A combination of a variant and a phenotype that cannot be definitively diagnosed
Please find example CSV file here
pid,uniqid,hp_uri,hp_label,clinvar_uri,hgvs_string,date
- pid - patient unique identifier
- uniqid: some row unique identifier, over all sessions (a millisecond timestamp, numerical only, is a good idea)
- hp_uri: the URI from the human phenotype ontology that describes the patient's primary phenotypic manifestation
- hp_label: the name for that Human Phenotype Ontology term
- clinvar_uri: the URL for the variant, either directly to NCBI ClinVar database (e.g. https://www.ncbi.nlm.nih.gov/clinvar/variation/597052/), or via the identifiers.org proxy (e.g. https://identifiers.org/clinvar:4886)
- hgvs_string: the string expression of that clinical variant, in HGVS format (e.g. "NM_003977.4(AIP):c.40C>T (p.Gln14Ter)") - be sure you enclose this in quotes!!
- date: date of the diagnosis (leave blank if not available)
Please find the YARRRML template for this module here