Tableinfo: phenotype_disease.tsv - nih-cfde/published-documentation GitHub Wiki

This table must not be manually created. Users should skip this, and all other tables marked "Built by script" in this summary, preparing only the rest of their datapackage's TSV files (those marked "Prepared by submitter") for submission. Once the "Prepared by submitter" tables are ready, users should then use the C2M2 submission prep script to automatically generate this table (and the other "Built by script" tables) using the information in the "Prepared by submitter" tables.

Each row in this table is equivalent to the statement "phenotype X (from HPO) is equivalent to disease Y (from the Disease Ontology)", for one particular (phenotype X, disease Y) pair; contents are autoloaded from HPO metadata by the submission prep script, which adds one row for every disease term associated with every phenotype term used in collection_phenotype.tsv or subject_phenotype.tsv.

USERS PLEASE NOTE: the creation of this table is currently stubbed pending reevaluation of its utility in the context of the CFDE portal. The submission prep script will generate a header-only version of the TSV for this table, independent of any included phenotype values. This is expected and will not invalidate your submission. phenotype_gene.tsv will (by contrast) be populated as expected, listing genes linked to any phenotype terms given in your submission.

All associations expressed in this table have been predetermined by the curators of the Human Phenotype Ontology: associations included in phenotype_disease.tsv for a given submission will be those that contain HPO phenotype terms in submitter-prepared tables.

Field	Field Description	Required?	Field Value Type	Extra Info
phenotype	A valid Human Phenotype Ontology term	Required	string	Human Phenotype Ontology lookup Examples: HP:0000349, HP:0012425
disease	A valid Disease Ontology term	Required	string	Disease Ontology lookup Examples: DOID:8778, DOID:0060249