biosample_in_collection.tsv

Sourced from the CFDE-CC Documentation Wiki

Assignment of a biosample as a member of a collection

If populated, biosample_in_collection.tsv will contain one row for every assignment of a biosample as a member of a collection.

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 biosamples contained in collections, this table should be left empty.
• If each biosample is contained in exactly one collection, this table will have the same number of rows as biosample.tsv.
• If each biosample is simultaneously a member of three collections, this table will have three times as many rows as biosample.tsv.

Usage note:

• If a biosample is a member of collection X, and collection X is itself a subcollection of some other collection Y (as expressed in the collection_in_collection table), then biosample_in_collection.tsv should only record the membership of the biosample in collection X: the biosample's (transitive) membership in collection Y will be automatically computed. In general, biosample_in_collection.tsv should record only the most specific (leaf-most) collection memberships: transitive membership of biosamples in ancestor/superset collections will be automatically inferred from the containment relationships expressed in collection_in_collection.

Field	Field Description	Required?	Field Value Type	Extra Info
biosample_id_namespace	Identifier namespace for this biosample	Required	string	This will be the value of id_namespace in the row in biosample.tsv corresponding to the biosample referenced in this row. If your program has not registered multiple CFDE identifier namespaces, this will be exactly the same value for all rows.
biosample_local_id	The ID of this biosample	Required	string	This will be the value of local_id in the row in biosample.tsv corresponding to the biosample referenced in this row.
collection_id_namespace	Identifier namespace for this collection	Required	string	This will be the value of id_namespace in the row in collection.tsv corresponding to the collection referenced in this row. If your program has not registered multiple CFDE identifier namespaces, this will be exactly the same value for all rows.
collection_local_id	The ID of this collection	Required	string	This will be the value of local_id in the row in collection.tsv corresponding to the collection referenced in this row.

Return to C2M2 Documentation