disease_history_csv_template.md

Disease History CDE

The CDE for disease history ("age" at onset, "age" at diagnosis)

CSV file

Example CSV file

Please find example CSV file here

Columns

pid, uniqid, onset_uri, onset_date, diagnosis_uri, diagnosis_date

Notes:

• pid - patient unique identifier
• iniqid: some row unique identifier, over all sessions (a millisecond timestamp, numerical only, is a good idea)
• onset_uri:
  • http://purl.obolibrary.org/obo/HP_0410280 (Pediatric onset)
  • http://purl.obolibrary.org/obo/HP_0003581 (Adult onset)
  • http://purl.obolibrary.org/obo/HP_0030674 (Antenatal onset)
  • http://purl.obolibrary.org/obo/HP_0003623 (Neonatal onset)
  • http://purl.obolibrary.org/obo/HP_0003577 (Congenital onset)
  • http://purl.obolibrary.org/obo/NCIT_C124294 (Undetermined)
  • http://purl.obolibrary.org/obo/NCIT_C25164 (Date) - use this when you are going to provide a date
• onset_date: ISO 8601 date (note that the CDE calls this "age", but it is annotated as being a date field...??)
• diagnosis_uri:
  • http://purl.obolibrary.org/obo/NCIT_C81318 (Prenatal)
  • http://purl.obolibrary.org/obo/NCIT_C81317 (Postnatal)
  • http://purl.obolibrary.org/obo/NCIT_C124294 (Undetermined)
  • http://purl.obolibrary.org/obo/NCIT_C25164 (Date) - use this when you are going to provide a date
• diagnosis_date: ISO 8601 date (note that the CDE calls this "age", but it is annotated as being a date field...??)

SPARQL NOTES: When querying, the patient attribute will be one of:

• http://purl.obolibrary.org/obo/NCIT_C156420 (Age at Diagnosis)
• http://purl.obolibrary.org/obo/HP_0003674 (symptom onset)

YARRRML

Please find the YARRRML template for this module here

TODO