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TableInfo: collection_taxonomy.tsv
mano-at-sdsc edited this page Oct 11, 2024
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Association between a collection and a NCBI Taxonomy ID
For collections with taxonomy metadata, this table will have one row for each taxon ID associated with each such 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 collections associated with taxa, this table should be left empty.
- If you have exactly one taxon associated with each collection, this table will have as many rows as collection.tsv.
- If you have five taxa associated with each collection, this table will have five times as many rows as collection.tsv.
- If some but not all of your collections are associated with one or more taxa, this table will contain one row for each taxon assigned to each such collection (and the resulting row count will not have any obvious relationship to the number of rows in collection.tsv, which is both expected and fine in such a case).
Field | Field Description | Required? | Field Value Type | Extra Info |
---|---|---|---|---|
collection_id_namespace | Identifier namespace for this collection [part 1 of 3-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 2 of 3-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. |
taxon | An NCBI Taxonomy Database ID identifying this taxon [part 3 of 3-component composite primary key] | Required | string | Example: NCBI:txid9606
|
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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