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fixing test csv headers
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costero-e committed Jan 17, 2025
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2 changes: 1 addition & 1 deletion csv/examples/test/cohorts.csv
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cohortDataTypes|id,cohortDataTypes|label,cohortDesign|id,cohortDesign|label,cohortSize,cohortType,collectionEvents|eventAgeRange|availability,collectionEvents|eventAgeRange|availabilityCount,collectionEvents|eventAgeRange|distribution,collectionEvents|eventDataTypes|availability,collectionEvents|eventDataTypes|availabilityCount,collectionEvents|eventDataTypes|distribution,collectionEvents|eventDiseases|availability,collectionEvents|eventDiseases|availabilityCount,collectionEvents|eventDiseases|distribution,collectionEvents|eventEthnicities|availability,collectionEvents|eventEthnicities|availabilityCount,collectionEvents|eventEthnicities|distribution,collectionEvents|eventGenders|availability,collectionEvents|eventGenders|availabilityCount,collectionEvents|eventGenders|distribution,collectionEvents|eventLocations|availability,collectionEvents|eventLocations|availabilityCount,collectionEvents|eventLocations|distribution,collectionEvents|eventPhenotypes|availability,collectionEvents|eventPhenotypes|availabilityCount,collectionEvents|eventPhenotypes|distribution,collectionEvents|eventTimeline|availability,collectionEvents|eventTimeline|availabilityCount,collectionEvents|eventTimeline|distribution,exclusionCriteria|ageRange|end|iso8601duration,exclusionCriteria|ageRange|start|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset,exclusionCriteria|diseaseConditions|diseaseCode|id,exclusionCriteria|diseaseConditions|diseaseCode|label,exclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|diseaseConditions|notes,exclusionCriteria|diseaseConditions|severity|id,exclusionCriteria|diseaseConditions|severity|label,exclusionCriteria|diseaseConditions|stage|id,exclusionCriteria|diseaseConditions|stage|label,exclusionCriteria|ethnicities|id,exclusionCriteria|ethnicities|label,exclusionCriteria|genders|id,exclusionCriteria|genders|label,exclusionCriteria|locations|id,exclusionCriteria|locations|label,exclusionCriteria|phenotypicConditions|evidence|evidenceCode,exclusionCriteria|phenotypicConditions|evidence|reference,exclusionCriteria|phenotypicConditions|excluded,exclusionCriteria|phenotypicConditions|featureType|id,exclusionCriteria|phenotypicConditions|featureType|label,exclusionCriteria|phenotypicConditions|modifiers,exclusionCriteria|phenotypicConditions|notes,exclusionCriteria|phenotypicConditions|onset,exclusionCriteria|phenotypicConditions|resolution,exclusionCriteria|phenotypicConditions|severity|id,exclusionCriteria|phenotypicConditions|severity|label,id,inclusionCriteria|ageRange|end|iso8601duration,inclusionCriteria|ageRange|start|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset,inclusionCriteria|diseaseConditions|diseaseCode|id,inclusionCriteria|diseaseConditions|diseaseCode|label,inclusionCriteria|diseaseConditions|familyHistory,inclusionCriteria|diseaseConditions|notes,inclusionCriteria|diseaseConditions|severity|id,inclusionCriteria|diseaseConditions|severity|label,inclusionCriteria|diseaseConditions|stage|id,inclusionCriteria|diseaseConditions|stage|label,inclusionCriteria|ethnicities|id,inclusionCriteria|ethnicities|label,inclusionCriteria|genders|id,inclusionCriteria|genders|label,inclusionCriteria|locations|id,inclusionCriteria|locations|label,inclusionCriteria|phenotypicConditions|evidence|evidenceCode,inclusionCriteria|phenotypicConditions|evidence|reference,inclusionCriteria|phenotypicConditions|excluded,inclusionCriteria|phenotypicConditions|featureType|id,inclusionCriteria|phenotypicConditions|featureType|label,inclusionCriteria|phenotypicConditions|modifiers,inclusionCriteria|phenotypicConditions|notes,inclusionCriteria|phenotypicConditions|onset,inclusionCriteria|phenotypicConditions|resolution,inclusionCriteria|phenotypicConditions|severity|id,inclusionCriteria|phenotypicConditions|severity|label,name
cohortDataTypes|id,cohortDataTypes|label,cohortDesign|id,cohortDesign|label,cohortSize,cohortType,collectionEvents|eventAgeRange|availability,collectionEvents|eventAgeRange|availabilityCount,collectionEvents|eventAgeRange|distribution,collectionEvents|eventDataTypes|availability,collectionEvents|eventDataTypes|availabilityCount,collectionEvents|eventDataTypes|distribution,collectionEvents|eventDiseases|availability,collectionEvents|eventDiseases|availabilityCount,collectionEvents|eventDiseases|distribution,collectionEvents|eventEthnicities|availability,collectionEvents|eventEthnicities|availabilityCount,collectionEvents|eventEthnicities|distribution,collectionEvents|eventGenders|availability,collectionEvents|eventGenders|availabilityCount,collectionEvents|eventGenders|distribution,collectionEvents|eventLocations|availability,collectionEvents|eventLocations|availabilityCount,collectionEvents|eventLocations|distribution,collectionEvents|eventPhenotypes|availability,collectionEvents|eventPhenotypes|availabilityCount,collectionEvents|eventPhenotypes|distribution,collectionEvents|eventTimeline|start,collectionEvents|eventTimeline|end,collectionEvents|eventSize,exclusionCriteria|ageRange|end|iso8601duration,exclusionCriteria|ageRange|start|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset,exclusionCriteria|diseaseConditions|diseaseCode|id,exclusionCriteria|diseaseConditions|diseaseCode|label,exclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|diseaseConditions|notes,exclusionCriteria|diseaseConditions|severity|id,exclusionCriteria|diseaseConditions|severity|label,exclusionCriteria|diseaseConditions|stage|id,exclusionCriteria|diseaseConditions|stage|label,exclusionCriteria|ethnicities|id,exclusionCriteria|ethnicities|label,exclusionCriteria|genders|id,exclusionCriteria|genders|label,exclusionCriteria|locations|id,exclusionCriteria|locations|label,exclusionCriteria|phenotypicConditions|evidence|evidenceCode,exclusionCriteria|phenotypicConditions|evidence|reference,exclusionCriteria|phenotypicConditions|excluded,exclusionCriteria|phenotypicConditions|featureType|id,exclusionCriteria|phenotypicConditions|featureType|label,exclusionCriteria|phenotypicConditions|modifiers,exclusionCriteria|phenotypicConditions|notes,exclusionCriteria|phenotypicConditions|onset,exclusionCriteria|phenotypicConditions|resolution,exclusionCriteria|phenotypicConditions|severity|id,exclusionCriteria|phenotypicConditions|severity|label,id,inclusionCriteria|ageRange|end|iso8601duration,inclusionCriteria|ageRange|start|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset,inclusionCriteria|diseaseConditions|diseaseCode|id,inclusionCriteria|diseaseConditions|diseaseCode|label,inclusionCriteria|diseaseConditions|familyHistory,inclusionCriteria|diseaseConditions|notes,inclusionCriteria|diseaseConditions|severity|id,inclusionCriteria|diseaseConditions|severity|label,inclusionCriteria|diseaseConditions|stage|id,inclusionCriteria|diseaseConditions|stage|label,inclusionCriteria|ethnicities|id,inclusionCriteria|ethnicities|label,inclusionCriteria|genders|id,inclusionCriteria|genders|label,inclusionCriteria|locations|id,inclusionCriteria|locations|label,inclusionCriteria|phenotypicConditions|evidence|evidenceCode,inclusionCriteria|phenotypicConditions|evidence|reference,inclusionCriteria|phenotypicConditions|excluded,inclusionCriteria|phenotypicConditions|featureType|id,inclusionCriteria|phenotypicConditions|featureType|label,inclusionCriteria|phenotypicConditions|modifiers,inclusionCriteria|phenotypicConditions|notes,inclusionCriteria|phenotypicConditions|onset,inclusionCriteria|phenotypicConditions|resolution,inclusionCriteria|phenotypicConditions|severity|id,inclusionCriteria|phenotypicConditions|severity|label,name
OGMS:0000015,clinical history,OMIABIS:0001019,longitudinal study design,20000,study-defined,TRUE,101,"{""ranges"": {""20-40"": 51,""50-60"": 50}}",TRUE,29,"{""datatypes"": {""OGMS:0000015"": 5,""OBI:0000070"": 8,""OMIABIS:0000060"": 16}}",TRUE,100,"{""diseases"":{""HP:0001645"": 50}}",TRUE,101,"{""ethnicities"": {""African"": 3,""European"": 90,""Latin American"": 8}}",TRUE,101,"{""genders"": {""female"": 51,""male"": 50}}",TRUE,101,"{""ethnicities"": {""GAZ:00004501"":101}}",TRUE,101,"{""Phenotype"": {""GAZ:00004501"":101}}",,,,P58Y,P18Y,"{""id"": ""NCIT:C49685"",""label"": ""Adult 18-65 Years Old""}",HP:0004789,lactose intolerance,FALSE,All this information is synthetic.,HP:0012828,Severe,OGMS:0000119,acute onset,NCIT:C43851,European,"NCIT:C16576|NCIT:C20197|NCIT:C1799","Female|male|uknown",GAZ:00000460,Eurasia,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0000002,Abnormality of body height,"{""id"": ""HP:0032500"",""label"": ""Exacerbated by tobacco use""}",Bear in mind that all this information is synthetic,"{""iso8601duration"": ""P58Y""}","{""iso8601duration"": ""P98Y""}",HP:0012828,Severe,EGA-testing,P59Y,P18Y,"{""id"": ""NCIT:C49685"",""label"": ""Adult 18-65 Years Old""}",HP:0004789,lactose intolerance,FALSE,All this information is synthetic.,HP:0012828,Severe,OGMS:0000119,acute onset,NCIT:C43851,European,"NCIT:C16576|NCIT:C20197|NCIT:C1799","Female|male|uknown",GAZ:00000460,Eurasia,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0000002,Abnormality of body height,"{""id"": ""HP:0032500"",""label"": ""Exacerbated by tobacco use""}",Bear in mind that all this information is synthetic,"{""iso8601duration"": ""P59Y""}","{""iso8601duration"": ""P98Y""}",HP:0012828,Severe,syntheticCohort
2 changes: 1 addition & 1 deletion csv/examples/test/individuals.csv
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diseases|ageOfOnset,diseases|ageOfOnset|days,diseases|ageOfOnset|end,diseases|ageOfOnset|end|iso8601duration,diseases|ageOfOnset|id,diseases|ageOfOnset|iso8601duration,diseases|ageOfOnset|label,diseases|ageOfOnset|start,diseases|ageOfOnset|start|iso8601duration,diseases|ageOfOnset|weeks,diseases|diseaseCode|id,diseases|diseaseCode|label,diseases|familyHistory,diseases|notes,diseases|severity|id,diseases|severity|label,diseases|stage|id,diseases|stage|label,ethnicity|id,ethnicity|label,exposures|ageAtExposure|iso8601duration,exposures|date,exposures|duration,exposures|exposureCode|id,exposures|exposureCode|label,exposures|unit|id,exposures|unit|label,geographicOrigin|id,geographicOrigin|label,id,info,interventionsOrProcedures|ageAtProcedure,interventionsOrProcedures|ageAtProcedure|days,interventionsOrProcedures|ageAtProcedure|end,interventionsOrProcedures|ageAtProcedure|end|iso8601duration,interventionsOrProcedures|ageAtProcedure|id,interventionsOrProcedures|ageAtProcedure|iso8601duration,interventionsOrProcedures|ageAtProcedure|label,interventionsOrProcedures|ageAtProcedure|start,interventionsOrProcedures|ageAtProcedure|start|iso8601duration,interventionsOrProcedures|ageAtProcedure|weeks,interventionsOrProcedures|bodySite|id,interventionsOrProcedures|bodySite|label,interventionsOrProcedures|dateOfProcedure,interventionsOrProcedures|procedureCode|id,interventionsOrProcedures|procedureCode|label,karyotypicSex,measures|assayCode|id,measures|assayCode|label,measures|date,measures|measurementValue|id,measures|measurementValue|label,measures|measurementValue|referenceRange|high,measures|measurementValue|referenceRange|low,measures|measurementValue|referenceRange|unit|id,measures|measurementValue|referenceRange|unit|label,measures|measurementValue|typedQuantities|quantity|referenceRange|high,measures|measurementValue|typedQuantities|quantity|referenceRange|low,measures|measurementValue|typedQuantities|quantity|referenceRange|unit,measures|measurementValue|typedQuantities|quantity|unit|id,measures|measurementValue|typedQuantities|quantity|unit|label,measures|measurementValue|typedQuantities|quantity|value,measures|measurementValue|unit|id,measures|measurementValue|unit|label,measures|measurementValue|value,measures|notes,measures|observationMoment,measures|observationMoment|days,measures|observationMoment|end,measures|observationMoment|end|iso8601duration,measures|observationMoment|id,measures|observationMoment|iso8601duration,measures|observationMoment|label,measures|observationMoment|start,measures|observationMoment|start|iso8601duration,measures|observationMoment|weeks,measures|procedure|ageAtProcedure,measures|procedure|bodySite|id,measures|procedure|bodySite|label,measures|procedure|dateOfProcedure,measures|procedure|procedureCode|id,measures|procedure|procedureCode|label,pedigrees|disease|ageOfOnset,pedigrees|disease|diseaseCode|id,pedigrees|disease|diseaseCode|label,pedigrees|disease|familyHistory,pedigrees|disease|notes,pedigrees|disease|severity|id,pedigrees|disease|severity|label,pedigrees|disease|stage|id,pedigrees|disease|stage|label,pedigrees|id,pedigrees|members|affected,pedigrees|members|memberId,pedigrees|members|role|id,pedigrees|members|role|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|evidence|reference|id,phenotypicFeatures|evidence|reference|notes,phenotypicFeatures|evidence|reference|reference,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset,phenotypicFeatures|onset|days,phenotypicFeatures|onset|end,phenotypicFeatures|onset|end|iso8601duration,phenotypicFeatures|onset|id,phenotypicFeatures|onset|iso8601duration,phenotypicFeatures|onset|label,phenotypicFeatures|onset|start,phenotypicFeatures|onset|start|iso8601duration,phenotypicFeatures|onset|weeks,phenotypicFeatures|resolution,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|end,phenotypicFeatures|resolution|end|iso8601duration,phenotypicFeatures|resolution|id,phenotypicFeatures|resolution|iso8601duration,phenotypicFeatures|resolution|label,phenotypicFeatures|resolution|start,phenotypicFeatures|resolution|start|iso8601duration,phenotypicFeatures|resolution|weeks,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sex|id,sex|label,treatments|ageAtOnset|iso8601duration,treatments|cumulativeDose|referenceRange|id,treatments|cumulativeDose|referenceRange|label,treatments|treatmentCode|id,treatments|treatmentCode|label,treatments|routeOfAdministration|id,treatments|routeOfAdministration|label,treatments|treatmentCode|id,treatments|treatmentCode|label
diseases|ageOfOnset,diseases|ageOfOnset|days,diseases|ageOfOnset|end,diseases|ageOfOnset|end|iso8601duration,diseases|ageOfOnset|id,diseases|ageOfOnset|iso8601duration,diseases|ageOfOnset|label,diseases|ageOfOnset|start,diseases|ageOfOnset|start|iso8601duration,diseases|ageOfOnset|weeks,diseases|diseaseCode|id,diseases|diseaseCode|label,diseases|familyHistory,diseases|notes,diseases|severity|id,diseases|severity|label,diseases|stage|id,diseases|stage|label,ethnicity|id,ethnicity|label,exposures|ageAtExposure|iso8601duration,exposures|date,exposures|duration,exposures|exposureCode|id,exposures|exposureCode|label,exposures|unit|id,exposures|unit|label,geographicOrigin|id,geographicOrigin|label,id,info,interventionsOrProcedures|ageAtProcedure,interventionsOrProcedures|ageAtProcedure|days,interventionsOrProcedures|ageAtProcedure|end,interventionsOrProcedures|ageAtProcedure|end|iso8601duration,interventionsOrProcedures|ageAtProcedure|id,interventionsOrProcedures|ageAtProcedure|iso8601duration,interventionsOrProcedures|ageAtProcedure|label,interventionsOrProcedures|ageAtProcedure|start,interventionsOrProcedures|ageAtProcedure|start|iso8601duration,interventionsOrProcedures|ageAtProcedure|weeks,interventionsOrProcedures|bodySite|id,interventionsOrProcedures|bodySite|label,interventionsOrProcedures|dateOfProcedure,interventionsOrProcedures|procedureCode|id,interventionsOrProcedures|procedureCode|label,karyotypicSex,measures|assayCode|id,measures|assayCode|label,measures|date,measures|measurementValue|id,measures|measurementValue|label,measures|measurementValue|referenceRange|high,measures|measurementValue|referenceRange|low,measures|measurementValue|referenceRange|unit|id,measures|measurementValue|referenceRange|unit|label,measures|measurementValue|typedQuantities|quantity|referenceRange|high,measures|measurementValue|typedQuantities|quantity|referenceRange|low,measures|measurementValue|typedQuantities|quantity|referenceRange|unit,measures|measurementValue|typedQuantities|quantity|unit|id,measures|measurementValue|typedQuantities|quantity|unit|label,measures|measurementValue|typedQuantities|quantity|value,measures|measurementValue|unit|id,measures|measurementValue|unit|label,measures|measurementValue|value,measures|notes,measures|observationMoment,measures|observationMoment|days,measures|observationMoment|end,measures|observationMoment|end|iso8601duration,measures|observationMoment|id,measures|observationMoment|iso8601duration,measures|observationMoment|label,measures|observationMoment|start,measures|observationMoment|start|iso8601duration,measures|observationMoment|weeks,measures|procedure|ageAtProcedure,measures|procedure|bodySite|id,measures|procedure|bodySite|label,measures|procedure|dateOfProcedure,measures|procedure|procedureCode|id,measures|procedure|procedureCode|label,pedigrees|disease|ageOfOnset,pedigrees|disease|diseaseCode|id,pedigrees|disease|diseaseCode|label,pedigrees|disease|familyHistory,pedigrees|disease|notes,pedigrees|disease|severity|id,pedigrees|disease|severity|label,pedigrees|disease|stage|id,pedigrees|disease|stage|label,pedigrees|id,pedigrees|members|affected,pedigrees|members|memberId,pedigrees|members|role|id,pedigrees|members|role|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|evidence|reference|id,phenotypicFeatures|evidence|reference|notes,phenotypicFeatures|evidence|reference|reference,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset,phenotypicFeatures|onset|days,phenotypicFeatures|onset|end,phenotypicFeatures|onset|end|iso8601duration,phenotypicFeatures|onset|id,phenotypicFeatures|onset|iso8601duration,phenotypicFeatures|onset|label,phenotypicFeatures|onset|start,phenotypicFeatures|onset|start|iso8601duration,phenotypicFeatures|onset|weeks,phenotypicFeatures|resolution,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|end,phenotypicFeatures|resolution|end|iso8601duration,phenotypicFeatures|resolution|id,phenotypicFeatures|resolution|iso8601duration,phenotypicFeatures|resolution|label,phenotypicFeatures|resolution|start,phenotypicFeatures|resolution|start|iso8601duration,phenotypicFeatures|resolution|weeks,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sex|id,sex|label,treatments|ageAtOnset|iso8601duration,treatments|cumulativeDose|referenceRange|unit|id,treatments|cumulativeDose|referenceRange|unit|label,treatments|treatmentCode|id,treatments|treatmentCode|label,treatments|routeOfAdministration|id,treatments|routeOfAdministration|label,treatments|treatmentCode|id,treatments|treatmentCode|label
,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,EGA-testing,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,XX,UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,"Ind001|Ind002|Ind003","NCIT:C64435|NCIT:C96572|NCIT:C111201","Proband|Father|Full Brother",ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,,,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure

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