RDT | 7, ELISA | 8,Other NAAT | 99, Unknown",,,,,,,This refers to the laboratory method used to test for the pathogen.,Select the single most appropriate option that represents the laboratory method used to test for the pathogen.,,,,,,1,1,1,1,1,1,1,,,,1,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_marker,checkbox,Lab marker,"1, NS1 Ag | 2, IgG | 3, IgM | 6, IgA | 4, Viral load / serotype (PCR/NAAT) | 5, Not applicable | 99, Unknown",,,,,,,This refers to the laboratory marker used to test for the pathogen,Select the single most appropriate option that represents the laboratory marker used to test for the pathogen.,,,,,,1,1,1,1,1,1,1,,,,1,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_naat,radio,NAAT subtype,"1, RT-PCR| 2, LAMP | 3, TMA / TMP | 88, Other | 99, Unknown ",,,,,[test_labtestmethod]='1' or [test_labtestmethod]='8',,,,,,,,,,,,,,,1,,,,,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_naat_other,text,Specify other NAAT subtype,,,,,,[test_naat]='88',,,,,,,,,,,,,,,1,,,,,, @@ -1162,7 +1162,7 @@ outcome,COMPLICATIONS: Experienced at any time from day of presentation to day o outcome,COMPLICATIONS: Experienced at any time from day of presentation to day of discharge / outcome.,compl_hypothermia,radio,Hypothermia,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,This refers to abnormally low body temperature.,"Indicate 'Yes', if the patient experienced this at any time during hospitalisation.",,,,,,,,,,1,,,,,,,, outcome,COMPLICATIONS: Experienced at any time from day of presentation to day of discharge / outcome.,compl_otherdesc,descriptive,Other Complications,,,,,,,Other,,,,,,,,1,1,1,1,1,1,1,,,,,, outcome,COMPLICATIONS: Experienced at any time from day of presentation to day of discharge / outcome.,compl_unlisted,list,Other complication(s),"1, Yes | 0, No | 99, Unknown",,,,conditions_Complications,,Other,This refers to other complication(s) not specified above.,"Specify all other complication(s), not listed above, the patient experienced at any time during hospitalisation.",,,,,clinical_features,1,1,1,1,1,1,1,,,,,, -outcome,INTERVENTIONS: Record interventions given or prescribed from day of presentation to day of discharge / outcome.,inter_ivfluid,radio,Intravenous (parenteral) fluids,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to intravenous fluid which includes crystalloid, albumin, gelatin, starches or other solutions.","Indicate 'Yes', if the patient received intravenous fluids at any time during hospitalisation.",,,,,,,,1,,,,,,,,,, +outcome,INTERVENTIONS: Record interventions given or prescribed from day of presentation to day of discharge / outcome.,inter_ivfluid,radio,Intravenous (parenteral) fluids,"1, Yes | 0, No | 99, Unknown",,,,,,,"This refers to intravenous fluid which includes crystalloid, albumin, gelatin, starches or other solutions.","Indicate 'Yes', if the patient received intravenous fluids at any time during hospitalisation.",,,,,,1,,1,,,,,,,,,, outcome,INTERVENTIONS: Record interventions given or prescribed from day of presentation to day of discharge / outcome.,inter_ivfluid_type,user_list,Intravenous fluid type,,,,,drugs_IVfluids,[inter_ivfluid]='1',,"This refers to the type of parenteral or intravenous (IV) fluid is prescribed as a replacement of fluid, electrolytes, calories, vitamins, and other nutritional substances. Intravenous fluids may be crystalloids (commonly including 0.9% Sodium Chloride (Normal Saline), Lactated Ringer(USP), 0.45% Sodium Chloride (Half-normal saline), 0.45% normal saline + 4% Glucose (Half-normal saline with dextrose), 0.18%-0.3% Sodium Chloride + 4% Glucose (Hypotonic saline with dextrose), 5% Glucose (Dextrose 5% in Water), Ringeracetate or Plasmalyte) or colloids (commonly including gelatins, starches or albumin).",Select the most appropriate option corresponding to the type of intravenous or parenteral fluid(s) administered.,,,,,,1,,1,,,,,,,,,, outcome,INTERVENTIONS: Record interventions given or prescribed from day of presentation to day of discharge / outcome.,inter_ivfluid_cryst,number,Total crystalloid volume given during admission (mL),,number,0,,,[inter_ivfluid]='1',,"Crystalloid fluids refer to aqueous solutions of mineral salts and other small, water-soluble molecules. They are commonly used for fluid resuscitation in the presence of hypovolemia, hemorrhage, sepsis, and dehydration Common crystalloids include 0.9% Sodium Chloride (Normal Saline), Lactated Ringer(USP), 0.45% Sodium Chloride (Half-normal saline), 0.45% normal saline + 4% Glucose (Half-normal saline with dextrose), 0.18%-0.3% Sodium Chloride + 4% Glucose (Hypotonic saline with dextrose), 5% Glucose (Dextrose 5% in Water), Ringeracetate or Plasmalyte.",Record the total volume of crystalloid fluids the patient received during admission in millilitres (mL).,,,,,,,,1,,,,,,,,,, outcome,INTERVENTIONS: Record interventions given or prescribed from day of presentation to day of discharge / outcome.,inter_ivfluid_colloid,number,Total colloid volume given during admission (mL),,number,0,,,[inter_ivfluid]='1',,"Colloid fluids are solutions that contain large molecules, such as proteins or polysaccharides, which remain in the bloodstream for a longer duration compared to crystalloids. These fluids help maintain or expand intravascular volume by drawing water into the blood vessels via oncotic pressure. Common colloids include gelatins, starches or albumin.",Record the total volume of colloid fluid the patient received during admission in millilitres (mL).,,,,,,,,1,,,,,,,,,, diff --git a/tests/test_skip_logic.py b/tests/test_skip_logic.py index 57e030e..d8690d4 100644 --- a/tests/test_skip_logic.py +++ b/tests/test_skip_logic.py @@ -215,21 +215,55 @@ def test_checkboxes(): @pytest.mark.medium @pytest.mark.parametrize("preset_column", PRESET_COLUMNS) def test_fields_exist_presets(preset_column): - """Check that fields mentioned in the skip logic exist""" + """Check that at least one valid OR-branch exists in skip logic for preset. + + For example, if skip logic is "(demog_age < 1 and demog_age_units = 1) OR + demog_calcage_days <365", and only demog_calcage_days is present in the + filtered preset, the test passes because that branch is fully valid. + """ arc = pd.read_csv( ARC_PATH, dtype="object", usecols=["Variable", "Skip Logic", preset_column] ) arc = arc.loc[arc[preset_column].isin(["1"])] - arc_skip_logic = extract_from_arc(arc) + valid_variables = set(arc["Variable"]) - condition = arc_skip_logic["skip_logic_field"].isin( - arc["Variable"] - ) | arc_skip_logic["skip_logic_field"].str.endswith(EXCEPTIONS_SUFFIX) - if not condition.all(): - invalid = invalid = arc_skip_logic.loc[ - ~condition, ["field_name", "skip_logic_field"] - ].to_dict(orient="records") - pytest.fail(f"Skip logic includes variable not in ARC: {invalid}") + invalid_rows = [] + + for idx in arc["Skip Logic"].dropna().index: + skip_logic = arc.loc[idx, "Skip Logic"] + + # Split by OR (case insensitive) to get separate branches + or_branches = re.split(r"\s+or\s+", skip_logic, flags=re.IGNORECASE) + + # Check if at least one branch has all its fields valid + has_valid_branch = False + for branch in or_branches: + branch_fields = extract(branch) + if not branch_fields: + continue + # Check if all fields in this branch are valid + all_valid = all( + f["skip_logic_field"] in valid_variables + or re.search(EXCEPTIONS_SUFFIX + "$", f["skip_logic_field"]) + for f in branch_fields + ) + if all_valid: + has_valid_branch = True + break + + if not has_valid_branch: + field_name = arc.loc[idx, "Variable"] + all_fields = extract(skip_logic) + invalid_rows.append( + { + "field_name": field_name, + "skip_logic_fields": [f["skip_logic_field"] for f in all_fields], + } + ) + + if invalid_rows: + formatted = "\n".join(str(row) for row in invalid_rows) + pytest.fail(f"Skip logic has no valid branches:\n{formatted}") @pytest.mark.high From ec65b00420775f177eeed41e4b01f18f21f0c414 Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 23 Mar 2026 16:43:15 +0000 Subject: [PATCH 2/7] Strips whitespace from List files --- Lists/conditions/Site.csv | 26 +++--- Lists/demographics/Occupation.csv | 2 +- Lists/drugs/Antibiotics.csv | 122 ++++++++++++++--------------- Lists/drugs/Anticoagulant.csv | 40 +++++----- Lists/drugs/Antiviral.csv | 66 ++++++++-------- Lists/drugs/IVfluids.csv | 2 +- Lists/drugs/Immunosuppressants.csv | 48 ++++++------ Lists/drugs/Other.csv | 60 +++++++------- Lists/drugs/Steroids.csv | 20 ++--- Lists/drugs/Type.csv | 20 ++--- Lists/drugs/nsaids.csv | 30 +++---- Lists/followup/outcome.csv | 2 +- Lists/inclusion/Diseases.csv | 18 ++--- Lists/outcome/Diseases.csv | 18 ++--- Lists/pathogens/All.csv | 12 +-- Lists/pathogens/Other.csv | 8 +- 16 files changed, 247 insertions(+), 247 deletions(-) diff --git a/Lists/conditions/Site.csv b/Lists/conditions/Site.csv index e7d8108..ef446ae 100644 --- a/Lists/conditions/Site.csv +++ b/Lists/conditions/Site.csv @@ -1,15 +1,15 @@ Site,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics+extended,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Syndromic CRF_ARI,preset_UserGenerated_Oropouche,preset_Score_CharlsonCI,preset_Module_Pregmpoxnompox,preset_Module_Pregnancy,preset_Module_Neonates,preset_Module_Paediatric,preset_Module_ExtendedMpoxPregnan,preset_Recommended Outcomes_Dengue,preset_Hospitalsed Outcomes_Dengue,preset_Early Stage Outcomes_Dengue,Value -Skin ,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,1 -Petechiae ,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,2 -Nose ,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,3 -Gums ,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,4 -GI tract ,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,5 +Skin,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,1 +Petechiae,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,2 +Nose,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,3 +Gums,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,4 +GI tract,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,5 Urinary tract,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,6 -Vagina ,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,7 -Intracranial ,,,,,,,,,,,,,,,,,,,1,1,1,8 -Intraspinal ,,,,,,,,,,,,,,,,,,,1,1,1,9 -Intraocular ,,,,,,,,,,,,,,,,,,,1,1,1,10 -Retroperitoneal ,,,,,,,,,,,,,,,,,,,1,1,1,11 -Intra-articular ,,,,,,,,,,,,,,,,,,,1,1,1,12 -Pericardial ,,,,,,,,,,,,,,,,,,,1,1,1,13 -Intramuscular (with compartment syndrome) ,,,,,,,,,,,,,,,,,,,1,1,1,14 +Vagina,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,7 +Intracranial,,,,,,,,,,,,,,,,,,,1,1,1,8 +Intraspinal,,,,,,,,,,,,,,,,,,,1,1,1,9 +Intraocular,,,,,,,,,,,,,,,,,,,1,1,1,10 +Retroperitoneal,,,,,,,,,,,,,,,,,,,1,1,1,11 +Intra-articular,,,,,,,,,,,,,,,,,,,1,1,1,12 +Pericardial,,,,,,,,,,,,,,,,,,,1,1,1,13 +Intramuscular (with compartment syndrome),,,,,,,,,,,,,,,,,,,1,1,1,14 diff --git a/Lists/demographics/Occupation.csv b/Lists/demographics/Occupation.csv index a25f199..4e7b012 100644 --- a/Lists/demographics/Occupation.csv +++ b/Lists/demographics/Occupation.csv @@ -1,6 +1,6 @@ Disease,Code,Library,Selected,preset_ARChetype Syndromic CRF_ARI,Value Abattoir Worker,,,1.0,1.0,1 -Beef Cattle Farm Worker ,,,1.0,1.0,2 +Beef Cattle Farm Worker,,,1.0,1.0,2 Dairy Farm Worker,,,1.0,1.0,3 Healthcare Worker,,,1.0,1.0,4 Live bird market worker,,,,1.0,5 diff --git a/Lists/drugs/Antibiotics.csv b/Lists/drugs/Antibiotics.csv index 4d86262..d7aa361 100644 --- a/Lists/drugs/Antibiotics.csv +++ b/Lists/drugs/Antibiotics.csv @@ -1,129 +1,129 @@ Drugs (Generic),Code,Library,Selected,preset_Respiratory,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Syndromic CRF_ARI,preset_ARChetype Syndromic CRF_Arbovirus,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,Comment,Value -"Amikacin (Amikin, Biodacin, Miacin) ",J01GB06 ,ATC ,1,,,,,,,,,,,,1 -"Amoxicillin (Amoxil, Moxatag, Trimox) ",J01CA04 ,ATC ,1,1,1,,,,,1,,,,,2 -"Amoxicillin/Beta-lactamase inhibitor (Amoxicillin/Clavulanate, Amoxicillin and clavulanic acid, Augmentin, Amoxyclav, Co-amoxiclav)",J01CR02 ,ATC ,1,1,1,,,,,1,,,,,3 -"Amphotericin (Amphotericin B, Amphocin, Fungizone, Fungilin) ",J02AA01 ,ATC , ,,,,,,,,,,,,4 +"Amikacin (Amikin, Biodacin, Miacin)",J01GB06,ATC,1,,,,,,,,,,,,1 +"Amoxicillin (Amoxil, Moxatag, Trimox)",J01CA04,ATC,1,1,1,,,,,1,,,,,2 +"Amoxicillin/Beta-lactamase inhibitor (Amoxicillin/Clavulanate, Amoxicillin and clavulanic acid, Augmentin, Amoxyclav, Co-amoxiclav)",J01CR02,ATC,1,1,1,,,,,1,,,,,3 +"Amphotericin (Amphotericin B, Amphocin, Fungizone, Fungilin)",J02AA01,ATC,,,,,,,,,,,,,4 Ampicillin (Polyflex),J01CA01,ATC,1,,,,,,,,,,,,5 -"Ampicillin/Beta-lactamase inhibitor (Ampicillin/Sulbactam, Sulacillin, Unasyn)",J01CR01 ,ATC ,1,,,,,,,,,,,,6 -"Atovaquone (Mepron, Wellvone) ",P01AX06,ATC,2,,,,,,,,,,,,7 -"Azithromycin (Sumamed, Zithromax, Zmax) ",J01FA10,ATC ,1,1,1,1,1,1,1,1,1,1,1,,8 +"Ampicillin/Beta-lactamase inhibitor (Ampicillin/Sulbactam, Sulacillin, Unasyn)",J01CR01,ATC,1,,,,,,,,,,,,6 +"Atovaquone (Mepron, Wellvone)",P01AX06,ATC,2,,,,,,,,,,,,7 +"Azithromycin (Sumamed, Zithromax, Zmax)",J01FA10,ATC,1,1,1,1,1,1,1,1,1,1,1,,8 "Aztreonam (Azactam, Cayston, Primbactam)",J01DF01,ATC,2,,,,,,,,,,,,9 "Bacampicillin (Penglobe, Spectrobid)",J01CA06,ATC,2,,,,,,,,,,,,10 Bacitracin (Baciguent),J01XX10,ATC,2,,,,,,,,,,,,11 Benzathine phenoxymethylpenicillin (Penicillin V),J01CE10,ATC,,,,,,,,,,,,,12 -"Benzylpenicillin (Penicillin G, Bactracillin G, )",J01CE01,ATC ,1,,,,,,,,,,,,13 +"Benzylpenicillin (Penicillin G, Bactracillin G)",J01CE01,ATC,1,,,,,,,,,,,,13 Capreomycin (Capastat),J04AB30,ATC,2,,,,,,,,,,,,14 -"Carbenicillin indanyl sodium (Anabactyl, Carbapen, Carindacillin, Pyopen)",J01CA05 ,ATC,2,,,,,,,,,,,,15 -Caspofungin (Cancidas) ,J02AX04,ATC, ,,,,,,,,,,,,16 +"Carbenicillin indanyl sodium (Anabactyl, Carbapen, Carindacillin, Pyopen)",J01CA05,ATC,2,,,,,,,,,,,,15 +Caspofungin (Cancidas),J02AX04,ATC,,,,,,,,,,,,,16 "Cefaclor (Biocef, Ceclor, Raniclor)",J01DC04,ATC,2,,,,,,,,,,,,17 Cefadroxil (Duricef),J01DB05,ATC,2,,,,,,,,,,,,18 -"Cefalexin (Cephalexin, Keflex, Daxbia) ",J01DB01,ATC,1,,,,,,,,,,,,19 +"Cefalexin (Cephalexin, Keflex, Daxbia)",J01DB01,ATC,1,,,,,,,,,,,,19 Cefamandole (Mandol),J01DC03,ATC,2,,,,,,,,,,,,20 -"Cefazolin (Ancef, Kefzol) ",J01DB04,ATC,1,,,,,,,,,,,,21 +"Cefazolin (Ancef, Kefzol)",J01DB04,ATC,1,,,,,,,,,,,,21 "Cefdinir (Cefzon, Omnicef)",J01DD15,ATC,2,,,,,,,,,,,,22 Cefditoren (Spectracef),J01DD16,ATC,2,,,,,,,,,,,,23 Cefepime (Maxipime),J01DE01,ATC,1,,,,,,,,,,,,24 Cefixime (Suprax),J01DD08,ATC,2,,,,,,,,,,,,25 Cefmetazole (Zefazone),J01DC09,ATC,2,,,,,,,,,,,,26 -Cefoperazone (Cefobid),J01DD12,ATC, ,,,,,,,,,,,,27 +Cefoperazone (Cefobid),J01DD12,ATC,,,,,,,,,,,,,27 Cefotaxime (Claforan),J01DD01,ATC,1,1,,,,,,,,,,,28 Cefotetan (Cefotan),J01DC05,ATC,2,,,,,,,,,,,,29 "Cefoxitin (Mefoxin, Renoxitin)",J01DC01,ATC,2,,,,,,,,,,,,30 -Cefpodoxime Proxetil (Vantin),J01DD13 ,ATC,2,,,,,,,,,,,,31 +Cefpodoxime Proxetil (Vantin),J01DD13,ATC,2,,,,,,,,,,,,31 "Cefprozil (Cefproxil, Cefproz, Cefzil)",J01DC10,ATC,2,,,,,,,,,,,,32 -"Ceftaroline Fosamil (Teflaro, Zinforo)",J01DI02 ,ATC,1,,,,,,,,,,,,33 -"Ceftazidime (Fortaz, Tazicef) ",J01DD02 ,ATC,1,1,,,,,,,,,,,34 +"Ceftaroline Fosamil (Teflaro, Zinforo)",J01DI02,ATC,1,,,,,,,,,,,,33 +"Ceftazidime (Fortaz, Tazicef)",J01DD02,ATC,1,1,,,,,,,,,,,34 "Ceftazidime/beta-lactamase inhibitor (ceftazidime/avibactam, Avycaz, Zavicefta)",J01DD52,ATC,,1,,,,,,,,,,,35 Ceftibuten (Cedax),J01DD14,ATC,2,,,,,,,,,,,,36 -Ceftizoxime (Cefizox),J01DD07,ATC, ,,,,,,,,,,,,37 -Ceftobiprole Medocaril (Zeftera),J01DI01 ,ATC,1,,,,,,,,,,,,38 -"Ceftriaxone (Rocephin, Wintriaxone) ",J01DD04 ,ATC,1,1,1,1,,,1,1,1,1,,,39 -"Cefuroxime (Ceftin, Zinacef) ",J01DC02,ATC,1,1,,,,,,,,,,,40 -"Cephalexin (Cefalexin, Keflex, Daxbia)",J01DB01 ,ATC,2,,,,,,,,,,,,41 -"Cephalothin (Cefalotin, ",J01DB03 ,ATC,2,,,,,,,,,,,,42 -"Cephapirin (Cefapirin, ",J01DB08,ATC,2,,,,,,,,,,,,43 +Ceftizoxime (Cefizox),J01DD07,ATC,,,,,,,,,,,,,37 +Ceftobiprole Medocaril (Zeftera),J01DI01,ATC,1,,,,,,,,,,,,38 +"Ceftriaxone (Rocephin, Wintriaxone)",J01DD04,ATC,1,1,1,1,,,1,1,1,1,,,39 +"Cefuroxime (Ceftin, Zinacef)",J01DC02,ATC,1,1,,,,,,,,,,,40 +"Cephalexin (Cefalexin, Keflex, Daxbia)",J01DB01,ATC,2,,,,,,,,,,,,41 +"Cephalothin (Cefalotin)",J01DB03,ATC,2,,,,,,,,,,,,42 +"Cephapirin (Cefapirin)",J01DB08,ATC,2,,,,,,,,,,,,43 "Cephradine (Cefradine, Velosef)",J01DB09,ATC,2,,,,,,,,,,,,44 -"Chloramphenicol (Chloromycetin, Viceton)",J01BA01,ATC, ,1,,,,,,,,,,,45 +"Chloramphenicol (Chloromycetin, Viceton)",J01BA01,ATC,,1,,,,,,,,,,,45 Cinoxacin (Cinobac),J01MB06,ATC,2,,,,,,,,,,,,46 "Ciprofloxacin (Cetraxal, Cipro, Ciloxan, Proquin)",J01MA02,ATC,1,,,,,,,,,,,,47 "Clarithromycin (Biaxin, Klacid)",J01FA09,ATC,1,1,,,,,,,,,,,48 "Clindamycin (Cleocin, Dalacin)",J01FF01,ATC,1,,,,,,,,,,,,49 -"Cloxacillin (Tegopen, Cloxapen)",J01CF02,ATC, ,,,,,,,,,,,,50 -"Colistin (Colistimethate, Coly Mycin M, Colobreathe, Xylistin)",J01XB01,ATC, ,,,,,,,,,,,,51 +"Cloxacillin (Tegopen, Cloxapen)",J01CF02,ATC,,,,,,,,,,,,,50 +"Colistin (Colistimethate, Coly Mycin M, Colobreathe, Xylistin)",J01XB01,ATC,,,,,,,,,,,,,51 Cycloserine (Seromycin),J04AB01,ATC,2,,,,,,,,,,,,52 -"Daptomycin (Dapzura, Cubicin)",J01XX09 ,ATC, ,,,,,,,,,,,,53 +"Daptomycin (Dapzura, Cubicin)",J01XX09,ATC,,,,,,,,,,,,,53 Demeclocycline (Declomycin),J01AA01,ATC,2,,,,,,,,,,,,54 "Dicloxacillin (Diclocil, Dycill, Dynapen)",J01CF01,ATC,2,,,,,,,,,,,,55 -Dirithromycin (Dynabac),J01FA13 ,ATC,2,,,,,,,,,,,,56 -"Doripenem (Doribax, Finibax)",J01DH04 ,ATC,2,,,,,,,,,,,,57 +Dirithromycin (Dynabac),J01FA13,ATC,2,,,,,,,,,,,,56 +"Doripenem (Doribax, Finibax)",J01DH04,ATC,2,,,,,,,,,,,,57 "Doxycycline (Vibramycin, Oracea, Monodox)",J01AA02,ATC,1,1,1,,1,1,,,,,1,,58 Enoxacin,J01MA04,ATC,2,,,,,,,,,,,,59 -Ertapenem (Invanz) ,J01DH03,ATC,1,,,,,,,,,,,,60 -"Erythromycin (Eryc, Erythrocin) ",J01FA01,ATC,1,1,,,,,,,,,,,61 +Ertapenem (Invanz),J01DH03,ATC,1,,,,,,,,,,,,60 +"Erythromycin (Eryc, Erythrocin)",J01FA01,ATC,1,1,,,,,,,,,,,61 Ethambutol,J04AK02,ATC,,,,,,,,,,,,,62 -"Flucloxacillin (Floxapen, Fluclox) ",J01CF05 ,ATC,1,,,,,,,,,,,,63 -Fluconazole (Diflucan) ,J02AC01 ,ATC,1,,,,,,,,,,,,64 -Fosfomycin (Monurol) ,J01XX01 ,ATC,1,,,,,,,,,,,,65 +"Flucloxacillin (Floxapen, Fluclox)",J01CF05,ATC,1,,,,,,,,,,,,63 +Fluconazole (Diflucan),J02AC01,ATC,1,,,,,,,,,,,,64 +Fosfomycin (Monurol),J01XX01,ATC,1,,,,,,,,,,,,65 Fusidic acid,J01XC01,ATC,,,,,,,,,,,,,66 -Gatifloxacin (Tequin) ,J01MA16,ATC, ,,,,,,,,,,,,67 +Gatifloxacin (Tequin),J01MA16,ATC,,,,,,,,,,,,,67 Gemifloxacin (Factive),J01MA15,ATC,2,,,,,,,,,,,,68 -"Gentamicin (Garamycin, Gentak, Genoptic) ",J01GB03,ATC,1,,,,,,,,,,,,69 +"Gentamicin (Garamycin, Gentak, Genoptic)",J01GB03,ATC,1,,,,,,,,,,,,69 Grepafloxacin,J01MA11,ATC,2,,,,,,,,,,,,70 -Imipenem/Cilastatin (Primaxin) ,J01DH51,ATC,1,,,,,,,,,,,,71 -"Isoniazid (Nydrazid, Laniazid) ",J04AC01,ATC,1,,,,,,,,,,,,72 -Kanamycin (Kantrex),J01GB04 ,ATC, ,,,,,,,,,,,,73 -"Levofloxacin (Levaquin, Levxin, Tavanic) ",J01MA12,ATC,1,1,,,,,1,1,,,,,74 +Imipenem/Cilastatin (Primaxin),J01DH51,ATC,1,,,,,,,,,,,,71 +"Isoniazid (Nydrazid, Laniazid)",J04AC01,ATC,1,,,,,,,,,,,,72 +Kanamycin (Kantrex),J01GB04,ATC,,,,,,,,,,,,,73 +"Levofloxacin (Levaquin, Levxin, Tavanic)",J01MA12,ATC,1,1,,,,,1,1,,,,,74 "Lincomycin (Linobac, Lincomed)",J01FF02,ATC,2,,,,,,,,,,,,75 Linezolid (Zyvox),J01XX08,ATC,1,1,,,,,,,,,,,76 Lomefloxacin,J01MA07,ATC,2,,,,,,,,,,,,77 -"Meropenem (Merrem, Meronem) ",J01DH02 ,ATC,1,1,,,,,,,,,,,78 -"Methenamine hippurate (Hiprex, Urex)",J01XX05 ,ATC,2,,,,,,,,,,,,79 +"Meropenem (Merrem, Meronem)",J01DH02,ATC,1,1,,,,,,,,,,,78 +"Methenamine hippurate (Hiprex, Urex)",J01XX05,ATC,2,,,,,,,,,,,,79 "Methicillin (Meticillin, Staphcillin)",J01CF03,ATC,2,,,,,,,,,,,,80 -"Metronidazole (Flagyl, Likmez) ",J01XD01,ATC,1,,,,,,,,,,,,81 -"Mezlocillin (Baypen, Melocin, Bezlin, Optocillin) ",J01CA10,ATC,2,,,,,,,,,,,,82 +"Metronidazole (Flagyl, Likmez)",J01XD01,ATC,1,,,,,,,,,,,,81 +"Mezlocillin (Baypen, Melocin, Bezlin, Optocillin)",J01CA10,ATC,2,,,,,,,,,,,,82 "Minocycline (Minocin, Ximino)",J01AA08,ATC,2,,,,,,,,,,,,83 -"Moxifloxacin (Avelox, Vigamox) ",J01MA14,ATC,1,,,,,,,,,,,,84 +"Moxifloxacin (Avelox, Vigamox)",J01MA14,ATC,1,,,,,,,,,,,,84 Nafcillin,J01CF06,ATC,2,,,,,,,,,,,,85 "Nalidixic Acid (NegGram, Wintomylon)",J01MB02,ATC,2,,,,,,,,,,,,86 Neomycin (Neovet),J01GB05,ATC,2,,,,,,,,,,,,87 -Netilmicin (Netromycin),J01GB07,ATC, ,,,,,,,,,,,,89 +Netilmicin (Netromycin),J01GB07,ATC,,,,,,,,,,,,,89 "Nitrofural (Aldomycin, Furacin, NFZ)",D08AF01,ATC,2,,,,,,,,,,,,90 -"Nitrofurantoin (Macrobid, Macrodantin) ",J01XE01 ,ATC,1,,,,,,,,,,,,91 +"Nitrofurantoin (Macrobid, Macrodantin)",J01XE01,ATC,1,,,,,,,,,,,,91 "Norfloxacin (Trizolin, Noroxin)",J01MA06,ATC,2,,,,,,,,,,,,92 Novobiocin (Albadry),90220005,SNOMED,2,,,,,,,,,,,,93 "Ofloxacin (Floxin, Ocuflox)",J01MA01,ATC,2,,,,,,,,,,,,94 Oxacillin (Bactocill),J01CF04,ATC,2,,,,,,,,,,,,95 "Oxytetracycline (Agrimycin, Noromycin)",J01AA06,ATC,2,,,,,,,,,,,,96 Piperacillin,J01CA12,ATC,,,,,,,,,,,,,97 -"Piperacillin/Beta-lactamase inhibitor (Piperacillin/Tazobactam, Pip-Taz, Tazocel, Tazocin, Zosyn, ",J01CR05 ,ATC,1,1,,,,,,,,,,,98 -Pivmecillinam (Selexid) ,J01CA08 ,ATC,1,,,,,,,,,,,,100 +"Piperacillin/Beta-lactamase inhibitor (Piperacillin/Tazobactam, Pip-Taz, Tazocel, Tazocin, Zosyn,",J01CR05,ATC,1,1,,,,,,,,,,,98 +Pivmecillinam (Selexid),J01CA08,ATC,1,,,,,,,,,,,,100 Plazomicin (Zemdri),J01GB14,ATC,,,,,,,,,,,,,101 -"Polymyxin B (Poly-Rx, Polysporin) ",J01XB02,ATC, ,,,,,,,,,,,,102 +"Polymyxin B (Poly-Rx, Polysporin)",J01XB02,ATC,,,,,,,,,,,,,102 "Procaine benzylpenicillin (Penicillin G, Bactracillin G, Norocillin)",J01CE09,ATC,,,,,,,,,,,,,103 Pyrazinamide,J04AK01,ATC,,,,,,,,,,,,,104 -Quinupristin/Dalfopristin (Synercid),J01FG02 ,ATC,2,,,,,,,,,,,,105 +Quinupristin/Dalfopristin (Synercid),J01FG02,ATC,2,,,,,,,,,,,,105 Retapamulin (Altabax),D06AX13,ATC,2,,,,,,,,,,,,106 -"Rifampicin (Rifadin, Rimactane) ",J04AB02 ,ATC,1,,,,,,,,,,,,107 +"Rifampicin (Rifadin, Rimactane)",J04AB02,ATC,1,,,,,,,,,,,,107 Rifapentine (Priftin),J04AB05,ATC,2,,,,,,,,,,,,108 -Rifaximin (Xifaxan) ,A07AA11,ATC,1,,,,,,,,,,,,109 +Rifaximin (Xifaxan),A07AA11,ATC,1,,,,,,,,,,,,109 "Roxithromycin (Biaxsig, Rulide)",J01FA06,ATC,,,,,,,,,,,,,110 -Sparfloxacin (Spacin),J01MA09 ,ATC,2,,,,,,,,,,,,111 +Sparfloxacin (Spacin),J01MA09,ATC,2,,,,,,,,,,,,111 Spectinomycin (SpectoGard),J01XX04,ATC,2,,,,,,,,,,,,112 Streptomycin,J01GA01,ATC,2,,,,,,,,,,,,113 Sulfadiazine,J01EC02,ATC,2,,,,,,,,,,,,114 -Sulfamethoxazole (Gantanol) ,J01EC01,ATC,1,,,,,,,,,,,,115 -"Sulfamethoxazole/Trimethoprim (Bactrim, Co-trimoxazole, Septra)",J01EE01 ,ATC,1,1,,,,,,,,,,,116 +Sulfamethoxazole (Gantanol),J01EC01,ATC,1,,,,,,,,,,,,115 +"Sulfamethoxazole/Trimethoprim (Bactrim, Co-trimoxazole, Septra)",J01EE01,ATC,1,1,,,,,,,,,,,116 "Sulfisoxazole (Sulfafurazole, Truxazole)",J01EB05,ATC,2,,,,,,,,,,,,117 -Teicoplanin (Targocid) ,J01XA02,ATC, ,1,,,,,,,,,,,118 +Teicoplanin (Targocid),J01XA02,ATC,,1,,,,,,,,,,,118 "Telavancin (Televancin, Vibativ)",J01XA03,ATC,2,,,,,,,,,,,,119 Telithromycin (Levviax),J01FA15,ATC,2,,,,,,,,,,,,120 "Tetracycline (Viabecline, Vitastem)",J01AA07,ATC,2,,,,,,,,,,,,121 Ticarcillin,J01CA13,ATC,2,,,,,,,,,,,,122 -Ticarcillin/Beta-lactamase inhibitor (Ticacillin/Clavulanate),J01CR03 ,ATC,2,,,,,,,,,,,,123 -Tigecycline (Tygacil),J01AA12 ,ATC,1,,,,,,,,,,,,124 +Ticarcillin/Beta-lactamase inhibitor (Ticacillin/Clavulanate),J01CR03,ATC,2,,,,,,,,,,,,123 +Tigecycline (Tygacil),J01AA12,ATC,1,,,,,,,,,,,,124 "Tobramycin (Nebcin, Tobrex, Tobi)",J01GB01,ATC,1,,,,,,,,,,,,125 Trimethoprim (Primsol),J01EA01,ATC,1,,,,,,,,,,,,126 -Trovafloxacin (Trovan),J01MA13 ,ATC, ,,,,,,,,,,,,127 +Trovafloxacin (Trovan),J01MA13,ATC,,,,,,,,,,,,,127 "Vancomycin (Vancocin, Vancocin HCl, Firvanq)",J01XA01,ATC,1,1,,,,,,1,,,,,128 -Voriconazole (Vfend),J02AC03 ,ATC, ,,,,,,,,,,,,129 +Voriconazole (Vfend),J02AC03,ATC,,,,,,,,,,,,,129 Xibornol,J01XX02,ATC,,,,,,,,,,,,,130 diff --git a/Lists/drugs/Anticoagulant.csv b/Lists/drugs/Anticoagulant.csv index ae3cf6f..be347f8 100644 --- a/Lists/drugs/Anticoagulant.csv +++ b/Lists/drugs/Anticoagulant.csv @@ -1,22 +1,22 @@ Drugs,Code,Library,Selected,preset_Respiratory,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,Comment,Value -Acetylsalicylic Acid (Aspirin),B01AC06 , ATC ,1,,,1,1,,,,,,1 -Alteplase (Activase),B01AD02, ATC ,,,,,,,,,,,2 -Apixaban (Eliquis),B01AF02 , ATC ,1,,1,1,1,,,,,,3 -Argatroban (Acova),B01AE03, ATC , ,,,,,,,,,,4 -Bivalirudin (Angiomax),B01AE06 , ATC , ,,,,,,,,,,5 -Clopidogrel (Plavix),B01AC04 , ATC ,1,,,,,,,,,,6 -Dabigatran Etexilate (Pradaxa),B01AE07 , ATC ,1,,,,,,,,,,7 -Dalteparin (Fragmin),B01AB04 , ATC , ,,,,,,,,,,8 -Desirudin (Iprivask),B01AE01, ATC , ,,,,,,,,,,9 -"Edoxaban (Savaysa, Lixiana)",B01AF03 , ATC , ,,,,,,,,,,10 -Enoxaparin (Lovenox),B01AB05 , ATC ,1,,1,1,1,,,1,,,11 -Fondaparinux (Arixtra),B01AX05 , ATC , ,,,,,,,,,,12 -Heparin (Unfractionated Heparin),B01AB01 , ATC ,1,,,1,1,,,1,,,13 -Lepirudin (Refludan),B01AE02, ATC , ,,,,,,,,,,14 -Rivaroxaban (Xarelto),B01AF01 , ATC ,1,,1,,,,,,,,15 -Streptokinase,B01AD01, ATC ,,,,,,,,,,,16 -Ticagrelor (Brilinta),B01AC24 , ATC ,1,,,,,,,,,,17 +Acetylsalicylic Acid (Aspirin),B01AC06,ATC,1,,,1,1,,,,,,1 +Alteplase (Activase),B01AD02,ATC,,,,,,,,,,,2 +Apixaban (Eliquis),B01AF02,ATC,1,,1,1,1,,,,,,3 +Argatroban (Acova),B01AE03,ATC,,,,,,,,,,,4 +Bivalirudin (Angiomax),B01AE06,ATC,,,,,,,,,,,5 +Clopidogrel (Plavix),B01AC04,ATC,1,,,,,,,,,,6 +Dabigatran Etexilate (Pradaxa),B01AE07,ATC,1,,,,,,,,,,7 +Dalteparin (Fragmin),B01AB04,ATC,,,,,,,,,,,8 +Desirudin (Iprivask),B01AE01,ATC,,,,,,,,,,,9 +"Edoxaban (Savaysa, Lixiana)",B01AF03,ATC,,,,,,,,,,,10 +Enoxaparin (Lovenox),B01AB05,ATC,1,,1,1,1,,,1,,,11 +Fondaparinux (Arixtra),B01AX05,ATC,,,,,,,,,,,12 +Heparin (Unfractionated Heparin),B01AB01,ATC,1,,,1,1,,,1,,,13 +Lepirudin (Refludan),B01AE02,ATC,,,,,,,,,,,14 +Rivaroxaban (Xarelto),B01AF01,ATC,1,,1,,,,,,,,15 +Streptokinase,B01AD01,ATC,,,,,,,,,,,16 +Ticagrelor (Brilinta),B01AC24,ATC,1,,,,,,,,,,17 Ticlopidine (Ticlid,B01AC05,ATC,,,,,,,,,,,18 -Tinzaparin (Innohep),B01AB10, ATC , ,,,,,,,,,,19 -Urokinase (Kinlytic),B01AD04, ATC ,,,,,,,,,,,20 -"Warfarin (Coumadin, Jantoven)",B01AA03 , ATC ,1,,,1,1,,,,,,21 +Tinzaparin (Innohep),B01AB10,ATC,,,,,,,,,,,19 +Urokinase (Kinlytic),B01AD04,ATC,,,,,,,,,,,20 +"Warfarin (Coumadin, Jantoven)",B01AA03,ATC,1,,,1,1,,,,,,21 diff --git a/Lists/drugs/Antiviral.csv b/Lists/drugs/Antiviral.csv index 4651b75..fbee3b6 100644 --- a/Lists/drugs/Antiviral.csv +++ b/Lists/drugs/Antiviral.csv @@ -1,39 +1,39 @@ Drugs,Code,Library,Selected,preset_Respiratory,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Syndromic CRF_ARI,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,Comment,Value -"Aciclovir (Acyclovir, Zovirax) ",J05AB01 ,ATC ,,,,,,,,,,,,,1 +"Aciclovir (Acyclovir, Zovirax)",J05AB01,ATC,,,,,,,,,,,,,1 "Amantadine (Gocovri, Osmolex ER, Symmetrel)",N04BB01,ATC,,,,,,,,,1,,,,2 -Atazanavir (Reyataz) ,J05AE08,ATC ,,,,,,,,,,,,,3 +Atazanavir (Reyataz),J05AE08,ATC,,,,,,,,,,,,,3 Baloxavir marboxil (Xofluza)​,782500006,SNOMED,,,,,,,,1,1,,,,4 -Brincidofovir,J05AB17,ATC ,1,,,,,1,1,,,,1,,5 -Bulevirtide (Hepcludex),J05AX28,ATC ,,,,,,,,,,,,,6 -Cidofovir (Vistide) ,J05AB12,ATC ,1,,,,,1,1,,,,1,,7 -Darunavir (Prezista) ,J05AE10,ATC ,,,,,,,,,,,,,8 -Dolutegravir (Tivicay) ,J05AJ03,ATC ,,,,,,,,,,,,,9 -Efavirenz (Sustiva) ,J05AG03,ATC ,,,,,,,,,,,,,10 -Emtricitabine (Emtriva) ,J05AF09,ATC ,,,,,,,,,,,,,11 -Famciclovir (Famvir) ,J05AB09,ATC ,,,,,,,,,,,,,12 -Favipiravir (Avigan) ,J05AX27,ATC ,,,1,,,,,1,1,1,,,13 -Fluoxetine,N06AB03,ATC ,,,,,,,,,,,,,14 -Ganciclovir (Cytovene) ,J05AB06,ATC ,,,,,,,,,,,,,15 -"Lamivudine (Epivir, 3TC) ",J05AF05,ATC ,,,,,,,,,,,,,16 +Brincidofovir,J05AB17,ATC,1,,,,,1,1,,,,1,,5 +Bulevirtide (Hepcludex),J05AX28,ATC,,,,,,,,,,,,,6 +Cidofovir (Vistide),J05AB12,ATC,1,,,,,1,1,,,,1,,7 +Darunavir (Prezista),J05AE10,ATC,,,,,,,,,,,,,8 +Dolutegravir (Tivicay),J05AJ03,ATC,,,,,,,,,,,,,9 +Efavirenz (Sustiva),J05AG03,ATC,,,,,,,,,,,,,10 +Emtricitabine (Emtriva),J05AF09,ATC,,,,,,,,,,,,,11 +Famciclovir (Famvir),J05AB09,ATC,,,,,,,,,,,,,12 +Favipiravir (Avigan),J05AX27,ATC,,,1,,,,,1,1,1,,,13 +Fluoxetine,N06AB03,ATC,,,,,,,,,,,,,14 +Ganciclovir (Cytovene),J05AB06,ATC,,,,,,,,,,,,,15 +"Lamivudine (Epivir, 3TC)",J05AF05,ATC,,,,,,,,,,,,,16 Laninamivir,OMOP5173449,RxNorm Extension,,,,,,,,1,,,,,17 -Lopinavir/Ritonavir (Kaletra) ,J05AR10 ,ATC ,,,1,,,,,,,,,,18 -Molnupiravir (Lagevrio) ,J05AB18 ,ATC ,,,,,,,,,,,,,19 -Nirmatrelvir/Retonavir (Paxlovid),J05AE30,ATC ,,,,,,,,,,,,,20 -Oseltamivir (Tamiflu) ,J05AH02 ,ATC ,,,1,,,,,1,1,,,,21 -Penciclovir (Denavir),J05AB13 ,ATC ,,,,,,,,,,,,,22 +Lopinavir/Ritonavir (Kaletra),J05AR10,ATC,,,1,,,,,,,,,,18 +Molnupiravir (Lagevrio),J05AB18,ATC,,,,,,,,,,,,,19 +Nirmatrelvir/Retonavir (Paxlovid),J05AE30,ATC,,,,,,,,,,,,,20 +Oseltamivir (Tamiflu),J05AH02,ATC,,,1,,,,,1,1,,,,21 +Penciclovir (Denavir),J05AB13,ATC,,,,,,,,,,,,,22 Peramivir,619693,RxNorm,,,,,,,,1,,,,,23 -Pleconaril,J05AX06,ATC ,,,,,,,,,,,,,24 +Pleconaril,J05AX06,ATC,,,,,,,,,,,,,24 Pocapavir,,,,,,,,,,,,,,,25 -Raltegravir (Isentress) ,J05AJ01,ATC ,,,,,,,,,,,,,26 -Remdesivir (Veklury) ,J05AB16,ATC ,,,1,,,,,,,1,,,27 -"Ribavirin (Rebetol, Copegus) ",J05AP01,ATC ,,,,,,,,,,1,,,28 -Rimantadine (Flumadine) ,J05AC02,ATC ,,,,,,,,,1,,,,29 -Tecovirimat,J05AX24,ATC ,1,,,,,1,1,,,,1,,30 -Tenofovir Disoproxil (Viread) ,J05AF07,ATC ,,,,,,,,,,,,,31 -Tenofovir alafenamide,J05AF13,ATC ,,,,,,,,,,,,,32 -Umifenovir (Arbidol) ,J05AX13,ATC ,,,,,,,,1,1,,,,33 -Valaciclovir (Valtrex) ,J05AB11,ATC ,,,,,,,,,,,,,34 -Valganciclovir (Valcyte) ,J05AB14,ATC ,,,,,,,,,,,,,35 -Zalcitabine,J05AF03,ATC ,,,,,,,,,,,,,36 -Zanamivir (Relenza) ,J05AH01,ATC ,,,1,,,,,1,1,,,,37 -"Zidovudine (Retrovir, AZT) ",J05AF01,ATC ,,,,,,,,,,,,,38 +Raltegravir (Isentress),J05AJ01,ATC,,,,,,,,,,,,,26 +Remdesivir (Veklury),J05AB16,ATC,,,1,,,,,,,1,,,27 +"Ribavirin (Rebetol, Copegus)",J05AP01,ATC,,,,,,,,,,1,,,28 +Rimantadine (Flumadine),J05AC02,ATC,,,,,,,,,1,,,,29 +Tecovirimat,J05AX24,ATC,1,,,,,1,1,,,,1,,30 +Tenofovir Disoproxil (Viread),J05AF07,ATC,,,,,,,,,,,,,31 +Tenofovir alafenamide,J05AF13,ATC,,,,,,,,,,,,,32 +Umifenovir (Arbidol),J05AX13,ATC,,,,,,,,1,1,,,,33 +Valaciclovir (Valtrex),J05AB11,ATC,,,,,,,,,,,,,34 +Valganciclovir (Valcyte),J05AB14,ATC,,,,,,,,,,,,,35 +Zalcitabine,J05AF03,ATC,,,,,,,,,,,,,36 +Zanamivir (Relenza),J05AH01,ATC,,,1,,,,,1,1,,,,37 +"Zidovudine (Retrovir, AZT)",J05AF01,ATC,,,,,,,,,,,,,38 diff --git a/Lists/drugs/IVfluids.csv b/Lists/drugs/IVfluids.csv index b1f2f35..a59cf27 100644 --- a/Lists/drugs/IVfluids.csv +++ b/Lists/drugs/IVfluids.csv @@ -1,5 +1,5 @@ Drugs,Code, Library,Selected,preset_Respiratory,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_UserGenerated_Oropouche,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,Comment,Value -0.18%-0.3% Sodium Chloride + 4% Glucose (Hypotonic saline with dextrose) ,,,,,,1,1,,,,1,1,,,1 +0.18%-0.3% Sodium Chloride + 4% Glucose (Hypotonic saline with dextrose),,,,,,1,1,,,,1,1,,,1 0.45% Sodium Chloride (Half-normal saline),,,,,,1,1,,,,1,1,,,2 0.45% normal saline + 4% Glucose (Half-normal saline with dextrose),,,,,,1,1,,,,1,1,,,3 0.9% Sodium Chloride (Normal Saline),,,,,,1,1,,,,1,1,,,4 diff --git a/Lists/drugs/Immunosuppressants.csv b/Lists/drugs/Immunosuppressants.csv index 16e2093..ecf3c44 100644 --- a/Lists/drugs/Immunosuppressants.csv +++ b/Lists/drugs/Immunosuppressants.csv @@ -1,28 +1,28 @@ Drugs,Code,Library,Selected,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,Value -Abatacept (Orencia) , L04AA24 , ATC , ,,,,1 -Adalimumab (Humira) , L04AB04 , ATC ,1,,,,2 -"Alemtuzumab (Campath, Lemtrada)", L04AA34, ATC ,,1,1,,3 -Anakinra ,L04AC03,ATC,,,,,4 -"Azathioprine (Imuran, Azasan) ", L04AX01 , ATC ,1,1,1,1,5 -Basiliximab (Simulect) , L04AC02, ATC , ,,,,6 -Belatacept (Nulojix) , L04AA28, ATC , ,,,,7 -"Ciclosporin (Neoral, Sandimmune, Gengraf) ", L04AD01 , ATC ,1,1,1,,8 -Etanercept (Enbrel) , L04AB01 , ATC ,1,,,,9 -"Everolimus (Afinitor, Zortress) ", L04AA18 , ATC , ,1,1,,10 -"Infliximab (Avsola, Inflectra, Remicade) ", L04AB02 , ATC ,1,,,,11 -Leflunomide (Arava) , L04AA13 , ATC , ,,,,12 +Abatacept (Orencia),L04AA24,ATC,,,,,1 +Adalimumab (Humira),L04AB04,ATC,1,,,,2 +"Alemtuzumab (Campath, Lemtrada)",L04AA34,ATC,,1,1,,3 +Anakinra,L04AC03,ATC,,,,,4 +"Azathioprine (Imuran, Azasan)",L04AX01,ATC,1,1,1,1,5 +Basiliximab (Simulect),L04AC02,ATC,,,,,6 +Belatacept (Nulojix),L04AA28,ATC,,,,,7 +"Ciclosporin (Neoral, Sandimmune, Gengraf)",L04AD01,ATC,1,1,1,,8 +Etanercept (Enbrel),L04AB01,ATC,1,,,,9 +"Everolimus (Afinitor, Zortress)",L04AA18,ATC,,1,1,,10 +"Infliximab (Avsola, Inflectra, Remicade)",L04AB02,ATC,1,,,,11 +Leflunomide (Arava),L04AA13,ATC,,,,,12 Mercaptopurine (Purixan),L01BB02,ATC,,,,,13 -"Methotrexate (Trexall, Rasuvo, Otrexup) ",L04AX03 ,ATC ,1,1,1,1,14 -Mycophenolate Mofetil (CellCept) , L04AA06 , ATC ,1,1,1,,15 -Mycophenolic Acid (Myfortic) , L04AA06, ATC ,1,,,1,16 -Natalizumab (Tysabri), L04AA23 , ATC , ,,,,17 +"Methotrexate (Trexall, Rasuvo, Otrexup)",L04AX03,ATC,1,1,1,1,14 +Mycophenolate Mofetil (CellCept),L04AA06,ATC,1,1,1,,15 +Mycophenolic Acid (Myfortic),L04AA06,ATC,1,,,1,16 +Natalizumab (Tysabri),L04AA23,ATC,,,,,17 Nivolumab (Opdivo),L01FF02,ATC,,,,,18 -"Rituximab (Rituxan, MabThera) ",L01FA01 , ATC ,1,1,1,1,19 -Sarilumab (Kevzara) , L04AC14, ATC ,1,,,,20 -Secukinumab (Cosentyx) , L04AC10 , ATC , ,,,,21 -Sirolimus (Rapamune) , L04AA10 , ATC , ,1,1,,22 -"Tacrolimus (Prograf, Advagraf, Protopic) ", L04AD02 , ATC ,1,1,1,,23 +"Rituximab (Rituxan, MabThera)",L01FA01,ATC,1,1,1,1,19 +Sarilumab (Kevzara),L04AC14,ATC,1,,,,20 +Secukinumab (Cosentyx),L04AC10,ATC,,,,,21 +Sirolimus (Rapamune),L04AA10,ATC,,1,1,,22 +"Tacrolimus (Prograf, Advagraf, Protopic)",L04AD02,ATC,1,1,1,,23 Thalidomide (Thalomid),L04AX02,ATC,,,,,24 -Tocilizumab (Actemra) , L04AC07 , ATC ,1,,,1,25 -Ustekinumab (Stelara) , L04AC05 , ATC , ,,,,26 -Vedolizumab (Entyvio) , L04AA33, ATC , ,,,,27 +Tocilizumab (Actemra),L04AC07,ATC,1,,,1,25 +Ustekinumab (Stelara),L04AC05,ATC,,,,,26 +Vedolizumab (Entyvio),L04AA33,ATC,,,,,27 diff --git a/Lists/drugs/Other.csv b/Lists/drugs/Other.csv index 9d498b3..42ba9e2 100644 --- a/Lists/drugs/Other.csv +++ b/Lists/drugs/Other.csv @@ -1,36 +1,36 @@ Drugs,Code,Library,Selected,preset_Respiratory,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Comment,Value -Aminophylline (Truphylline) , R03DA05 , ATC ,,,,,,,,,,,1 -"Beclometasone (Qvar, Beconase AQ) ", R03BA01 , ATC ,,,,,,,,,,,2 -Caspofungin (Cancidas) , J02AX04 , ATC ,,,,,,,,,,,3 -Chloroquine (Aralen) , P01BA01 , ATC ,,,1.0,,,,,,1.0,,4 -"Clobetasol (Temovate, Olux, Impoyz) ",D07AD01,ATC,,,,,,,,,,Topical,5 -Fluconazole (Diflucan) , J02AC01 , ATC ,,,,,,,,,,,6 -"Fluticasone (Flovent, Flonase) ", R03BA05 , ATC ,,,,,,,,,,,7 -Fluticasone furoate, R03BA09, ATC ,,,,,,,,,,,8 -"Formoterol (Foradil, Perforomist) ", R03AC13, ATC ,,,,,,,,,,,9 -Formoterol and Beclometasone (Fostair) , R03AK11 , ATC ,,,,,,,,,,,10 -Formoterol and Budesonide (Symbicort) , R03AK07 , ATC ,,,,,,,,,,,11 -Glycopyrronium Bromide (Seebri) , R03BB06 , ATC ,,,,,,,,,,,12 -Hydroxychloroquine (Plaquenil) , P01BA02 , ATC ,,,,,,,,,,,13 -"Imiquimod (Aldara, Zyclara)",D06BB10 ,ATC,,,,,,,,,,Topical/Locally acting,14 -Indacaterol and Glycopyrronium Bromide (Ultibro Breezhaler), R03AL04, ATC ,,,,,,,,,,,15 -Interferon Alpha , L03AB01 , ATC ,,,1.0,,,,,,1.0,,16 -Interferon Beta , L03AB02 , ATC ,,,1.0,,,,,,1.0,,17 -Ipratropium Bromide (Atrovent) , R03BB01 , ATC ,,,,,,,,,,,18 -Ivermectin (Stromectol) , P02CF01 , ATC ,,,,,,,,,,,19 +Aminophylline (Truphylline),R03DA05,ATC,,,,,,,,,,,1 +"Beclometasone (Qvar, Beconase AQ)",R03BA01,ATC,,,,,,,,,,,2 +Caspofungin (Cancidas),J02AX04,ATC,,,,,,,,,,,3 +Chloroquine (Aralen),P01BA01,ATC,,,1.0,,,,,,1.0,,4 +"Clobetasol (Temovate, Olux, Impoyz)",D07AD01,ATC,,,,,,,,,,Topical,5 +Fluconazole (Diflucan),J02AC01,ATC,,,,,,,,,,,6 +"Fluticasone (Flovent, Flonase)",R03BA05,ATC,,,,,,,,,,,7 +Fluticasone furoate,R03BA09,ATC,,,,,,,,,,,8 +"Formoterol (Foradil, Perforomist)",R03AC13,ATC,,,,,,,,,,,9 +Formoterol and Beclometasone (Fostair),R03AK11,ATC,,,,,,,,,,,10 +Formoterol and Budesonide (Symbicort),R03AK07,ATC,,,,,,,,,,,11 +Glycopyrronium Bromide (Seebri),R03BB06,ATC,,,,,,,,,,,12 +Hydroxychloroquine (Plaquenil),P01BA02,ATC,,,,,,,,,,,13 +"Imiquimod (Aldara, Zyclara)",D06BB10,ATC,,,,,,,,,,Topical/Locally acting,14 +Indacaterol and Glycopyrronium Bromide (Ultibro Breezhaler),R03AL04,ATC,,,,,,,,,,,15 +Interferon Alpha,L03AB01,ATC,,,1.0,,,,,,1.0,,16 +Interferon Beta,L03AB02,ATC,,,1.0,,,,,,1.0,,17 +Ipratropium Bromide (Atrovent),R03BB01,ATC,,,,,,,,,,,18 +Ivermectin (Stromectol),P02CF01,ATC,,,,,,,,,,,19 Mafenide (Sulfamylon),D06BA03,ATC,,,,,,,,,,Topical,20 -"Mometasone (Asmanex, Nasonex)", R03BA07, ATC ,,,,,,,,,,,21 -Montelukast (Singulair) , R03DC03 , ATC ,,,,,,,,,,,22 +"Mometasone (Asmanex, Nasonex)",R03BA07,ATC,,,,,,,,,,,21 +Montelukast (Singulair),R03DC03,ATC,,,,,,,,,,,22 Mupirocin (Bactroban),D06AX09,ATC,,,,,,,,,,Topical/Locally acting,23 "Nystatin (Bio-statin, Nyamyc)",A02AA01,ATC,,,,,,,,,,Locally acting,24 -"Podophyllotoxin (Podofilox, Condylox)",D06BB04 ,ATC,,,,,,,,,,Topical,25 -Primaquine , P01BA03 , ATC ,,,,,,,,,,,26 -"Salbutamol (Ventolin, Proventil) ", R03AC02 , ATC ,,,,,,,,,,,27 -Salmeterol (Serevent) , R03AC12 , ATC ,1.0,,,,,,,,,,28 -"Salmeterol and Fluticasone (Advair, Seretide) ", R03AK06 , ATC ,,,,,,,,,,,29 +"Podophyllotoxin (Podofilox, Condylox)",D06BB04,ATC,,,,,,,,,,Topical,25 +Primaquine,P01BA03,ATC,,,,,,,,,,,26 +"Salbutamol (Ventolin, Proventil)",R03AC02,ATC,,,,,,,,,,,27 +Salmeterol (Serevent),R03AC12,ATC,1.0,,,,,,,,,,28 +"Salmeterol and Fluticasone (Advair, Seretide)",R03AK06,ATC,,,,,,,,,,,29 "Sulphur, precipitated in petrolatum",D10AB02,ATC,,,,,,,,,,Topical,30 -"Theophylline (Theo-24, Elixophyllin) ", R03DA04 , ATC ,,,,,,,,,,,31 -Tiotropium Bromide (Spiriva) , R03BB04 , ATC ,,,,,,,,,,,32 +"Theophylline (Theo-24, Elixophyllin)",R03DA04,ATC,,,,,,,,,,,31 +Tiotropium Bromide (Spiriva),R03BB04,ATC,,,,,,,,,,,32 Trichloroacetic acid,78151001,SNOMED,,,,,,,,,,Topical,33 -Vilanterol and Fluticasone Furoate (Breo Ellipta) , R03AK10 , ATC ,,,,,,,,,,,34 -Vilanterol and Umeclidinium Bromide (Anoro Ellipta) ,R03AL03, ATC ,1.0,,,,,,,,,,35 +Vilanterol and Fluticasone Furoate (Breo Ellipta),R03AK10,ATC,,,,,,,,,,,34 +Vilanterol and Umeclidinium Bromide (Anoro Ellipta),R03AL03,ATC,1.0,,,,,,,,,,35 diff --git a/Lists/drugs/Steroids.csv b/Lists/drugs/Steroids.csv index 33de145..f9d0fa5 100644 --- a/Lists/drugs/Steroids.csv +++ b/Lists/drugs/Steroids.csv @@ -1,14 +1,14 @@ Drugs,Code,Library,Selected,preset_Respiratory,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_Syndrome_VHF,preset_ARChetype Syndromic CRF_ARI,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,Comment,Value "Beclomethasone (Beclometasone, Beconase)",R03BA01,ATC,,,,,,,,,,,,,1 -"Betamethasone (Celestone, Betnelan) ",H02AB01,ATC, ,,,,,,,,,,,,2 +"Betamethasone (Celestone, Betnelan)",H02AB01,ATC,,,,,,,,,,,,,2 Budesonide (Pulmicort),R03BA02,ATC,,,,,,,,,,,,,3 -Cortisone (Cortone) ,H02AB10 ,ATC,,,,,,,,1,,,,,4 -"Dexamethasone (Decadron, Dexasone, Diodex) ",H02AB02,ATC,1,,1,1,1,1,1,,1,1,1,,5 +Cortisone (Cortone),H02AB10,ATC,,,,,,,,1,,,,,4 +"Dexamethasone (Decadron, Dexasone, Diodex)",H02AB02,ATC,1,,1,1,1,1,1,,1,1,1,,5 "Fludrocortisone (Astonin, Florinef)",H02AA02,ATC,,,,,,,,,,,,,6 -"Fluticasone (Flovent, Flonase) ",R03BA05,ATC,,,,,,,,,,,,,7 -"Hydrocortisone (Cortef, Solu-Cortef) ",H02AB09,ATC,1,,1,1,1,1,1,,1,1,1,,8 -"Methylprednisolone (Medrol, Solu-Medrol) ",H02AB04 ,ATC,1,,1,1,1,1,1,,1,1,1,,9 -"Mometasone (Asmanex, Elocon, Nasonex) ",R03BA07,ATC,,,,,,,,,,,,,10 -"Prednisolone (Prelone, Orapred) ",H02AB06 ,ATC,1,,1,1,1,,,,1,1,,,11 -Prednisone (Deltasone) ,H02AB07 ,ATC,1,,,1,1,1,1,,,,1,,12 -"Triamcinolone (Kenalog, Aristocort) ",H02AB08 ,ATC, ,,,,,,,,,,,,13 +"Fluticasone (Flovent, Flonase)",R03BA05,ATC,,,,,,,,,,,,,7 +"Hydrocortisone (Cortef, Solu-Cortef)",H02AB09,ATC,1,,1,1,1,1,1,,1,1,1,,8 +"Methylprednisolone (Medrol, Solu-Medrol)",H02AB04,ATC,1,,1,1,1,1,1,,1,1,1,,9 +"Mometasone (Asmanex, Elocon, Nasonex)",R03BA07,ATC,,,,,,,,,,,,,10 +"Prednisolone (Prelone, Orapred)",H02AB06,ATC,1,,1,1,1,,,,1,1,,,11 +Prednisone (Deltasone),H02AB07,ATC,1,,,1,1,1,1,,,,1,,12 +"Triamcinolone (Kenalog, Aristocort)",H02AB08,ATC,,,,,,,,,,,,,13 diff --git a/Lists/drugs/Type.csv b/Lists/drugs/Type.csv index c81f00e..1da3604 100644 --- a/Lists/drugs/Type.csv +++ b/Lists/drugs/Type.csv @@ -1,17 +1,17 @@ Drugs,Code,Library,Selected,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value -Analgesic ,373265006 |Analgesic (substance)|,SNOMED,1.0,,1.0,,1 -Antibiotic ,255631004 |Antibiotic (product)|,SNOMED,1.0,1.0,,1.0,2 +Analgesic,373265006 |Analgesic (substance)|,SNOMED,1.0,,1.0,,1 +Antibiotic,255631004 |Antibiotic (product)|,SNOMED,1.0,1.0,,1.0,2 Anticoagulant,372862008 |Anticoagulant (substance)|,SNOMED,,1.0,,1.0,3 -Antifungal ,373219008 |Substance with antifungal mechanism of action (substance)|,SNOMED,1.0,1.0,,1.0,4 +Antifungal,373219008 |Substance with antifungal mechanism of action (substance)|,SNOMED,1.0,1.0,,1.0,4 Antihistamine,6425004 |Product containing histamine receptor antagonist (product)|,SNOMED,,,,,5 Antiprotozoal,788027008 |Medicinal product acting as antiprotozoal agent (product)|,SNOMED,,,,,6 -Antipruritic ,312067003 |Local antipruritic agent (product)|,SNOMED,1.0,,,,7 -Antiviral ,372701006,SNOMED,1.0,1.0,1.0,1.0,8 -Convalescent plasma ,1179779000,SNOMED,,,,,9 -Corticosteroid ,116566001,SNOMED,1.0,1.0,1.0,1.0,10 +Antipruritic,312067003 |Local antipruritic agent (product)|,SNOMED,1.0,,,,7 +Antiviral,372701006,SNOMED,1.0,1.0,1.0,1.0,8 +Convalescent plasma,1179779000,SNOMED,,,,,9 +Corticosteroid,116566001,SNOMED,1.0,1.0,1.0,1.0,10 Diuretics,372695000,SNOMED,,,,,11 Immunomodulator,372558009,SNOMED,,,1.0,,12 Immunosuppressive drugs (non-steroid),69431002,SNOMED,,,1.0,,13 -Inotropes / vasopressor ,373213009 |Inotropic agent (substance)|870406003 |Vasopressor (substance)|,SNOMED,,1.0,,1.0,14 -Intravenous immunoglobulin ,698802001,SNOMED,,,1.0,,15 -Topical antibiotic ,255631004 |Antibiotic (product)| 6064005 |Topical route (qualifier value)|,SNOMED,1.0,,,,16 +Inotropes / vasopressor,373213009 |Inotropic agent (substance)|870406003 |Vasopressor (substance)|,SNOMED,,1.0,,1.0,14 +Intravenous immunoglobulin,698802001,SNOMED,,,1.0,,15 +Topical antibiotic,255631004 |Antibiotic (product)| 6064005 |Topical route (qualifier value)|,SNOMED,1.0,,,,16 diff --git a/Lists/drugs/nsaids.csv b/Lists/drugs/nsaids.csv index 8c501eb..897fda2 100644 --- a/Lists/drugs/nsaids.csv +++ b/Lists/drugs/nsaids.csv @@ -1,16 +1,16 @@ Drugs,Code,Library,Selected,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,Value -"Acetylsalicylic acid (Aspirin, Ascriptin, Ecotrin)",N02BA01, ATC ,1,1,1,1,1 -Celecoxib (Celebrex), M01AH01 , ATC ,1,1,1,1,2 -"Diclofenac (Voltaren, Cataflam)", M01AB05 , ATC ,1,1,1,1,3 -Etoricoxib (Arcoxia), M01AH05 , ATC , , , , ,4 -"Flurbiprofen (Ansaid, Ocufen)", M01AE09 , ATC , , , , ,5 -"Ibuprofen (Advil, Motrin)", M01AE01 , ATC ,1,1,1,1,6 -Indomethacin (Indocin), M01AB01 , ATC ,1,1,1,1,7 -"Ketoprofen (Orudis, Oruvail)", M01AE03 , ATC , , , , ,8 -Ketorolac (Toradol), M01AB15 , ATC , , , , ,9 -Mefenamic Acid (Ponstel), M01AG01 , ATC , , , , ,10 -Meloxicam (Mobic), M01AC06 , ATC , , , , ,11 -Nabumetone (Relafen), M01AX01 , ATC , , , , ,12 -"Naproxen (Aleve, Naprosyn)", M01AE02 , ATC ,1,1,1,1,13 -Piroxicam (Feldene), M01AC01 , ATC , , ,, ,14 -Sulindac (Clinoril), M01AB02 , ATC , , ,, ,15 +"Acetylsalicylic acid (Aspirin, Ascriptin, Ecotrin)",N02BA01,ATC,1,1,1,1,1 +Celecoxib (Celebrex),M01AH01,ATC,1,1,1,1,2 +"Diclofenac (Voltaren, Cataflam)",M01AB05,ATC,1,1,1,1,3 +Etoricoxib (Arcoxia),M01AH05,ATC,,,,,4 +"Flurbiprofen (Ansaid, Ocufen)",M01AE09,ATC,,,,,5 +"Ibuprofen (Advil, Motrin)",M01AE01,ATC,1,1,1,1,6 +Indomethacin (Indocin),M01AB01,ATC,1,1,1,1,7 +"Ketoprofen (Orudis, Oruvail)",M01AE03,ATC,,,,,8 +Ketorolac (Toradol),M01AB15,ATC,,,,,9 +Mefenamic Acid (Ponstel),M01AG01,ATC,,,,,10 +Meloxicam (Mobic),M01AC06,ATC,,,,,11 +Nabumetone (Relafen),M01AX01,ATC,,,,,12 +"Naproxen (Aleve, Naprosyn)",M01AE02,ATC,1,1,1,1,13 +Piroxicam (Feldene),M01AC01,ATC,,,,,14 +Sulindac (Clinoril),M01AB02,ATC,,,,,15 diff --git a/Lists/followup/outcome.csv b/Lists/followup/outcome.csv index 22312ab..1850950 100644 --- a/Lists/followup/outcome.csv +++ b/Lists/followup/outcome.csv @@ -2,7 +2,7 @@ Outcome,Code,Selected,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease All lesions are completely resolved and no serious complications,,,1.0,1.0,1.0,,1 All lesions are no longer active and no serious complications,,,1.0,1.0,1.0,,2 Death,,1.0,1.0,1.0,1.0,1.0,3 -Discharged alive - medical grounds ,,1.0,1.0,1.0,1.0,1.0,4 +Discharged alive - medical grounds,,1.0,1.0,1.0,1.0,1.0,4 Discharged alive - patient's preference,,1.0,1.0,1.0,1.0,1.0,5 Early withdrawal,,1.0,1.0,1.0,1.0,1.0,6 Loss to follow-up,,1.0,1.0,1.0,1.0,1.0,7 diff --git a/Lists/inclusion/Diseases.csv b/Lists/inclusion/Diseases.csv index 3cbc3d0..bc4528a 100644 --- a/Lists/inclusion/Diseases.csv +++ b/Lists/inclusion/Diseases.csv @@ -1,19 +1,19 @@ -Disease,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_UserGenerated_Oropouche,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,Value +Disease,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_UserGenerated_Oropouche,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,Value Adenovirus,,,,,,,,1,,,,,,1 Andes virus infection (hantavirus),359761005,SNOMED,,,,,,,,1,,,,2 Argentine haemorrhagic fever (Junin virus),58868000,SNOMED,,,,,,,,1,,,,3 -Avian influenza A H7N9/ H5N1/ H5N8/ H7N7 ,NEW CODE (609444009 | Influenza A virus subtype H7N9 (organism) |772827006 | Influenza A virus subtype H5N1 (organism) |715346008 | Influenza A virus subtype H7N7 (organism) |708527000 | Influenza A virus subtype H5N8 (organism) |,,,,,,,1,,,,,,4 +Avian influenza A H7N9/ H5N1/ H5N8/ H7N7,NEW CODE (609444009 | Influenza A virus subtype H7N9 (organism) |772827006 | Influenza A virus subtype H5N1 (organism) |715346008 | Influenza A virus subtype H7N7 (organism) |708527000 | Influenza A virus subtype H5N8 (organism) |,,,,,,,1,,,,,,4 Bacterial infection,87628006,SNOMED,,,,,,,,,,,,5 Bolivian haemorrhagic fever (Machupo virus),67247008,SNOMED,,,,,,,,1,,,,6 -COVID-19 (SARS-CoV-2) ,840539006,SNOMED,1,1,,,,1,,,,,1,7 +COVID-19 (SARS-CoV-2),840539006,SNOMED,1,1,,,,1,,,,,1,7 Chickenpox (Varicella),58750007,SNOMED,,,,1,1,,,,1,,,8 Crimean Congo haemorrhagic fever (CCHF),43489008,SNOMED,,,,,,,,1,,,,9 -Dengue ,38362002,SNOMED,1,,1,,,,,1,,1,,10 +Dengue,38362002,SNOMED,1,,1,,,,,1,,1,,10 Ebola virus disease (EVD),37109004,SNOMED,,,,,,,,1,,,,11 Enterovirus,53648006,SNOMED,,,,,,,,,,,,12 Exposure to CBRN agent,,,,,,,,,,,,,,13 Exposure to Harmful Energy,,,,,,,,,,,,,,14 -HSV ,88594005,SNOMED,,,,,,,,,,,,15 +HSV,88594005,SNOMED,,,,,,,,,,,,15 "Hepatitis (general, unspecified)",40468003,SNOMED,,,1,,,,,,,,,16 Herpes simplex virus infection (HSV),88594005,SNOMED,,,,1,1,,,,1,,,17 Human immunodeficiency virus infection (HIV infection),86406008,SNOMED,,,,1,1,,,,1,,,18 @@ -25,18 +25,18 @@ Influenza A H7N9,609444009,SNOMED,,,,,,,,,,,,23 Influenza A virus,407479009,SNOMED,,,,,,,,,,,,24 Influenza B virus,407480007,SNOMED,,,,,,,,,,,,25 Influenza virus,725894000,SNOMED,,,,,,,,,1,,,26 -JE ,52947006,SNOMED,,,,,,,,,,,,27 +JE,52947006,SNOMED,,,,,,,,,,,,27 Lassa fever,19065005,SNOMED,,,,,,,,1,,,,28 Lujo virus disease,721784007,SNOMED,,,,,,,,1,,,,29 Marburg virus disease (MVD),77503002,SNOMED,,,,,,,,1,,,,30 Measles,14189004,SNOMED,,,,,,,,,,,,31 Middle East respiratory syndrome (MERS),6.51E+11,SNOMED,,,,,,,,,,,,32 -Mpox ,359814004,SNOMED,1,,,1,1,,,,1,,,33 -Nipah ,406597005,SNOMED,,,,,,,,,,,,34 +Mpox,359814004,SNOMED,1,,,1,1,,,,1,,,33 +Nipah,406597005,SNOMED,,,,,,,,,,,,34 Oropouche,72880002,SNOMED,,,,,,,1,,,1,,35 Pneumonic plague (Yersinia pestis),38976008,SNOMED,,,,,,,,,,,,36 Respiratory syncytial virus infection (RSV),55256001,SNOMED,,,,,,,,,,,1,37 -Severe Acute paediatric hepatitis ,37871000 | Acute hepatitis (disorder) |24484000 | Severe (severity modifier) (qualifier value) |255398004 | Childhood (qualifier value) |,SNOMED,,,,,,,,,,,,38 +Severe Acute paediatric hepatitis,37871000 | Acute hepatitis (disorder) |24484000 | Severe (severity modifier) (qualifier value) |255398004 | Childhood (qualifier value) |,SNOMED,,,,,,,,,,,,38 Severe acute respiratory syndrome (SARS-not COVID-19),398447004,SNOMED,,,,,,,,,,,1,39 Severe fever with thrombocytopaenia syndrome (SFTS),722401001,SNOMED,,,,,,,,,,,,40 Undefined influenza,155559006,SNOMED,,,,,,,,,,,1,41 diff --git a/Lists/outcome/Diseases.csv b/Lists/outcome/Diseases.csv index 5a275f8..e6e936c 100644 --- a/Lists/outcome/Diseases.csv +++ b/Lists/outcome/Diseases.csv @@ -1,19 +1,19 @@ -Disease,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_UserGenerated_Oropouche,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,Value +Disease,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_UserGenerated_Oropouche,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,Value Adenovirus,,,,,,,,1,,,,,,1 Andes virus infection (hantavirus),359761005,SNOMED,,,,,,,,1,,,,2 Argentine haemorrhagic fever (Junin virus),58868000,SNOMED,,,,,,,,1,,,,3 -Avian influenza A H7N9/ H5N1/ H5N8/ H7N7 ,NEW CODE (609444009 | Influenza A virus subtype H7N9 (organism) |772827006 | Influenza A virus subtype H5N1 (organism) |715346008 | Influenza A virus subtype H7N7 (organism) |708527000 | Influenza A virus subtype H5N8 (organism) |,,,,,,,1,,,,,,4 +Avian influenza A H7N9/ H5N1/ H5N8/ H7N7,NEW CODE (609444009 | Influenza A virus subtype H7N9 (organism) |772827006 | Influenza A virus subtype H5N1 (organism) |715346008 | Influenza A virus subtype H7N7 (organism) |708527000 | Influenza A virus subtype H5N8 (organism) |,,,,,,,1,,,,,,4 Bacterial infection,87628006,SNOMED,1,1,1,1,1,1,1,1,1,,1,5 Bolivian haemorrhagic fever (Machupo virus),67247008,SNOMED,,,,,,,,1,,,,6 -COVID-19 (SARS-CoV-2) ,840539006,SNOMED,,1,,,,1,,,,,1,7 +COVID-19 (SARS-CoV-2),840539006,SNOMED,,1,,,,1,,,,,1,7 Chickenpox (Varicella),58750007,SNOMED,,,,1,1,,,,1,,,8 Crimean Congo haemorrhagic fever (CCHF),43489008,SNOMED,,,,,,,,1,,,,9 -Dengue ,38362002,SNOMED,,,1,,,,,1,,1,,10 +Dengue,38362002,SNOMED,,,1,,,,,1,,1,,10 Ebola virus disease (EVD),37109004,SNOMED,,,,,,,,1,,,,11 Enterovirus,53648006,SNOMED,,,,,,,,,,,,12 Exposure to CBRN agent,,,,,,,,,,,,,,13 Exposure to Harmful Energy,,,,,,,,,,,,,,14 -HSV ,88594005,SNOMED,,,,,,,,,,,,15 +HSV,88594005,SNOMED,,,,,,,,,,,,15 Hepatitis,40468003,SNOMED,,,1,,,,,,,1,,16 Herpes simplex virus infection (HSV),88594005,SNOMED,,,,1,1,,,,1,,,17 Human immunodeficiency virus infection (HIV infection),86406008,SNOMED,,,,1,1,,,,1,,,18 @@ -25,18 +25,18 @@ Influenza A H7N9,609444009,SNOMED,,,,,,,,,,,,23 Influenza A virus,407479009,SNOMED,,,,,,,,,,,,24 Influenza B virus,407480007,SNOMED,,,,,,,,,,,,25 Influenza virus,725894000,SNOMED,,,,,,,,,,,,26 -JE ,52947006,SNOMED,,,,,,,,,,,,27 +JE,52947006,SNOMED,,,,,,,,,,,,27 Lassa fever,19065005,SNOMED,,,,,,,,1,,,,28 Lujo virus disease,721784007,SNOMED,,,,,,,,1,,,,29 Marburg virus disease (MVD),77503002,SNOMED,,,,,,,,1,,,,30 Measles,14189004,SNOMED,,,,,,,,,,,,31 Middle East respiratory syndrome (MERS),6.51E+11,SNOMED,,,,,,,,,,,,32 -Mpox ,359814004,SNOMED,1,,,1,1,,,,1,,,33 -Nipah ,406597005,SNOMED,,,,,,,,,,,,34 +Mpox,359814004,SNOMED,1,,,1,1,,,,1,,,33 +Nipah,406597005,SNOMED,,,,,,,,,,,,34 Oropouche,72880002,SNOMED,,,,,,,1,,,1,,35 Pneumonic plague (Yersinia pestis),38976008,SNOMED,,,,,,,,,,,,36 Respiratory syncytial virus infection (RSV),55256001,SNOMED,,,,,,,,,,,,37 -Severe Acute paediatric hepatitis ,37871000 | Acute hepatitis (disorder) |24484000 | Severe (severity modifier) (qualifier value) |255398004 | Childhood (qualifier value) |,SNOMED,,,,,,,,,,,,38 +Severe Acute paediatric hepatitis,37871000 | Acute hepatitis (disorder) |24484000 | Severe (severity modifier) (qualifier value) |255398004 | Childhood (qualifier value) |,SNOMED,,,,,,,,,,,,38 Severe acute respiratory syndrome (SARS-not COVID-19),398447004,SNOMED,,,,,,,,,,,,39 Severe fever with thrombocytopaenia syndrome (SFTS),722401001,SNOMED,,,,,,,,,,,,40 Undefined influenza,155559006,SNOMED,,,,,,,,,,,,41 diff --git a/Lists/pathogens/All.csv b/Lists/pathogens/All.csv index c6b268b..31d5ca5 100644 --- a/Lists/pathogens/All.csv +++ b/Lists/pathogens/All.csv @@ -1,4 +1,4 @@ -Microorganism,Code,Library,Type,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,preset_Recommended Outcomes_Dengue,Comment,Value +Microorganism,Code,Library,Type,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_Syndrome_VHF,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_Arbovirus,preset_ARChetype Syndromic CRF_ARI,preset_Recommended Outcomes_Dengue,Comment,Value Achromobacter,91620006.0,SNOMED,bacteria,,,,,,,,,,,,,1 Achromobacter xylosoxidans,413424009.0,SNOMED,bacteria,,,,,,,,,,,,,2 Acinetobacter,7757008.0,SNOMED,bacteria,,,,,,,,,,,,,3 @@ -188,7 +188,7 @@ Influenza B virus,407480007.0,SNOMED,virus,1,,,,,1,,,,1,,,189 Influenza virus,725894000.0,SNOMED,virus,1,,,,,1,,1,,1,,,190 Isospora belli,12633005.0,SNOMED,"parasite, protozoa",,,,,,,,,,,,,191 Japanese encephalitis virus (JEV),243603004.0,SNOMED,virus,,,,,,,,,,,,,192 -Junin virus ,26352009.0,SNOMED,virus,,,,,,,,,,,,,193 +Junin virus,26352009.0,SNOMED,virus,,,,,,,,,,,,,193 Klebsiella,75032006.0,SNOMED,bacteria,,,,,,,,,,,,,194 Klebsiella aerogenes,62592009.0,SNOMED,bacteria,,,,,,,,,,,,,195 Klebsiella oxytoca,40886007.0,SNOMED,bacteria,,,,,,,,,,,,,196 @@ -210,7 +210,7 @@ Listeria monocytogenes,36094007.0,SNOMED,bacteria,,,,,,,,,,,,,211 Lomentospora prolificans (Scedosporium prlificans),69564000.0,SNOMED,fungi,,,,,,,,,,,,,212 Lujo virus,450622000.0,SNOMED,virus,,,,,,,,,,,,,213 Lymphocytic choriomeningitis virus (LCMV),82518003.0,SNOMED,virus,,,,,,,,,,,,,214 -MERS-CoV ,697932005.0,SNOMED,virus,,,,,,,,,,1,,,215 +MERS-CoV,697932005.0,SNOMED,virus,,,,,,,,,,1,,,215 Machupo virus,71489006.0,SNOMED,virus,,1,,,,,,,,,,,216 Madurella,23009007.0,SNOMED,fungi,,,,,,,,,,,,,217 Malassezia pachydermatis,51257000.0,SNOMED,fungi,,,,,,,,,,,,,218 @@ -295,7 +295,7 @@ SARS-CoV-2 Eta - B.1.525,840533010.0,SNOMED,virus,,,,,,,,,,,,,296 SARS-CoV-2 Gamma - P.1,840533011,SNOMED,virus,,,,,,,,,,,,,297 SARS-CoV-2 Iota - B.1.526,840533012.0,SNOMED,virus,,,,,,,,,,,,,298 SARS-CoV-2 Kappa - B.1.617.1,840533013.0,SNOMED,virus,,,,,,,,,,,,,299 -SARS-CoV-2 Omicron ,840533014.0,SNOMED,virus,,,,,,,,,,,,,300 +SARS-CoV-2 Omicron,840533014.0,SNOMED,virus,,,,,,,,,,,,,300 SARS-CoV-2 Omicron - B.1.1.529,840533015.0,SNOMED,virus,,,,,,,,,,,,,301 SARS-CoV-2 Omicron - B.1.1.529.2 BA.2,840533016.0,SNOMED,virus,,,,,,,,,,,,,302 SARS-CoV-2 Omicron - B.1.1.529.5 BA.5,840533017.0,SNOMED,virus,,,,,,,,,,,,,303 @@ -324,7 +324,7 @@ Serratia marcescens,33522002.0,SNOMED,bacteria,,,,,,,,,,,,,325 Serratia ureilytica,450416004.0,SNOMED,bacteria,,,,,,,,,,,,,326 Severe Acute Respiratory Syndrome Coronavirus 2,1240000000000000.0,SNOMED,virus,,,,,,,,,,,,,327 Severe Acute Respiratory Syndrome-Related Coronavirus,415360003.0,SNOMED,virus,,,,,,,,,,,,,328 -Severe fever with thrombocytopaenia syndrome (SFTS) ,722401001,SNOMED,virus,,,,,,,,,,,,,329 +Severe fever with thrombocytopaenia syndrome (SFTS),722401001,SNOMED,virus,,,,,,,,,,,,,329 Shigella,77352002.0,SNOMED,bacteria,,,,,,,,,,,,,330 Shigella boydii,55462008.0,SNOMED,bacteria,,,,,,,,,,,,,331 Shigella dysenteriae,43612004.0,SNOMED,bacteria,,,,,,,,,,,,,332 @@ -395,4 +395,4 @@ Yeast,62093005.0,SNOMED,fungi,,,,,,,,,,,,,396 Yersinia pestis,54365000.0,SNOMED,bacteria,,,,,,,,,,,,,397 Zika virus,50471002.0,SNOMED,virus,,,,,,,,,1,,,,398 Chikungunya virus,,,virus,,,,,,,,,1,,,,399 -Oropouche virus ,,,virus,,,,,,,,,1,,,,400 +Oropouche virus,,,virus,,,,,,,,,1,,,,400 diff --git a/Lists/pathogens/Other.csv b/Lists/pathogens/Other.csv index 99acf3c..e701330 100644 --- a/Lists/pathogens/Other.csv +++ b/Lists/pathogens/Other.csv @@ -109,7 +109,7 @@ Influenza B virus,407480007,SNOMED,virus,109,1 Influenza virus,725894000,SNOMED,virus,110,1 Isospora belli,12633005,SNOMED,"parasite, protozoa",111,1 Japanese encephalitis virus (JEV),243603004,SNOMED,virus,112,1 -Junin virus ,26352009,SNOMED,virus,113,1 +Junin virus,26352009,SNOMED,virus,113,1 Lassa virus,85944001,SNOMED,virus,114,1 Leishmania,79357004,SNOMED,"parasite, protozoa",115,1 Leishmania Viannia,712933004,SNOMED,"parasite, protozoa",116,1 @@ -120,7 +120,7 @@ Lichthiemia,734206002,SNOMED,fungi,120,1 Lomentospora prolificans (Scedosporium prlificans),69564000,SNOMED,fungi,121,1 Lujo virus,450622000,SNOMED,virus,122,1 Lymphocytic choriomeningitis virus (LCMV),82518003,SNOMED,virus,123,1 -MERS-CoV ,697932005,SNOMED,virus,124,1 +MERS-CoV,697932005,SNOMED,virus,124,1 Machupo virus,71489006,SNOMED,virus,125,1 Madurella,23009007,SNOMED,fungi,126,1 Malassezia pachydermatis,51257000,SNOMED,fungi,127,1 @@ -173,7 +173,7 @@ SARS-CoV-2 Eta - B.1.525,,,virus,173,1 SARS-CoV-2 Gamma - P.1,,,virus,174,1 SARS-CoV-2 Iota - B.1.526,,,virus,175,1 SARS-CoV-2 Kappa - B.1.617.1,,,virus,176,1 -SARS-CoV-2 Omicron ,,,virus,177,1 +SARS-CoV-2 Omicron,,,virus,177,1 SARS-CoV-2 Omicron - B.1.1.529,,,virus,178,1 SARS-CoV-2 Omicron - B.1.1.529.2 BA.2,,,virus,179,1 SARS-CoV-2 Omicron - B.1.1.529.5 BA.5,,,virus,180,1 @@ -196,7 +196,7 @@ Schistosoma mansoni,11168007,SNOMED,"parasite, helminth",196,1 Schistosoma mekongi,75475007,SNOMED,"parasite, helminth",197,1 Severe Acute Respiratory Syndrome Coronavirus 2,1240000000000000,SNOMED,virus,198,1 Severe Acute Respiratory Syndrome-Related Coronavirus,415360003,SNOMED,virus,199,1 -Severe fever with thrombocytopaenia syndrome (SFTS) ,722401001,SNOMED,virus,200,1 +Severe fever with thrombocytopaenia syndrome (SFTS),722401001,SNOMED,virus,200,1 Simplexvirus (Genus),314797000,SNOMED,virus,201,1 Sporothrix schenckii,32662000,SNOMED,fungi,202,1 Strongyloides stercoralis,42625000,SNOMED,"parasite, helminth",203,1 From bfa88456909086ed2d18003d1e7ee030b37ff84f Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 23 Mar 2026 16:50:51 +0000 Subject: [PATCH 3/7] Preset value selection columns must be int not float --- Lists/conditions/Site.csv | 14 +++++++------- Lists/conditions/Symptoms.csv | 20 +++++++++---------- Lists/demographics/Occupation.csv | 20 +++++++++---------- Lists/drugs/Other.csv | 6 +++--- Lists/drugs/Type.csv | 20 +++++++++---------- Lists/followup/outcome.csv | 26 ++++++++++++------------- Lists/followup/sequelae.csv | 26 ++++++++++++------------- Lists/pathogens/SampleType.csv | 32 +++++++++++++++---------------- 8 files changed, 82 insertions(+), 82 deletions(-) diff --git a/Lists/conditions/Site.csv b/Lists/conditions/Site.csv index ef446ae..97c9a01 100644 --- a/Lists/conditions/Site.csv +++ b/Lists/conditions/Site.csv @@ -1,11 +1,11 @@ Site,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics+extended,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Syndromic CRF_ARI,preset_UserGenerated_Oropouche,preset_Score_CharlsonCI,preset_Module_Pregmpoxnompox,preset_Module_Pregnancy,preset_Module_Neonates,preset_Module_Paediatric,preset_Module_ExtendedMpoxPregnan,preset_Recommended Outcomes_Dengue,preset_Hospitalsed Outcomes_Dengue,preset_Early Stage Outcomes_Dengue,Value -Skin,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,1 -Petechiae,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,2 -Nose,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,3 -Gums,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,4 -GI tract,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,5 -Urinary tract,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,6 -Vagina,,,,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,,,,,,,1,1,1,7 +Skin,,,,1,1,1,1,1,1,1,1,1,,,,,,,1,1,1,1 +Petechiae,,,,1,1,1,1,1,1,1,1,1,,,,,,,1,1,1,2 +Nose,,,,1,1,1,1,1,1,1,1,1,,,,,,,1,1,1,3 +Gums,,,,1,1,1,1,1,1,1,1,1,,,,,,,1,1,1,4 +GI tract,,,,1,1,1,1,1,1,1,1,1,,,,,,,1,1,1,5 +Urinary tract,,,,1,1,1,1,1,1,1,1,1,,,,,,,1,1,1,6 +Vagina,,,,1,1,1,1,1,1,1,1,1,,,,,,,1,1,1,7 Intracranial,,,,,,,,,,,,,,,,,,,1,1,1,8 Intraspinal,,,,,,,,,,,,,,,,,,,1,1,1,9 Intraocular,,,,,,,,,,,,,,,,,,,1,1,1,10 diff --git a/Lists/conditions/Symptoms.csv b/Lists/conditions/Symptoms.csv index c6befea..a509aeb 100644 --- a/Lists/conditions/Symptoms.csv +++ b/Lists/conditions/Symptoms.csv @@ -14,13 +14,13 @@ Cardiac arrhythmia,I49.9,ICD10,698247007,SNOMED,,,,12 Changes in menstruation (Irregular menstruation),N92.6,ICD10,80182007,SNOMED,,,,13 Changes in skin texture,R23.4,ICD10,274672009,SNOMED,,,,14 Chest pain,R07.9,ICD10,29857009,SNOMED,,,,15 -Chest pain on breathing,R07.1,ICD10,274664007,SNOMED,,,1.0,16 +Chest pain on breathing,R07.1,ICD10,274664007,SNOMED,,,1,16 Chills (without fever),R68.83,ICD10,43724002,SNOMED,,,,17 Cognitive impairment (Unspecified intellectual disabilities),F79,ICD10,386806002,SNOMED,,,,18 Conjunctivitis,H10.9,ICD10,9826008,SNOMED,,,,19 Constipation,K59.0,ICD10,14760008,SNOMED,,,,20 Convulsions,R56.9,ICD10,91175000,SNOMED,,,,21 -Cough,R05,ICD10,49727002,SNOMED,,,1.0,22 +Cough,R05,ICD10,49727002,SNOMED,,,1,22 Diarrhea,R19.7,ICD10,267060006,SNOMED,,,,23 Difficulty eating or drinking (Dysphagia),R13.10,ICD10,40739000,SNOMED,,,,24 Difficulty in walking,R26.2,ICD10,719232003,SNOMED,,,,25 @@ -33,7 +33,7 @@ Erectile dysfunction,N52.9,ICD10,860914002,SNOMED,,,,31 Fainting / blackouts (Syncope and collapse),R55,ICD10,309585006,SNOMED,,,,32 Fecal incontinence,R15,ICD10,72042002,SNOMED,,,,33 Feeding difficulty,R63.3,ICD10,78164000,SNOMED,,,,34 -Fever,R50.9,ICD10,386661006,SNOMED,1.0,1.0,1.0,35 +Fever,R50.9,ICD10,386661006,SNOMED,1.0,1,1,35 Gastrointestinal bleeding (Gastrointestinal hemorrhage),K92.2,ICD10,74474003,SNOMED,,,,36 Headache,R51,ICD10,25064002,SNOMED,,,,37 Hepatomegaly,R16.0,ICD10,80515008,SNOMED,,,,38 @@ -52,10 +52,10 @@ Loss of taste (Parageusia),R43.2,ICD10,271801002,SNOMED,,,,50 Lymphadenitis,I88,ICD10,19471005,SNOMED,,,,51 Malaise and fatigue,R53,ICD10,271795006,SNOMED,,,,52 Mouth ulcers (Recurrent oral aphthae),K12.0,ICD10,26284000,SNOMED,,,,53 -Mucosal lesion,,,427752005,SNOMED,1.0,1.0,,54 +Mucosal lesion,,,427752005,SNOMED,1.0,1,,54 Muscle aches (Myalgia),M79.1,ICD10,68962001,SNOMED,,,,55 Muscle weakness,M62.81,ICD10,26544005,SNOMED,,,,56 -Nasal congestion,R09.81,ICD10,68235000,SNOMED,,,1.0,57 +Nasal congestion,R09.81,ICD10,68235000,SNOMED,,,1,57 Nausea or vomiting,R11,ICD10,16932000,SNOMED,,,,58 Pain during urination (Dysuria),R30.0,ICD10,49650001,SNOMED,,,,59 Pallor,R23.1,ICD10,398979000,SNOMED,,,,60 @@ -66,12 +66,12 @@ Pruritus,L29,ICD10,418363000,SNOMED,,,,64 Rapid heart beat/Pulse (Tachycardia),R00.0,ICD10,3424008,SNOMED,,,,65 Rashes or skin lesions,R21,ICD10,271807003,SNOMED,,,,66 Retention of urine,R33.9,ICD10,267064002,SNOMED,,,,67 -Shortness of breath (Dyspnea),R06.0,ICD10,267036007,SNOMED,,,1.0,68 +Shortness of breath (Dyspnea),R06.0,ICD10,267036007,SNOMED,,,1,68 Skin lesion,,,,SNOMED,1.0,,,69 -Skin rash,R21,ICD10,271807003,SNOMED,,1.0,,70 +Skin rash,R21,ICD10,271807003,SNOMED,,1,,70 Sleep disorder,F51.9,ICD10,39898005,SNOMED,,,,71 -Sneezing,R06.7,ICD10,162367006,SNOMED,,,1.0,72 -Sore throat (Pain in throat),R07.0,ICD10,267102003,SNOMED,,,1.0,73 +Sneezing,R06.7,ICD10,162367006,SNOMED,,,1,72 +Sore throat (Pain in throat),R07.0,ICD10,267102003,SNOMED,,,1,73 Speech disturbances,R47.9,ICD10,29164008,SNOMED,,,,74 Spontaneous bruising (Spontaneous ecchymoses),R23.3,ICD10,161887000,SNOMED,,,,75 Sweating (hyperhidrosis),R61,ICD10,312230002,SNOMED,,,,76 @@ -80,4 +80,4 @@ Tinnitus,H93.1,ICD10,60862001,SNOMED,,,,78 Tremor,R25.1,ICD10,26079004,SNOMED,,,,79 Urinary incontinence,R32,ICD10,165232002,SNOMED,,,,80 Visual disturbances,H53,ICD10,63102001,SNOMED,,,,81 -Wheezing,R06.2,ICD10,56018004,SNOMED,,,1.0,82 +Wheezing,R06.2,ICD10,56018004,SNOMED,,,1,82 diff --git a/Lists/demographics/Occupation.csv b/Lists/demographics/Occupation.csv index 4e7b012..7534fed 100644 --- a/Lists/demographics/Occupation.csv +++ b/Lists/demographics/Occupation.csv @@ -1,13 +1,13 @@ Disease,Code,Library,Selected,preset_ARChetype Syndromic CRF_ARI,Value -Abattoir Worker,,,1.0,1.0,1 -Beef Cattle Farm Worker,,,1.0,1.0,2 -Dairy Farm Worker,,,1.0,1.0,3 -Healthcare Worker,,,1.0,1.0,4 -Live bird market worker,,,,1.0,5 -Other live animal market worker,,,,1.0,6 -Poultry Farm Worker,,,1.0,1.0,7 -Poultry culler,,,,1.0,8 +Abattoir Worker,,,1.0,1,1 +Beef Cattle Farm Worker,,,1.0,1,2 +Dairy Farm Worker,,,1.0,1,3 +Healthcare Worker,,,1.0,1,4 +Live bird market worker,,,,1,5 +Other live animal market worker,,,,1,6 +Poultry Farm Worker,,,1.0,1,7 +Poultry culler,,,,1,8 Public Transport Worker,,,,,9 Sanitation Worker,,,,,10 -Swine farm worker,,,,1.0,11 -Veterinarian,,,1.0,1.0,12 +Swine farm worker,,,,1,11 +Veterinarian,,,1.0,1,12 diff --git a/Lists/drugs/Other.csv b/Lists/drugs/Other.csv index 42ba9e2..6d08bd6 100644 --- a/Lists/drugs/Other.csv +++ b/Lists/drugs/Other.csv @@ -2,7 +2,7 @@ Drugs,Code,Library,Selected,preset_Respiratory,preset_ARChetype Disease CRF_Covi Aminophylline (Truphylline),R03DA05,ATC,,,,,,,,,,,1 "Beclometasone (Qvar, Beconase AQ)",R03BA01,ATC,,,,,,,,,,,2 Caspofungin (Cancidas),J02AX04,ATC,,,,,,,,,,,3 -Chloroquine (Aralen),P01BA01,ATC,,,1.0,,,,,,1.0,,4 +Chloroquine (Aralen),P01BA01,ATC,,,1,,,,,,1,,4 "Clobetasol (Temovate, Olux, Impoyz)",D07AD01,ATC,,,,,,,,,,Topical,5 Fluconazole (Diflucan),J02AC01,ATC,,,,,,,,,,,6 "Fluticasone (Flovent, Flonase)",R03BA05,ATC,,,,,,,,,,,7 @@ -14,8 +14,8 @@ Glycopyrronium Bromide (Seebri),R03BB06,ATC,,,,,,,,,,,12 Hydroxychloroquine (Plaquenil),P01BA02,ATC,,,,,,,,,,,13 "Imiquimod (Aldara, Zyclara)",D06BB10,ATC,,,,,,,,,,Topical/Locally acting,14 Indacaterol and Glycopyrronium Bromide (Ultibro Breezhaler),R03AL04,ATC,,,,,,,,,,,15 -Interferon Alpha,L03AB01,ATC,,,1.0,,,,,,1.0,,16 -Interferon Beta,L03AB02,ATC,,,1.0,,,,,,1.0,,17 +Interferon Alpha,L03AB01,ATC,,,1,,,,,,1,,16 +Interferon Beta,L03AB02,ATC,,,1,,,,,,1,,17 Ipratropium Bromide (Atrovent),R03BB01,ATC,,,,,,,,,,,18 Ivermectin (Stromectol),P02CF01,ATC,,,,,,,,,,,19 Mafenide (Sulfamylon),D06BA03,ATC,,,,,,,,,,Topical,20 diff --git a/Lists/drugs/Type.csv b/Lists/drugs/Type.csv index 1da3604..baaa3c5 100644 --- a/Lists/drugs/Type.csv +++ b/Lists/drugs/Type.csv @@ -1,17 +1,17 @@ Drugs,Code,Library,Selected,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value -Analgesic,373265006 |Analgesic (substance)|,SNOMED,1.0,,1.0,,1 -Antibiotic,255631004 |Antibiotic (product)|,SNOMED,1.0,1.0,,1.0,2 -Anticoagulant,372862008 |Anticoagulant (substance)|,SNOMED,,1.0,,1.0,3 -Antifungal,373219008 |Substance with antifungal mechanism of action (substance)|,SNOMED,1.0,1.0,,1.0,4 +Analgesic,373265006 |Analgesic (substance)|,SNOMED,1.0,,1,,1 +Antibiotic,255631004 |Antibiotic (product)|,SNOMED,1.0,1,,1,2 +Anticoagulant,372862008 |Anticoagulant (substance)|,SNOMED,,1,,1,3 +Antifungal,373219008 |Substance with antifungal mechanism of action (substance)|,SNOMED,1.0,1,,1,4 Antihistamine,6425004 |Product containing histamine receptor antagonist (product)|,SNOMED,,,,,5 Antiprotozoal,788027008 |Medicinal product acting as antiprotozoal agent (product)|,SNOMED,,,,,6 Antipruritic,312067003 |Local antipruritic agent (product)|,SNOMED,1.0,,,,7 -Antiviral,372701006,SNOMED,1.0,1.0,1.0,1.0,8 +Antiviral,372701006,SNOMED,1.0,1,1,1,8 Convalescent plasma,1179779000,SNOMED,,,,,9 -Corticosteroid,116566001,SNOMED,1.0,1.0,1.0,1.0,10 +Corticosteroid,116566001,SNOMED,1.0,1,1,1,10 Diuretics,372695000,SNOMED,,,,,11 -Immunomodulator,372558009,SNOMED,,,1.0,,12 -Immunosuppressive drugs (non-steroid),69431002,SNOMED,,,1.0,,13 -Inotropes / vasopressor,373213009 |Inotropic agent (substance)|870406003 |Vasopressor (substance)|,SNOMED,,1.0,,1.0,14 -Intravenous immunoglobulin,698802001,SNOMED,,,1.0,,15 +Immunomodulator,372558009,SNOMED,,,1,,12 +Immunosuppressive drugs (non-steroid),69431002,SNOMED,,,1,,13 +Inotropes / vasopressor,373213009 |Inotropic agent (substance)|870406003 |Vasopressor (substance)|,SNOMED,,1,,1,14 +Intravenous immunoglobulin,698802001,SNOMED,,,1,,15 Topical antibiotic,255631004 |Antibiotic (product)| 6064005 |Topical route (qualifier value)|,SNOMED,1.0,,,,16 diff --git a/Lists/followup/outcome.csv b/Lists/followup/outcome.csv index 1850950..ed0d7a2 100644 --- a/Lists/followup/outcome.csv +++ b/Lists/followup/outcome.csv @@ -1,14 +1,14 @@ Outcome,Code,Selected,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value -All lesions are completely resolved and no serious complications,,,1.0,1.0,1.0,,1 -All lesions are no longer active and no serious complications,,,1.0,1.0,1.0,,2 -Death,,1.0,1.0,1.0,1.0,1.0,3 -Discharged alive - medical grounds,,1.0,1.0,1.0,1.0,1.0,4 -Discharged alive - patient's preference,,1.0,1.0,1.0,1.0,1.0,5 -Early withdrawal,,1.0,1.0,1.0,1.0,1.0,6 -Loss to follow-up,,1.0,1.0,1.0,1.0,1.0,7 -No lesions ever developed and no serious complications,,,1.0,1.0,1.0,,8 -One or more lesion(s) are active and no serious complications,,,1.0,1.0,1.0,,9 -Palliative Care,,,,,,1.0,10 -Serious complication and/or re-hospitalisation due to infection with pathogen of interest,,,1.0,1.0,1.0,1.0,11 -Still hospitalised,,1.0,1.0,1.0,1.0,1.0,12 -Transfer to other facility,,1.0,1.0,1.0,1.0,1.0,13 +All lesions are completely resolved and no serious complications,,,1,1,1,,1 +All lesions are no longer active and no serious complications,,,1,1,1,,2 +Death,,1.0,1,1,1,1,3 +Discharged alive - medical grounds,,1.0,1,1,1,1,4 +Discharged alive - patient's preference,,1.0,1,1,1,1,5 +Early withdrawal,,1.0,1,1,1,1,6 +Loss to follow-up,,1.0,1,1,1,1,7 +No lesions ever developed and no serious complications,,,1,1,1,,8 +One or more lesion(s) are active and no serious complications,,,1,1,1,,9 +Palliative Care,,,,,,1,10 +Serious complication and/or re-hospitalisation due to infection with pathogen of interest,,,1,1,1,1,11 +Still hospitalised,,1.0,1,1,1,1,12 +Transfer to other facility,,1.0,1,1,1,1,13 diff --git a/Lists/followup/sequelae.csv b/Lists/followup/sequelae.csv index f384d61..6ef8c79 100644 --- a/Lists/followup/sequelae.csv +++ b/Lists/followup/sequelae.csv @@ -1,14 +1,14 @@ Sequelae,Code,Selected,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value -Blindness,,1.0,1.0,1.0,1.0,,1 -Cardiovascular Effects,,,,,,1.0,2 -Decreased vision,,1.0,1.0,1.0,1.0,,3 -Depression,,1.0,1.0,1.0,1.0,,4 -Dyspareunia,,1.0,1.0,1.0,1.0,,5 -Immunological Consequence,,,,,,1.0,6 -Neurological Complications,,,,,,1.0,7 -Psychological Impacts,,,,,,1.0,8 -Rectal stricture,,1.0,1.0,1.0,1.0,,9 -Respiratory Complications,,,,,,1.0,10 -Systemic Effects,,,,,,1.0,11 -Urethral stricture,,1.0,1.0,1.0,1.0,,12 -Vaginal stricture,,1.0,1.0,1.0,1.0,,13 +Blindness,,1.0,1,1,1,,1 +Cardiovascular Effects,,,,,,1,2 +Decreased vision,,1.0,1,1,1,,3 +Depression,,1.0,1,1,1,,4 +Dyspareunia,,1.0,1,1,1,,5 +Immunological Consequence,,,,,,1,6 +Neurological Complications,,,,,,1,7 +Psychological Impacts,,,,,,1,8 +Rectal stricture,,1.0,1,1,1,,9 +Respiratory Complications,,,,,,1,10 +Systemic Effects,,,,,,1,11 +Urethral stricture,,1.0,1,1,1,,12 +Vaginal stricture,,1.0,1,1,1,,13 diff --git a/Lists/pathogens/SampleType.csv b/Lists/pathogens/SampleType.csv index 922e1eb..8f95c18 100644 --- a/Lists/pathogens/SampleType.csv +++ b/Lists/pathogens/SampleType.csv @@ -1,21 +1,21 @@ Sample_Type,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value Amniotic fluid,TEMP,TEMP,,,,,,,,,1 -BAL (Bronchoalveolar Lavage),TEMP,TEMP,1.0,1.0,,,,1.0,,1.0,2 -Blood,TEMP,TEMP,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,3 +BAL (Bronchoalveolar Lavage),TEMP,TEMP,1.0,1,,,,1,,1,2 +Blood,TEMP,TEMP,1.0,1,1,1,1,1,1,1,3 Breast milk,TEMP,TEMP,,,,,,,,,4 -Buccal swab,TEMP,TEMP,,,,1.0,1.0,,1.0,,5 -CSF (Cerebrospinal Fluid),TEMP,TEMP,,,1.0,1.0,1.0,,1.0,,6 -Combined nasal/NP + throat swab,TEMP,TEMP,1.0,1.0,,,,1.0,,1.0,7 -ETA (Endotracheal aspirate),TEMP,TEMP,1.0,1.0,,,,1.0,,1.0,8 -Eye swab,TEMP,TEMP,,,,1.0,1.0,,1.0,1.0,9 -Faeces/rectal swab,TEMP,TEMP,,,,1.0,1.0,,1.0,,10 -Lesion/crust (skin) swab,TEMP,TEMP,,,,1.0,1.0,,1.0,,11 -Nasal/NP swab,TEMP,TEMP,1.0,1.0,,,,1.0,,1.0,12 -Neonate-blood,TEMP,TEMP,,,1.0,,,,,,13 -Semen,TEMP,TEMP,,,,1.0,1.0,,1.0,,14 -Sputum,TEMP,TEMP,1.0,1.0,,,,1.0,,1.0,15 +Buccal swab,TEMP,TEMP,,,,1,1,,1,,5 +CSF (Cerebrospinal Fluid),TEMP,TEMP,,,1,1,1,,1,,6 +Combined nasal/NP + throat swab,TEMP,TEMP,1.0,1,,,,1,,1,7 +ETA (Endotracheal aspirate),TEMP,TEMP,1.0,1,,,,1,,1,8 +Eye swab,TEMP,TEMP,,,,1,1,,1,1,9 +Faeces/rectal swab,TEMP,TEMP,,,,1,1,,1,,10 +Lesion/crust (skin) swab,TEMP,TEMP,,,,1,1,,1,,11 +Nasal/NP swab,TEMP,TEMP,1.0,1,,,,1,,1,12 +Neonate-blood,TEMP,TEMP,,,1,,,,,,13 +Semen,TEMP,TEMP,,,,1,1,,1,,14 +Sputum,TEMP,TEMP,1.0,1,,,,1,,1,15 Stool sample,TEMP,TEMP,,,,,,,,,16 -Throat swab,TEMP,TEMP,1.0,1.0,,1.0,1.0,1.0,1.0,1.0,17 +Throat swab,TEMP,TEMP,1.0,1,,1,1,1,1,1,17 Urethral swab,TEMP,TEMP,,,,,,,,,18 -Urine,TEMP,TEMP,,,,1.0,1.0,,1.0,,19 -Vaginal swab,TEMP,TEMP,,,,1.0,1.0,,1.0,,20 +Urine,TEMP,TEMP,,,,1,1,,1,,19 +Vaginal swab,TEMP,TEMP,,,,1,1,,1,,20 From 92273b9b6cb78c07f3a33e5fd40694c878399cdc Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 23 Mar 2026 16:57:26 +0000 Subject: [PATCH 4/7] Convert float '1.0' to 1 for 'Selected' column in List files --- Lists/conditions/Symptoms.csv | 6 +++--- Lists/demographics/Occupation.csv | 12 ++++++------ Lists/drugs/Antifungal.csv | 6 +++--- Lists/drugs/Other.csv | 4 ++-- Lists/drugs/Type.csv | 14 +++++++------- Lists/followup/outcome.csv | 14 +++++++------- Lists/followup/sequelae.csv | 14 +++++++------- Lists/pathogens/GenomicRepository.csv | 4 ++-- Lists/pathogens/SampleType.csv | 14 +++++++------- 9 files changed, 44 insertions(+), 44 deletions(-) diff --git a/Lists/conditions/Symptoms.csv b/Lists/conditions/Symptoms.csv index a509aeb..97a90d1 100644 --- a/Lists/conditions/Symptoms.csv +++ b/Lists/conditions/Symptoms.csv @@ -33,7 +33,7 @@ Erectile dysfunction,N52.9,ICD10,860914002,SNOMED,,,,31 Fainting / blackouts (Syncope and collapse),R55,ICD10,309585006,SNOMED,,,,32 Fecal incontinence,R15,ICD10,72042002,SNOMED,,,,33 Feeding difficulty,R63.3,ICD10,78164000,SNOMED,,,,34 -Fever,R50.9,ICD10,386661006,SNOMED,1.0,1,1,35 +Fever,R50.9,ICD10,386661006,SNOMED,1,1,1,35 Gastrointestinal bleeding (Gastrointestinal hemorrhage),K92.2,ICD10,74474003,SNOMED,,,,36 Headache,R51,ICD10,25064002,SNOMED,,,,37 Hepatomegaly,R16.0,ICD10,80515008,SNOMED,,,,38 @@ -52,7 +52,7 @@ Loss of taste (Parageusia),R43.2,ICD10,271801002,SNOMED,,,,50 Lymphadenitis,I88,ICD10,19471005,SNOMED,,,,51 Malaise and fatigue,R53,ICD10,271795006,SNOMED,,,,52 Mouth ulcers (Recurrent oral aphthae),K12.0,ICD10,26284000,SNOMED,,,,53 -Mucosal lesion,,,427752005,SNOMED,1.0,1,,54 +Mucosal lesion,,,427752005,SNOMED,1,1,,54 Muscle aches (Myalgia),M79.1,ICD10,68962001,SNOMED,,,,55 Muscle weakness,M62.81,ICD10,26544005,SNOMED,,,,56 Nasal congestion,R09.81,ICD10,68235000,SNOMED,,,1,57 @@ -67,7 +67,7 @@ Rapid heart beat/Pulse (Tachycardia),R00.0,ICD10,3424008,SNOMED,,,,65 Rashes or skin lesions,R21,ICD10,271807003,SNOMED,,,,66 Retention of urine,R33.9,ICD10,267064002,SNOMED,,,,67 Shortness of breath (Dyspnea),R06.0,ICD10,267036007,SNOMED,,,1,68 -Skin lesion,,,,SNOMED,1.0,,,69 +Skin lesion,,,,SNOMED,1,,,69 Skin rash,R21,ICD10,271807003,SNOMED,,1,,70 Sleep disorder,F51.9,ICD10,39898005,SNOMED,,,,71 Sneezing,R06.7,ICD10,162367006,SNOMED,,,1,72 diff --git a/Lists/demographics/Occupation.csv b/Lists/demographics/Occupation.csv index 7534fed..5b1c594 100644 --- a/Lists/demographics/Occupation.csv +++ b/Lists/demographics/Occupation.csv @@ -1,13 +1,13 @@ Disease,Code,Library,Selected,preset_ARChetype Syndromic CRF_ARI,Value -Abattoir Worker,,,1.0,1,1 -Beef Cattle Farm Worker,,,1.0,1,2 -Dairy Farm Worker,,,1.0,1,3 -Healthcare Worker,,,1.0,1,4 +Abattoir Worker,,,1,1,1 +Beef Cattle Farm Worker,,,1,1,2 +Dairy Farm Worker,,,1,1,3 +Healthcare Worker,,,1,1,4 Live bird market worker,,,,1,5 Other live animal market worker,,,,1,6 -Poultry Farm Worker,,,1.0,1,7 +Poultry Farm Worker,,,1,1,7 Poultry culler,,,,1,8 Public Transport Worker,,,,,9 Sanitation Worker,,,,,10 Swine farm worker,,,,1,11 -Veterinarian,,,1.0,1,12 +Veterinarian,,,1,1,12 diff --git a/Lists/drugs/Antifungal.csv b/Lists/drugs/Antifungal.csv index c691819..bf8d590 100644 --- a/Lists/drugs/Antifungal.csv +++ b/Lists/drugs/Antifungal.csv @@ -1,10 +1,10 @@ Drugs,Code,Library,Selected,Value -Amphotericin B,714520003,http://snomed.info/sct,1.0,1 +Amphotericin B,714520003,http://snomed.info/sct,1,1 Clotrimazole,5797005,http://snomed.info/sct,,2 Econazole,18952006,http://snomed.info/sct,,3 -Fluconazole,31865003,http://snomed.info/sct,1.0,4 +Fluconazole,31865003,http://snomed.info/sct,1,4 Ketoconazole,40232005,http://snomed.info/sct,,5 -Liposomal amphotericin,773379008,http://snomed.info/sct,1.0,6 +Liposomal amphotericin,773379008,http://snomed.info/sct,1,6 Miconazole,42720001,http://snomed.info/sct,,7 Nystatin,12096000,http://snomed.info/sct,,8 Terbinafine,108925005,http://snomed.info/sct,,9 diff --git a/Lists/drugs/Other.csv b/Lists/drugs/Other.csv index 6d08bd6..37c2788 100644 --- a/Lists/drugs/Other.csv +++ b/Lists/drugs/Other.csv @@ -26,11 +26,11 @@ Mupirocin (Bactroban),D06AX09,ATC,,,,,,,,,,Topical/Locally acting,23 "Podophyllotoxin (Podofilox, Condylox)",D06BB04,ATC,,,,,,,,,,Topical,25 Primaquine,P01BA03,ATC,,,,,,,,,,,26 "Salbutamol (Ventolin, Proventil)",R03AC02,ATC,,,,,,,,,,,27 -Salmeterol (Serevent),R03AC12,ATC,1.0,,,,,,,,,,28 +Salmeterol (Serevent),R03AC12,ATC,1,,,,,,,,,,28 "Salmeterol and Fluticasone (Advair, Seretide)",R03AK06,ATC,,,,,,,,,,,29 "Sulphur, precipitated in petrolatum",D10AB02,ATC,,,,,,,,,,Topical,30 "Theophylline (Theo-24, Elixophyllin)",R03DA04,ATC,,,,,,,,,,,31 Tiotropium Bromide (Spiriva),R03BB04,ATC,,,,,,,,,,,32 Trichloroacetic acid,78151001,SNOMED,,,,,,,,,,Topical,33 Vilanterol and Fluticasone Furoate (Breo Ellipta),R03AK10,ATC,,,,,,,,,,,34 -Vilanterol and Umeclidinium Bromide (Anoro Ellipta),R03AL03,ATC,1.0,,,,,,,,,,35 +Vilanterol and Umeclidinium Bromide (Anoro Ellipta),R03AL03,ATC,1,,,,,,,,,,35 diff --git a/Lists/drugs/Type.csv b/Lists/drugs/Type.csv index baaa3c5..7917eff 100644 --- a/Lists/drugs/Type.csv +++ b/Lists/drugs/Type.csv @@ -1,17 +1,17 @@ Drugs,Code,Library,Selected,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value -Analgesic,373265006 |Analgesic (substance)|,SNOMED,1.0,,1,,1 -Antibiotic,255631004 |Antibiotic (product)|,SNOMED,1.0,1,,1,2 +Analgesic,373265006 |Analgesic (substance)|,SNOMED,1,,1,,1 +Antibiotic,255631004 |Antibiotic (product)|,SNOMED,1,1,,1,2 Anticoagulant,372862008 |Anticoagulant (substance)|,SNOMED,,1,,1,3 -Antifungal,373219008 |Substance with antifungal mechanism of action (substance)|,SNOMED,1.0,1,,1,4 +Antifungal,373219008 |Substance with antifungal mechanism of action (substance)|,SNOMED,1,1,,1,4 Antihistamine,6425004 |Product containing histamine receptor antagonist (product)|,SNOMED,,,,,5 Antiprotozoal,788027008 |Medicinal product acting as antiprotozoal agent (product)|,SNOMED,,,,,6 -Antipruritic,312067003 |Local antipruritic agent (product)|,SNOMED,1.0,,,,7 -Antiviral,372701006,SNOMED,1.0,1,1,1,8 +Antipruritic,312067003 |Local antipruritic agent (product)|,SNOMED,1,,,,7 +Antiviral,372701006,SNOMED,1,1,1,1,8 Convalescent plasma,1179779000,SNOMED,,,,,9 -Corticosteroid,116566001,SNOMED,1.0,1,1,1,10 +Corticosteroid,116566001,SNOMED,1,1,1,1,10 Diuretics,372695000,SNOMED,,,,,11 Immunomodulator,372558009,SNOMED,,,1,,12 Immunosuppressive drugs (non-steroid),69431002,SNOMED,,,1,,13 Inotropes / vasopressor,373213009 |Inotropic agent (substance)|870406003 |Vasopressor (substance)|,SNOMED,,1,,1,14 Intravenous immunoglobulin,698802001,SNOMED,,,1,,15 -Topical antibiotic,255631004 |Antibiotic (product)| 6064005 |Topical route (qualifier value)|,SNOMED,1.0,,,,16 +Topical antibiotic,255631004 |Antibiotic (product)| 6064005 |Topical route (qualifier value)|,SNOMED,1,,,,16 diff --git a/Lists/followup/outcome.csv b/Lists/followup/outcome.csv index ed0d7a2..5121fd0 100644 --- a/Lists/followup/outcome.csv +++ b/Lists/followup/outcome.csv @@ -1,14 +1,14 @@ Outcome,Code,Selected,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value All lesions are completely resolved and no serious complications,,,1,1,1,,1 All lesions are no longer active and no serious complications,,,1,1,1,,2 -Death,,1.0,1,1,1,1,3 -Discharged alive - medical grounds,,1.0,1,1,1,1,4 -Discharged alive - patient's preference,,1.0,1,1,1,1,5 -Early withdrawal,,1.0,1,1,1,1,6 -Loss to follow-up,,1.0,1,1,1,1,7 +Death,,1,1,1,1,1,3 +Discharged alive - medical grounds,,1,1,1,1,1,4 +Discharged alive - patient's preference,,1,1,1,1,1,5 +Early withdrawal,,1,1,1,1,1,6 +Loss to follow-up,,1,1,1,1,1,7 No lesions ever developed and no serious complications,,,1,1,1,,8 One or more lesion(s) are active and no serious complications,,,1,1,1,,9 Palliative Care,,,,,,1,10 Serious complication and/or re-hospitalisation due to infection with pathogen of interest,,,1,1,1,1,11 -Still hospitalised,,1.0,1,1,1,1,12 -Transfer to other facility,,1.0,1,1,1,1,13 +Still hospitalised,,1,1,1,1,1,12 +Transfer to other facility,,1,1,1,1,1,13 diff --git a/Lists/followup/sequelae.csv b/Lists/followup/sequelae.csv index 6ef8c79..5e120b3 100644 --- a/Lists/followup/sequelae.csv +++ b/Lists/followup/sequelae.csv @@ -1,14 +1,14 @@ Sequelae,Code,Selected,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value -Blindness,,1.0,1,1,1,,1 +Blindness,,1,1,1,1,,1 Cardiovascular Effects,,,,,,1,2 -Decreased vision,,1.0,1,1,1,,3 -Depression,,1.0,1,1,1,,4 -Dyspareunia,,1.0,1,1,1,,5 +Decreased vision,,1,1,1,1,,3 +Depression,,1,1,1,1,,4 +Dyspareunia,,1,1,1,1,,5 Immunological Consequence,,,,,,1,6 Neurological Complications,,,,,,1,7 Psychological Impacts,,,,,,1,8 -Rectal stricture,,1.0,1,1,1,,9 +Rectal stricture,,1,1,1,1,,9 Respiratory Complications,,,,,,1,10 Systemic Effects,,,,,,1,11 -Urethral stricture,,1.0,1,1,1,,12 -Vaginal stricture,,1.0,1,1,1,,13 +Urethral stricture,,1,1,1,1,,12 +Vaginal stricture,,1,1,1,1,,13 diff --git a/Lists/pathogens/GenomicRepository.csv b/Lists/pathogens/GenomicRepository.csv index fd4c2b9..3883a27 100644 --- a/Lists/pathogens/GenomicRepository.csv +++ b/Lists/pathogens/GenomicRepository.csv @@ -1,4 +1,4 @@ Repository,URL,Selected,Value DNA Data Bank of Japan (DDBJ),https://www.ddbj.nig.ac.jp,,1 -EMBL - European Bioinformatics Institute(EBI),https://www.ebi.ac.uk/,1.0,2 -GenBank,https://www.ncbi.nlm.nih.gov/genbank,1.0,3 +EMBL - European Bioinformatics Institute(EBI),https://www.ebi.ac.uk/,1,2 +GenBank,https://www.ncbi.nlm.nih.gov/genbank,1,3 diff --git a/Lists/pathogens/SampleType.csv b/Lists/pathogens/SampleType.csv index 8f95c18..6037b95 100644 --- a/Lists/pathogens/SampleType.csv +++ b/Lists/pathogens/SampleType.csv @@ -1,21 +1,21 @@ Sample_Type,Code,Library,Selected,preset_ARChetype Disease CRF_Covid,preset_ARChetype Disease CRF_Dengue,preset_ARChetype Disease CRF_Mpox,preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric,preset_ARChetype Disease CRF_H5Nx,preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics,preset_ARChetype Syndromic CRF_ARI,Value Amniotic fluid,TEMP,TEMP,,,,,,,,,1 -BAL (Bronchoalveolar Lavage),TEMP,TEMP,1.0,1,,,,1,,1,2 -Blood,TEMP,TEMP,1.0,1,1,1,1,1,1,1,3 +BAL (Bronchoalveolar Lavage),TEMP,TEMP,1,1,,,,1,,1,2 +Blood,TEMP,TEMP,1,1,1,1,1,1,1,1,3 Breast milk,TEMP,TEMP,,,,,,,,,4 Buccal swab,TEMP,TEMP,,,,1,1,,1,,5 CSF (Cerebrospinal Fluid),TEMP,TEMP,,,1,1,1,,1,,6 -Combined nasal/NP + throat swab,TEMP,TEMP,1.0,1,,,,1,,1,7 -ETA (Endotracheal aspirate),TEMP,TEMP,1.0,1,,,,1,,1,8 +Combined nasal/NP + throat swab,TEMP,TEMP,1,1,,,,1,,1,7 +ETA (Endotracheal aspirate),TEMP,TEMP,1,1,,,,1,,1,8 Eye swab,TEMP,TEMP,,,,1,1,,1,1,9 Faeces/rectal swab,TEMP,TEMP,,,,1,1,,1,,10 Lesion/crust (skin) swab,TEMP,TEMP,,,,1,1,,1,,11 -Nasal/NP swab,TEMP,TEMP,1.0,1,,,,1,,1,12 +Nasal/NP swab,TEMP,TEMP,1,1,,,,1,,1,12 Neonate-blood,TEMP,TEMP,,,1,,,,,,13 Semen,TEMP,TEMP,,,,1,1,,1,,14 -Sputum,TEMP,TEMP,1.0,1,,,,1,,1,15 +Sputum,TEMP,TEMP,1,1,,,,1,,1,15 Stool sample,TEMP,TEMP,,,,,,,,,16 -Throat swab,TEMP,TEMP,1.0,1,,1,1,1,1,1,17 +Throat swab,TEMP,TEMP,1,1,,1,1,1,1,1,17 Urethral swab,TEMP,TEMP,,,,,,,,,18 Urine,TEMP,TEMP,,,,1,1,,1,,19 Vaginal swab,TEMP,TEMP,,,,1,1,,1,,20 From c7a8c403e6ee6c9c2330dddf9b77bf7478a8cc0a Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 23 Mar 2026 17:11:28 +0000 Subject: [PATCH 5/7] Make list test parameterisations clearer with labels --- tests/test_lists.py | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/tests/test_lists.py b/tests/test_lists.py index afbe1ad..ce10e63 100644 --- a/tests/test_lists.py +++ b/tests/test_lists.py @@ -6,6 +6,7 @@ ARC_PATH = BASE_DIR / "ARC.csv" TEST_PATH = pathlib.Path(__file__) LIST_FILES = [x for x in pathlib.Path("Lists").rglob("*") if x.is_file()] +LIST_FILE_NAMES = [f"{f.parent.stem}_{f.stem}" for f in LIST_FILES] REQUIRED_COLUMNS = ["Selected", "Value"] LIST_FILES_WITH_ARCHETYPE_PRESETS = [ @@ -44,7 +45,7 @@ def test_list_file_used_in_arc(): @pytest.mark.high -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_list_csv_loads(file): """Check loads correctly with no encoding""" try: @@ -59,7 +60,7 @@ def test_list_csv_loads(file): @pytest.mark.high -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_list_required_columns_exist(file): """Check required columns exist""" header = pd.read_csv(file, nrows=0, dtype="object").columns @@ -69,7 +70,7 @@ def test_list_required_columns_exist(file): @pytest.mark.high -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_list_other_value(file): """Check required columns exist""" df = pd.read_csv(file, dtype="object") @@ -82,7 +83,7 @@ def test_list_other_value(file): @pytest.mark.medium -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_arc_strip(file): """Check if each required column has empty spaces at the beginning/end""" df = pd.read_csv(file, dtype="object") @@ -96,7 +97,7 @@ def test_arc_strip(file): @pytest.mark.medium -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_list_valid_selected_values(file): """Selected column must be NaN or 1 (not 1.0)""" df = pd.read_csv(file, dtype="object", usecols=["Selected"]) @@ -109,7 +110,7 @@ def test_list_valid_selected_values(file): @pytest.mark.medium -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_list_valid_preset_values(file): """Preset columns column must be NaN or 1 (not 1.0)""" df = pd.read_csv(file, dtype="object") @@ -123,7 +124,7 @@ def test_list_valid_preset_values(file): @pytest.mark.medium -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_too_many_presets(file): """Check if the Lists file has the same presets as ARC""" arc = pd.read_csv(ARC_PATH, nrows=0, dtype="object") @@ -141,7 +142,7 @@ def test_too_many_presets(file): @pytest.mark.high -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_unique_labels(file): """Check if the Lists file has the same presets as ARC""" df = pd.read_csv(file, dtype="object") @@ -149,13 +150,11 @@ def test_unique_labels(file): condition = df[df.columns[0]].str.strip().duplicated(keep=False) if condition.any(): invalid = df.loc[condition, df.columns[0]] - pytest.fail( - f"{str(file)} has repeated labels: {invalid}" - ) + pytest.fail(f"{str(file)} has repeated labels: {invalid}") @pytest.mark.medium -@pytest.mark.parametrize("file", LIST_FILES) +@pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_unique_codes(file): """Check if the Lists file has the same presets as ARC""" df = pd.read_csv(file, dtype="object") @@ -165,11 +164,12 @@ def test_unique_codes(file): if condition.any(): invalid = df.loc[ condition, - [df.columns[0], "Code"], + [df.columns[0], "Code", "Value"], ].to_dict(orient="records") - pytest.fail( - f"{str(file)} has repeated labels: {invalid}" + formatted = "\n".join( + str(row) for row in sorted(invalid, key=lambda x: x["Code"]) ) + pytest.fail(f"{str(file)} has repeated labels:\n{formatted}") @pytest.mark.high From 3d6009455659576746b89ef7841d8efc1581561f Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 23 Mar 2026 17:14:29 +0000 Subject: [PATCH 6/7] Run both critical and medium tests on push/pull --- .github/workflows/test-critical-high.yml | 2 +- .github/workflows/test-medium-low.yml | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-critical-high.yml b/.github/workflows/test-critical-high.yml index dbc3743..2f66377 100644 --- a/.github/workflows/test-critical-high.yml +++ b/.github/workflows/test-critical-high.yml @@ -8,7 +8,7 @@ on: jobs: build: - name: Tests + name: Tests (critical/high) runs-on: ubuntu-latest steps: diff --git a/.github/workflows/test-medium-low.yml b/.github/workflows/test-medium-low.yml index bc9f5c9..6f86f04 100644 --- a/.github/workflows/test-medium-low.yml +++ b/.github/workflows/test-medium-low.yml @@ -1,6 +1,9 @@ name: Run tests marked as medium or low on: + push: + pull_request: + branches: [main] workflow_dispatch: jobs: From 19187e8720f58306323fb563ce4240cb40d64337 Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Tue, 24 Mar 2026 12:19:08 +0000 Subject: [PATCH 7/7] Remove some more trailing whitespace, switch out some min/max tests, edit some docstrings --- ARC.csv | 16 ++++++++-------- tests/test_arc.py | 32 +++++++++++++++++++++++--------- tests/test_lists.py | 4 ++-- 3 files changed, 33 insertions(+), 19 deletions(-) diff --git a/ARC.csv b/ARC.csv index bba9b4c..6384268 100644 --- a/ARC.csv +++ b/ARC.csv @@ -327,13 +327,13 @@ presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from ons presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_dizzy,radio,Feeling dizzy / faint,"1, Yes | 0, No | 99, Unknown",,,,,[demog_calcage_days]>=1825,Systemic/General,"This refers to the subjective feeling of light-headedness or dizziness which may precede an episode of syncope or a sensation of unsteadiness, spinning or rocking.","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"248223005, Feeling faint","C0581879, Felt faint",,clinical_features,,1,,,1,1,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_myalgia,radio,Muscle aches (myalgia),"1, Yes | 0, No | 99, Unknown",,,,,[demog_calcage_days]>=365,Systemic/General,This refers to pain localised to a muscle or group of muscles.,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"68962001, Muscle pain","C0231528, Myalgia",,clinical_features,1,1,1,1,1,1,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_arthralgia,radio,Joint pain (arthralgia),"1, Yes | 0, No | 99, Unknown",,,,,[demog_calcage_days]>=365,Systemic/General,"This refers to a sensation of marked discomfort or pain localised to one or more joints, including small and big joints.","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"57676002, Joint pain","C3805780, Arthralgia",,clinical_features,1,1,1,1,1,1,1,,,,,, -presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointswell,radio,Joint swelling,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,Defined as the buildup of fluid in the soft tissue SURROUNDING the joint or in the joint itself,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation. ",SNOMED,"271771009, Joint swelling",,,clinical_features,,,,,,,1,,,,,, +presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointswell,radio,Joint swelling,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,Defined as the buildup of fluid in the soft tissue SURROUNDING the joint or in the joint itself,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"271771009, Joint swelling",,,clinical_features,,,,,,,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointswell_site,checkbox,Site where joint swelling occurred,"1, Fingers | 2, Wrists | 3, Shoulders | 4, Elbow | 5, Hips | 8, Knees | 9, Ankles | 10, Toes | 99, Unknown | 88, Other",,,,,[adsym_jointswell]= '1',Systemic/General,This refers to the location where joint swelling first occurred,,,,,,clinical_features,,,,,,,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointswell_site_oth,text,Specify other first joint swelling location,,,,,,[adsym_jointswell_site(88)]='1',Systemic/General,This refers to the location where joint swelling first occurred,,,,,,clinical_features,,,,,,,1,,,,,, -presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointtender,radio,Joint tenderness,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,"Defined as pain and discomfort in a joint, often accompanied by sensitivity to touch","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation. ",SNOMED,"110288007, Tenderness of joint",,,clinical_features,,,,,,,1,,,,,, +presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointtender,radio,Joint tenderness,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,"Defined as pain and discomfort in a joint, often accompanied by sensitivity to touch","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"110288007, Tenderness of joint",,,clinical_features,,,,,,,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointtender_site,checkbox,Site where joint tenderness occurred,"1, Fingers | 2, Wrists | 3, Shoulders | 4, Elbow | 5, Hips | 8, Knees | 9, Ankles | 10, Toes | 99, Unknown | 88, Other",,,,,[adsym_jointtender]= '1',Systemic/General,This refers to the location where joint tenderness first occurred,,,,,,clinical_features,,,,,,,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_jointtender_site_oth,text,Specify other first joint tenderness location,,,,,,[adsym_jointtender_site(88)]='1',Systemic/General,This refers to the location where joint tenderness first occurred,,,,,,clinical_features,,,,,,,1,,,,,, -presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_stissueswell,radio,Small tissue swelling,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,"Defined as painful swelling of the interphalangeal tissue, leading to tension and pain when flexing the fingers","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation. ",SNOMED,"298349001, Soft tissue swelling",,,clinical_features,,,,,,,1,,,,,, +presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_stissueswell,radio,Small tissue swelling,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,"Defined as painful swelling of the interphalangeal tissue, leading to tension and pain when flexing the fingers","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"298349001, Soft tissue swelling",,,clinical_features,,,,,,,1,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_backpain,radio,Back Pain,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,,,,,,,,,,,,,,,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_neckpain,radio,Neck Pain,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,,,,,,,,,,,,,,,,,,,, presentation,SYMPTOMS ON ADMISSION: Indicate if experienced at any time from onset of this illness to the day of presentation.,adsym_skinrash,radio,Skin rash,"1, Yes | 0, No | 99, Unknown",,,,,,Systemic/General,"This refers to any change in the skin which affects its appearance or texture. A rash may be localized to one part of the body or affect all the skin. Rashes may cause the skin to change colour, itch, become warm, bumpy, dry, cracked, or blistered, swell and may be painful.","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"271807003, Eruption of skin","C4227880, Skin Rash",,clinical_features,1,1,1,1,1,1,1,,,,,, @@ -499,7 +499,7 @@ presentation,PREGNANCY PRESENTATION,preg_brefed,radio,Breastfeeding,"1, Yes-curr presentation,PREGNANCY PRESENTATION,preg_brefedduration,number,How long did breastfeeding last? (weeks),,number,0,,,[preg_postpartum] = '1',,"Total duration from initiation of breastfeeding to complete cessation, recorded in completed weeks.",,,,,,,,,,,1,,,,,,,1,1 presentation,PREGNANCY PRESENTATION,pregdet_labour,radio,Is the patient in labour at presentation?,"1, Yes | 0, No | 99, Unknown",,,,,[preg_pregnant] = '1',,,,,,,,,,,,,1,,,,,,,,1 presentation,PREGNANCY PRESENTATION,preg_bbtest,radio,Baby tested for mother's infection of interest,"1, Yes | 0, No | 99, Unknown",,,,,[preg_postpartum] = '1',,This refers to testing the baby for the mother's infection of interest.,Indicate 'Yes' if the baby was tested for the mother's infection of interest.,,,,,,1,1,1,1,,1,1,,,,,, -presentation,PREGNANCY PRESENTATION,preg_bbresl,radio,If yes: specify test result from mother's infection of interest ,"1, Positive | 0, Negative | 99, Unknown",,,,,[preg_bbtest] = '1',,This refers to the result of testing the baby for the mother's infection of interest.,Indicate the test result.,,,,,,1,1,1,1,,1,1,,,,,, +presentation,PREGNANCY PRESENTATION,preg_bbresl,radio,If yes: specify test result from mother's infection of interest,"1, Positive | 0, Negative | 99, Unknown",,,,,[preg_bbtest] = '1',,This refers to the result of testing the baby for the mother's infection of interest.,Indicate the test result.,,,,,,1,1,1,1,,1,1,,,,,, presentation,INFANT: LESS THAN 12 MONTHS OLD,infa_neonate,descriptive,The patient is a neonate. Please do not forget to complete the neonate-specific form.,,,,,,[demog_calcage_days]<=28,,,,,,,,,,,,,1,,,,,,,1, presentation,INFANT: LESS THAN 12 MONTHS OLD,infa_brtwei,number,Birth weight (select units),,number,0,,,([demog_age] <= 1 and [demog_age_units]='1') or ([demog_age] <= 12 and [demog_age_units]='2') or ([demog_age] <= 365 and [demog_age_units]='3') or [demog_calcage_days]<=1,,This refers to the first weight of a newborn obtained after birth.,Indicate the birth weight.,SNOMED,"47340003, Birth weight (finding)","C0005612, Birth weight",,,1,1,,1,1,1,,,,,,1, presentation,INFANT: LESS THAN 12 MONTHS OLD,infa_brtwei_units,radio,Birth weight (select units),"1, g | 2, lb",units,,,,([demog_age] <= 1 and [demog_age_units]='1') or ([demog_age] <= 12 and [demog_age_units]='2') or ([demog_age] <= 365 and [demog_age_units]='3') or [demog_calcage_days]<=1,,,,SNOMED,"47340003, Birth weight (finding)","C0005612, Birth weight",,,1,1,,1,1,1,,,,,,1, @@ -553,13 +553,13 @@ daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessm daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_dizzy,radio,Feeling dizzy / faint,"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata]='1' and [initial_assessment_arm_1][demog_calcage_days]>=1825,Systemic/General,"This refers to the subjective feeling of light-headedness or dizziness which may precede an episode of syncope or a sensation of unsteadiness, spinning or rocking.","Indicate 'Yes', if the patient experienced this at any time during the date of assessment.",SNOMED,SNOMED,"C0581879, Felt faint",,clinical_features,,1,,,1,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_myalgia,radio,Muscle aches (myalgia),"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata]='1' and [initial_assessment_arm_1][demog_calcage_days]>=365,Systemic/General,This refers to pain localised to a muscle or group of muscles.,"Indicate 'Yes', if the patient experienced this at any time during the date of assessment.",SNOMED,SNOMED,"C0231528, Myalgia",,clinical_features,,1,,1,1,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_arthralgia,radio,Joint pain (arthralgia),"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata]='1' and [initial_assessment_arm_1][demog_calcage_days]>=365,Systemic/General,"This refers to a sensation of marked discomfort or pain localised to one or more joints, including small and big joints.","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C3805780, Arthralgia",,clinical_features,,1,,1,1,,1,,,,,, -daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointswell,radio,Joint swelling,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,Defined as the buildup of fluid in the soft tissue SURROUNDING the joint or in the joint itself,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation. ",SNOMED,"271771009, Joint swelling",,,,,,,,,,1,,,,,, +daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointswell,radio,Joint swelling,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,Defined as the buildup of fluid in the soft tissue SURROUNDING the joint or in the joint itself,"Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"271771009, Joint swelling",,,,,,,,,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointswell_site,checkbox,Site where joint swelling occurred,"1, Fingers | 2, Wrists | 3, Shoulders | 4, Elbow | 5, Hips | 8, Knees | 9, Ankles | 10, Toes | 99, Unknown | 88, Other",,,,,[sympt_jointswell]= '1',,This refers to the location where joint swelling occurred,,,,,,,,,,,,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointswell_site_oth,text,Specify other first joint swelling location,,,,,,[sympt_jointswell_site(88)]='1',,This refers to the location where joint swelling occurred,,,,,,,,,,,,,1,,,,,, -daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointtender,radio,Joint tenderness,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,"Defined as pain and discomfort in a joint, often accompanied by sensitivity to touch","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation. ",SNOMED,"110288007, Tenderness of joint",,,,,,,,,,1,,,,,, +daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointtender,radio,Joint tenderness,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,"Defined as pain and discomfort in a joint, often accompanied by sensitivity to touch","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"110288007, Tenderness of joint",,,,,,,,,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointtender_site,checkbox,Site where joint tenderness occurred,"1, Fingers | 2, Wrists | 3, Shoulders | 4, Elbow | 5, Hips | 8, Knees | 9, Ankles | 10, Toes | 99, Unknown | 88, Other",,,,,[sympt_jointtender]= '1',,This refers to the location where joint tenderness occurred,,,,,,,,,,,,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_jointtender_site_oth,text,Specify other first joint tenderness location,,,,,,[sympt_jointtender_site(88)]='1',,This refers to the location where joint tenderness occurred,,,,,,,,,,,,,1,,,,,, -daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_stissueswell,radio,Small tissue swelling,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,"Defined as painful swelling of the interphalangeal tissue, leading to tension and pain when flexing the fingers","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation. ",SNOMED,"298349001, Soft tissue swelling",,,,,,,,,,1,,,,,, +daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_stissueswell,radio,Small tissue swelling,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,"Defined as painful swelling of the interphalangeal tissue, leading to tension and pain when flexing the fingers","Indicate 'Yes', if the patient has experienced this at any time from onset of this illness to presentation.",SNOMED,"298349001, Soft tissue swelling",,,,,,,,,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_skinrash,radio,Skin rash,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,"This refers to any change in the skin which affects its appearance or texture. A rash may be localized to one part of the body or affect all the skin. Rashes may cause the skin to change colour, itch, become warm, bumpy, dry, cracked, or blistered, swell and may be painful.","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",SNOMED,SNOMED,"C4227880, Skin Rash",,clinical_features,,1,,,,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_paresthesia,radio,Skin paresthesia,"1, Yes | 0, No | 99, Unknown",,,,,[daily_arm_1][sympt_dailydata]='1' and [initial_assessment_arm_1][demog_calcage_days]>=365,Systemic/General,"This refers to percieved cutaneous sensations (e.g., cold, warmth, tingling, pressure, etc.) that are experienced spontaneously in the absence of stimulation.","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,,,,,1,,1,,,,,, daily,SYMPTOMS: Indicate if experienced between 00:00 to 24:00 on day of assessment.,sympt_skinchange,radio,Changes in skin texture,"1, Yes | 0, No | 99, Unknown",,,,,[sympt_dailydata]='1',Systemic/General,"This refers to alterations in the surface appearance and feel of the skin, such as roughness, unevenness, or the presence of bumps.","Indicate 'Yes', if the patient experienced this between 00:00 to 24:00 on day of assessment.",,,,,,,,,,1,,,,,,,, @@ -1062,7 +1062,7 @@ pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen t pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_pathtested,user_list,Pathogen tested / detected,,,,,pathogens_All,,,This refers to the pathogen(s) tested for using the biological sample.,Indicate the pathogen(s) which were tested for using the biological sample.,,,,,,1,1,1,1,1,1,1,,,,1,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_labtestmethod,radio,Lab test method,"1, PCR (NAAT) | 3, Culture | 6, RDT | 7, ELISA | 8,Other NAAT | 99, Unknown",,,,,,,This refers to the laboratory method used to test for the pathogen.,Select the single most appropriate option that represents the laboratory method used to test for the pathogen.,,,,,,1,1,1,1,1,1,1,,,,1,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_marker,checkbox,Lab marker,"1, NS1 Ag | 2, IgG | 3, IgM | 6, IgA | 4, Viral load / serotype (PCR/NAAT) | 5, Not applicable | 99, Unknown",,,,,,,This refers to the laboratory marker used to test for the pathogen,Select the single most appropriate option that represents the laboratory marker used to test for the pathogen.,,,,,,1,1,1,1,1,1,1,,,,1,, -pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_naat,radio,NAAT subtype,"1, RT-PCR| 2, LAMP | 3, TMA / TMP | 88, Other | 99, Unknown ",,,,,[test_labtestmethod]='1' or [test_labtestmethod]='8',,,,,,,,,,,,,,,1,,,,,, +pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_naat,radio,NAAT subtype,"1, RT-PCR | 2, LAMP | 3, TMA / TMP | 88, Other | 99, Unknown",,,,,[test_labtestmethod]='1' or [test_labtestmethod]='8',,,,,,,,,,,,,,,1,,,,,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_naat_other,text,Specify other NAAT subtype,,,,,,[test_naat]='88',,,,,,,,,,,,,,,1,,,,,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_result,radio,Pathogen test result,"1, Detected | 0, Not detected | 2, Equivocal | 99, Unknown",,,,,,,This refers to the results of the pathogen(s) tested for using the biological sample.,Select the single most appropriate option that represents results of the pathogen(s) tested for using the biological sample.,,,,,,1,1,1,1,1,1,1,,,,1,, pathogen_testing,PATHOGEN TESTING: Results of all types of sample and pathogen testing,test_denguetyp,radio,Dengue virus type,"1, DENV1 | 2, DENV2 | 3, DENV3 | 4, DENV4",,,,,[test_labtestmethod] = '1' and [test_pathtested]='96',,"This refers to the serotype label of the viral species of Dengue virus, which is a single-stranded, positive-sense RNA virus of the Flaviviridae family and Flavivirus genus, detected using the PCR test.",Select the single most appropriate option that represents the serotype label of the viral species of Dengue virus detected using the PCR test.,SNOMED,"60588009, Dengue virus, type 1 (organism) | 41328007, Dengue virus, type 2 (organism) | 8467002, Dengue virus, type 3 (organism) | 36700002, Dengue virus, type 4 (organism)",,,,,,1,,,,1,,,,,, diff --git a/tests/test_arc.py b/tests/test_arc.py index eccdfa6..28cd9bb 100644 --- a/tests/test_arc.py +++ b/tests/test_arc.py @@ -268,7 +268,9 @@ def test_arc_minimum_maximum_correct_type(): ) -@pytest.mark.low +@pytest.mark.skip( + reason="Not currently required. Maximum may not always make sense and can be left blank." +) def test_arc_minimum_maximum_exists(): """Minimum and maximum must exist for numbers.""" arc = pd.read_csv( @@ -285,19 +287,31 @@ def test_arc_minimum_maximum_exists(): @pytest.mark.low -def test_arc_minimum_maximum_exists_dates(): - """Maximum should exist for dates/times.""" +def test_arc_minimum_less_than_maximum(): + """Minimum must be less than Maximum for numbers.""" arc = pd.read_csv( ARC_PATH, - dtype="object", - usecols=["Variable", "Validation", "Maximum"], + usecols=["Variable", "Validation", "Minimum", "Maximum"], ) - condition = ~arc["Validation"].isin(["date_dmy", "datetime_dmy", "time"]) | ( - arc["Maximum"].notna() + + numeric_arc = arc[arc["Validation"] == "number"] + + condition = ( + numeric_arc["Minimum"].isna() + | numeric_arc["Maximum"].isna() + | ( + pd.to_numeric(numeric_arc["Minimum"]) + < pd.to_numeric(numeric_arc["Maximum"]) + ) ) + if not condition.all(): - invalid = arc.loc[~condition].set_index("Variable").to_dict(orient="index") - pytest.fail(f"ARC has no Maximum for date Variables: {invalid}") + invalid = ( + numeric_arc.loc[~condition].set_index("Variable").to_dict(orient="index") + ) + pytest.fail( + f"ARC has Minimum values greater than Maximum for Variables: {invalid}" + ) @pytest.mark.medium diff --git a/tests/test_lists.py b/tests/test_lists.py index ce10e63..433a47c 100644 --- a/tests/test_lists.py +++ b/tests/test_lists.py @@ -144,7 +144,7 @@ def test_too_many_presets(file): @pytest.mark.high @pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_unique_labels(file): - """Check if the Lists file has the same presets as ARC""" + """Check each option in a List file has a unique name""" df = pd.read_csv(file, dtype="object") condition = df[df.columns[0]].str.strip().duplicated(keep=False) @@ -156,7 +156,7 @@ def test_unique_labels(file): @pytest.mark.medium @pytest.mark.parametrize("file", LIST_FILES, ids=LIST_FILE_NAMES) def test_unique_codes(file): - """Check if the Lists file has the same presets as ARC""" + """Check each option in a List file has a unique code""" df = pd.read_csv(file, dtype="object") if "Code" in df.columns: