Merge pull request #144 from adknowledgeportal/clear-ad-updates-v2

Clear-ad-updates-v2

Author: MasterPastures

AD.model.csv

@@ -835,7 +835,7 @@ CMO,Cholesterol-modified oligonucleotide sample barcode anchor.,,,,,libraryType,
 HTO,Hashtag oligonucelotide; oligo-tagged antibodies against ubiquitously expressed surface proteins with different barcodes are used to uniquely label cells from distinct samples.,,,,,libraryType,,https://doi.org/10.1186/s13059-018-1603-1,,string,sequencing
 LMO,Lipid-modified oligonucleotide sample barcode anchor.,,,,,libraryType,,https://doi.org/10.1038/s41592-019-0433-8,,string,sequencing
 plasmid DNA,A small cellular inclusion consisting of a ring of DNA that is not in a chromosome but is capable of autonomous replication.,,,,,libraryType,,http://purl.obolibrary.org/obo/NCIT_C754,,string,sequencing
- recent/active, remote/inactive," unknown""",,,False,ManifestColumn,,sage.annotations-demographics.hypercholesterolemias-0.0.2,,string,demographics
+ recent/active, remote/inactive," unknown""",,,False,ManifestColumn,,sage.annotations-demographics.hypercholesterolemia-0.0.2,,string,demographics
 ADNC,ADNC severity score,"Not AD, Low, Intermediate, High, missing or unknown",,,True,ManifestColumn,,sage-annotations-clinical.ADNC-0.0.2,string,,clinical
 ageAssessment,Age of clinical or behavioral assessment.,,,,False,ManifestColumn,,sage.annotations-experimentalData.ageAssessment-0.0.2,,number,experimentalData
 ageAssessmentUnits,Age of assessment units.,"days, gestational weeks, months, PCW, weeks, years",,,False,ManifestColumn,,sage.annotations-experimentalData.ageAssessmentUnits-0.0.2,,string,experimentalData
@@ -1058,7 +1058,7 @@ assay_wholeExomeSeq_metadata_template,SysBio wholeExomeSeq metadata template sch
 assay_wholeGenomeSeq_metadata_template,SysBio wholeGenomeSeq (aka WGS) metadata template schema,,"Component, specimenID, libraryID, assay, platform, referenceSet, dnaBatch, sequencingBatch, libraryPrep, libraryPreparationMethod, readLength, runType, totalReads, numberCells, ratio260over280, ratio260over230, GQN",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.wholeGenomeSeq,,,template
 biospecimen_drosophila_metadata_template,SysBio drosophila biospecimen metadata template schema,,"Component, specimenID, bodyPart, tissueWeight, nucleicAcidSource, genotype, ageDays, nIndividuals, nMale, nFemale, temperature",,False,ManifestTemplate,,sysbio.metadataTemplates-biospecimen.drosophila,,,template
 biospecimen_invitro_metadata_template,SysBio in vitro biospecimen metadata template schema,,"Component, individualID, specimenID, specimenIdSource, modelSystemType, sourceCell, cellType, reprogrammingMethod, differentiationMethod, passage, terminalDifferentiationPoint, samplingAge, samplingAgeUnits, treatmentType, nucleicAcidSource, assay",,False,ManifestTemplate,,sysbio.metadataTemplates-biospecimen.invitro,,,template
-biospecimen_metadata_template,SysBio AD biospecimen metadata template schema,,"Component, individualID, specimenID, specimenIdSource, organ, tissue, isPostMortem, BrodmannArea, nucleicAcidSource, cellType, samplingAge, samplingAgeUnits, sampleStatus, fastingState, visitNumber, assay, treatmentType, treatmentDose",,False,ManifestTemplate,,sysbio.metadataTemplates-ad.biospecimen,,,template
+biospecimen_metadata_template,SysBio AD biospecimen metadata template schema,,"Component, individualID, specimenID, specimenIdSource, collectionMethod, freezeThawCycles, organ, tissue, isPostMortem, BrodmannArea, nucleicAcidSource, cellType, samplingAge, samplingAgeUnits, sampleStatus, fastingState, visitNumber, assay, treatmentType, treatmentDose",,False,ManifestTemplate,,sysbio.metadataTemplates-ad.biospecimen,,,template
 file_annotation_template,AD file annotation template schema,,"Component, Filename, individualID, specimenID, isMultiSpecimen, assay, fileFormat, consortium, study, grant, resourceType, dataType, dataSubtype, metadataType, analysisType, isModelSystem, chromosome",,False,ManifestTemplate,,sysbio.metadataTemplates-ad.manifest,,,template
 individual_animal_metadata_template,SysBio individual animal metadata template schema,,"Component, individualID, individualIdSource, species, sexChromosome, dateBirth, dateDeath, sex, genotype, genotypeBackground, room, litter, matingID, treatmentDose, modelSystemName",,False,ManifestTemplate,,sysbio.metadataTemplates-individual.animal,,,template
 individual_animal_MODEL-AD_metadata_template,individual animal metadata template schema for MODEL-AD Consortium,,"Component, individualID, climbID, microchipID, birthID, matingID, individualIdSource, materialOrigin, sex, species, generation, dateBirth, ageDeath, ageDeathUnits, brainWeight, rodentWeight, rodentDiet, bedding, room, waterpH, treatmentDose, treatmentType, stockNumber, genotype, genotypeBackground, modelSystemName, strainOfficialName",,False,ManifestTemplate,,sysbio.metadataTemplates-modelad.individual.animal,,,template

AD.model.jsonld

@@ -33108,6 +33108,12 @@
                 {
                     "@id": "bts:SpecimenIdSource"
                 },
+                {
+                    "@id": "bts:CollectionMethod"
+                },
+                {
+                    "@id": "bts:FreezeThawCycles"
+                },
                 {
                     "@id": "bts:Organ"
                 },

modules/demographics/Hypercholesterolemia.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-hypercholesterolemia, For CLEAR AD. UDSV3 IVP Form A5 Subject Health History Question 5c.  AND OR UDSV3 IVP Form D1 Clinician Diagnosis Question 8., "absent, recent/active, remote/inactive, unknown",,,False,ManifestColumn,,sage.annotations-demographics.hypercholesterolemias-0.0.2,,string,demographics
+hypercholesterolemia, For CLEAR AD. UDSV3 IVP Form A5 Subject Health History Question 5c. AND OR UDSV3 IVP Form D1 Clinician Diagnosis Question 8., "absent, recent/active, remote/inactive, unknown",,,False,ManifestColumn,,sage.annotations-demographics.hypercholesterolemia-0.0.2,,string,demographics

modules/template/templates.csv

@@ -20,7 +20,7 @@ assay_wholeExomeSeq_metadata_template,SysBio wholeExomeSeq metadata template sch
 assay_wholeGenomeSeq_metadata_template,SysBio wholeGenomeSeq (aka WGS) metadata template schema,,"Component, specimenID, libraryID, assay, platform, referenceSet, dnaBatch, sequencingBatch, libraryPrep, libraryPreparationMethod, readLength, runType, totalReads, numberCells, ratio260over280, ratio260over230, GQN",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.wholeGenomeSeq,,,template
 biospecimen_drosophila_metadata_template,SysBio drosophila biospecimen metadata template schema,,"Component, specimenID, bodyPart, tissueWeight, nucleicAcidSource, genotype, ageDays, nIndividuals, nMale, nFemale, temperature",,False,ManifestTemplate,,sysbio.metadataTemplates-biospecimen.drosophila,,,template
 biospecimen_invitro_metadata_template,SysBio in vitro biospecimen metadata template schema,,"Component, individualID, specimenID, specimenIdSource, modelSystemType, sourceCell, cellType, reprogrammingMethod, differentiationMethod, passage, terminalDifferentiationPoint, samplingAge, samplingAgeUnits, treatmentType, nucleicAcidSource, assay",,False,ManifestTemplate,,sysbio.metadataTemplates-biospecimen.invitro,,,template
-biospecimen_metadata_template,SysBio AD biospecimen metadata template schema,,"Component, individualID, specimenID, specimenIdSource, organ, tissue, isPostMortem, BrodmannArea, nucleicAcidSource, cellType, samplingAge, samplingAgeUnits, sampleStatus, fastingState, visitNumber, assay, treatmentType, treatmentDose",,False,ManifestTemplate,,sysbio.metadataTemplates-ad.biospecimen,,,template
+biospecimen_metadata_template,SysBio AD biospecimen metadata template schema,,"Component, individualID, specimenID, specimenIdSource, collectionMethod, freezeThawCycles, organ, tissue, isPostMortem, BrodmannArea, nucleicAcidSource, cellType, samplingAge, samplingAgeUnits, sampleStatus, fastingState, visitNumber, assay, treatmentType, treatmentDose",,False,ManifestTemplate,,sysbio.metadataTemplates-ad.biospecimen,,,template
 file_annotation_template,AD file annotation template schema,,"Component, Filename, individualID, specimenID, isMultiSpecimen, assay, fileFormat, consortium, study, grant, resourceType, dataType, dataSubtype, metadataType, analysisType, isModelSystem, chromosome",,False,ManifestTemplate,,sysbio.metadataTemplates-ad.manifest,,,template
 individual_animal_metadata_template,SysBio individual animal metadata template schema,,"Component, individualID, individualIdSource, species, sexChromosome, dateBirth, dateDeath, sex, genotype, genotypeBackground, room, litter, matingID, treatmentDose, modelSystemName",,False,ManifestTemplate,,sysbio.metadataTemplates-individual.animal,,,template
 individual_animal_MODEL-AD_metadata_template,individual animal metadata template schema for MODEL-AD Consortium,,"Component, individualID, climbID, microchipID, birthID, matingID, individualIdSource, materialOrigin, sex, species, generation, dateBirth, ageDeath, ageDeathUnits, brainWeight, rodentWeight, rodentDiet, bedding, room, waterpH, treatmentDose, treatmentType, stockNumber, genotype, genotypeBackground, modelSystemName, strainOfficialName",,False,ManifestTemplate,,sysbio.metadataTemplates-modelad.individual.animal,,,template