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

Association between a subject and a Human Phenotype Ontology term

For subjects with phenotype metadata, this table will have one row for each phenotype associated with each such subject, along with an association_type field distinguishing "phenotype present" from "phenotype specifically ruled out."

All fields are required: this table can be empty (header-row only), but any non-header rows must leave no fields blank.

Some examples:

• If you don't have any subjects associated with phenotypes, this table should be left empty.
• If you have exactly one phenotype associated with each subject, this table will have as many rows as subject.tsv.
• If you have five phenotypes associated with each subject, this table will have five times as many rows as subject.tsv.
• If some but not all of your subjects are associated with one or more phenotypes, this table will contain one row for each phenotype assigned to each such subject (and the resulting row count will not have any obvious relationship to the number of rows in subject.tsv, which is both expected and fine in such a case).

Field	Field Description	Required?	Field Value Type	Extra Info
subject_id_namespace	Identifier namespace for this subject	Required	string	This will be the value of id_namespace in the row in subject.tsv corresponding to the subject referenced in this row. If your program has not registered multiple CFDE identifier namespaces, this will be exactly the same value for all rows.
subject_local_id	The ID of this subject	Required	string	This will be the value of local_id in the row in subject.tsv corresponding to the subject referenced in this row.
association_type	An indicator distinguishing "phenotype present" from "phenotype ruled out"	Required	one of cfde_phenotype_association_type:0 (meaning "phenotype ruled out") or cfde_phenotype_association_type:1 (meaning "phenotype observed")
phenotype	A valid Human Phenotype Ontology term	Required	string	Human Phenotype Ontology lookup Examples: HP:0000349, HP:0012425