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TableInfo: file_in_collection.tsv
mano-at-sdsc edited this page Oct 11, 2024
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Assignment of a file as a member of a collection
If populated, file_in_collection.tsv
will contain one row for every assignment of a file 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 files contained in collections, this table should be left empty.
- If each file is contained in exactly one collection, this table will have the same number of rows as file.tsv.
- If each file is simultaneously a member of three collections, this table will have three times as many rows as file.tsv.
Usage note:
- If a file is a member of collection
X
, and collectionX
is itself a subcollection of some other collectionY
(as expressed in the collection_in_collection table), thenfile_in_collection.tsv
should only record the membership of the file in collectionX
: the file's (transitive) membership in collectionY
will be automatically computed. In general,file_in_collection.tsv
should record only the most specific (leaf-most) collection memberships: transitive membership of files 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 |
---|---|---|---|---|
file_id_namespace | Identifier namespace for this file [part 1 of 4-component composite primary key] | Required | string | This will be the value of id_namespace in the row in file.tsv corresponding to the file referenced in this row. If your program has not registered multiple CFDE identifier namespaces, this will be exactly the same value for all rows. |
file_local_id | The ID of this file [part 2 of 4-component composite primary key] | Required | string | This will be the value of local_id in the row in file.tsv corresponding to the file referenced in this row. |
collection_id_namespace | Identifier namespace for this collection [part 3 of 4-component composite primary key] | 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 [part 4 of 4-component composite primary key] | Required | string | This will be the value of local_id in the row in collection.tsv corresponding to the collection referenced in this row. |
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Tutorials
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C2M2 Table Guide
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Table Summary
- analysis_type.tsv
- anatomy.tsv
- assay_type.tsv
- biofluid.tsv
- biosample.tsv
- biosample_disease.tsv
- biosample_from_subject.tsv
- biosample_gene.tsv
- biosample_in_collection.tsv
- biosample_substance.tsv
- collection.tsv
- collection_anatomy.tsv
- collection_biofluid.tsv
- collection_compound.tsv
- collection_defined_by_project.tsv
- collection_disease.tsv
- collection_gene.tsv
- collection_in_collection.tsv
- collection_phenotype.tsv
- collection_protein.tsv
- collection_substance.tsv
- collection_taxonomy.tsv
- compound.tsv
- data_type.tsv
- dcc.tsv (formerly
primary_dcc_contact.tsv
- disease.tsv
- file.tsv
- file_describes_biosample.tsv
- file_describes_collection.tsv
- file_describes_subject.tsv
- file_format.tsv
- file_in_collection.tsv
- gene.tsv
- id_namespace.tsv
- ncbi_taxonomy.tsv
- phenotype.tsv
- phenotype_disease.tsv
- phenotype_gene.tsv
- project.tsv
- project_in_project.tsv
- protein.tsv
- protein_gene.tsv
- subject.tsv
- subject_disease.tsv
- subject_in_collection.tsv
- subject_phenotype.tsv
- subject_race.tsv
- subject_role_taxonomy.tsv
- subject_substance.tsv
- substance.tsv
- Reference Tables
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Table Summary