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3 changes: 2 additions & 1 deletion AD.model.csv
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ missing or unknown,ADNC severity score is missing or unknown,,,,,ADNC,,CLEAR-AD,
Not AD,Not AD,,,,,ADNC,,ADSP,,string,clinical
days,"Age measured in days, a period of 24 hours.",,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C25301,,string,experimentalData
gestational weeks,"Gestational age (written with both weeks and days, e.g. 39 weeks and 0 days) is calculated using the best obstetrical estimated due date (EDD) based on the following formula: Gestational Age = (280 - (EDD - Reference Date))/ 7. Note: Reference Date is the date on which you are trying to determine gestational age.",,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C81253,,string,experimentalData
hours,Age measured in hours (60 minutes),,,,,ageAssessmentUnits,,TBD,,string,experimentalData
months,Age measured in calendar months (approximately 30 days or 4 weeks).,,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C29846,,string,experimentalData
PCW,Post-Conception Weeks,,,,,ageAssessmentUnits,,https://embryology.med.unsw.edu.au/embryology/index.php/Timeline_human_development,,string,experimentalData
weeks,"Age measured in weeks, a period of 7 consecutive days.",,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C29844,,string,experimentalData
Expand Down Expand Up @@ -821,7 +822,7 @@ LMO,Lipid-modified oligonucleotide sample barcode anchor.,,,,,libraryType,,https
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
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
ageAssessmentUnits,Age of assessment units.,"days, gestational weeks, months, PCW, weeks, years, hours",,,False,ManifestColumn,,sage.annotations-experimentalData.ageAssessmentUnits-0.0.2,,string,experimentalData
ageDays,Average age in days of the Drosophila individuals in the sample,,,,False,ManifestColumn,,sage.annotations-demographics.ageDays-0.0.2,,number,drosophila
ageDeath,"Age of death (note that ages > 89 must be censored to ""90+"")",,,,False,ManifestColumn,,sage.annotations-demographics.ageDeath-0.0.2,required^^#IndividualHumanMetadataTemplate,number,demographics
ageDeathUnits,The death age unit of measure,"days, gestational weeks, months, PCW, weeks, years",,,False,ManifestColumn,,sage.annotations-demographics.ageDeathUnits-0.0.4,required^^#IndividualHumanMetadataTemplate,string,demographics
Expand Down
114 changes: 60 additions & 54 deletions AD.model.jsonld
Original file line number Diff line number Diff line change
Expand Up @@ -385,6 +385,66 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Hours",
"@type": "rdfs:Class",
"rdfs:comment": "Age measured in hours (60 minutes)",
"rdfs:label": "Hours",
"rdfs:subClassOf": [
{
"@id": "bts:AgeAssessmentUnits"
},
{
"@id": "bts:PmiUnits"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "hours",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:AgeAssessmentUnits",
"@type": "rdfs:Class",
"rdfs:comment": "Age of assessment units.",
"rdfs:label": "AgeAssessmentUnits",
"rdfs:subClassOf": [
{
"@id": "bts:ManifestColumn"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:Days"
},
{
"@id": "bts:Gestationalweeks"
},
{
"@id": "bts:Months"
},
{
"@id": "bts:PCW"
},
{
"@id": "bts:Weeks"
},
{
"@id": "bts:Years"
},
{
"@id": "bts:Hours"
}
],
"sms:displayName": "ageAssessmentUnits",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Months",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -18114,43 +18174,6 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:AgeAssessmentUnits",
"@type": "rdfs:Class",
"rdfs:comment": "Age of assessment units.",
"rdfs:label": "AgeAssessmentUnits",
"rdfs:subClassOf": [
{
"@id": "bts:ManifestColumn"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:Days"
},
{
"@id": "bts:Gestationalweeks"
},
{
"@id": "bts:Months"
},
{
"@id": "bts:PCW"
},
{
"@id": "bts:Weeks"
},
{
"@id": "bts:Years"
}
],
"sms:displayName": "ageAssessmentUnits",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:AgeDays",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -24285,23 +24308,6 @@
"NeuropathMetadataTemplate": "required"
}
},
{
"@id": "bts:Hours",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "Hours",
"rdfs:subClassOf": [
{
"@id": "bts:PmiUnits"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "hours",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Minutes",
"@type": "rdfs:Class",
Expand Down
3 changes: 2 additions & 1 deletion modules/experimentalData/ageAssessmentUnits.csv
Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
ageAssessmentUnits,Age of assessment units.,"days, gestational weeks, months, PCW, weeks, years",,,False,ManifestColumn,,sage.annotations-experimentalData.ageAssessmentUnits-0.0.2,,string,experimentalData
ageAssessmentUnits,Age of assessment units.,"days, gestational weeks, months, PCW, weeks, years, hours",,,False,ManifestColumn,,sage.annotations-experimentalData.ageAssessmentUnits-0.0.2,,string,experimentalData
days,"Age measured in days, a period of 24 hours.",,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C25301,,string,experimentalData
gestational weeks,"Gestational age (written with both weeks and days, e.g. 39 weeks and 0 days) is calculated using the best obstetrical estimated due date (EDD) based on the following formula: Gestational Age = (280 - (EDD - Reference Date))/ 7. Note: Reference Date is the date on which you are trying to determine gestational age.",,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C81253,,string,experimentalData
months,Age measured in calendar months (approximately 30 days or 4 weeks).,,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C29846,,string,experimentalData
PCW,Post-Conception Weeks,,,,,ageAssessmentUnits,,https://embryology.med.unsw.edu.au/embryology/index.php/Timeline_human_development,,string,experimentalData
weeks,"Age measured in weeks, a period of 7 consecutive days.",,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C29844,,string,experimentalData
years,Age measured in years (approximately 365 days).,,,,,ageAssessmentUnits,,http://purl.obolibrary.org/obo/NCIT_C29848,,string,experimentalData
hours,Age measured in hours (60 minutes),,,,,ageAssessmentUnits,,TBD,,string,experimentalData