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TableInfo: file_describes_biosample.tsv
Amanda Charbonneau edited this page Mar 4, 2021
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If fully filled, file_describes_biosample.tsv will contain one row for every combination of file and biosample in your program.
If a row is filled, it must be filled for all columns, but there is no minimum number of rows that must be filled. You can choose any subset of files/biosamples.
Some examples:
- If you have exactly one biosample in each file, this table will have the same number of rows as file.tsv
- If you have two biosamples in every file, this table will have two rows for each file, each linking to a single biosample
- If you have 3 files for each biosample, this table will have 3 rows for each biosample, each linking to a single file
| Field | Field Description | Required? | Attributes | Extra Info |
|---|---|---|---|---|
| file_id_namespace | Identifier namespace for this file | Required if table is populated | If a row has this value, it must have a value for every column Value type is string |
For each row this will be the value of id_namespace in file.tsv for this file. If your program has not implemented multiple id_namespaces, this will be exactly the same for all rows and in the collection_id_namespace column |
| file_local_id | The ID of this file | Required if table is populated | For each row this will be the value of local_id in file.tsv for the file that describes this biosample. If a biosample has multiple files, it should have multiple rows. Concatenating values in this column will invalidate your submission
|
|
| biosample_id_namespace | Identifier namespace for this biosample | Required if table is populated | If a row has this value, it must have a value for every column Value type is string |
For each row this will be the value of id_namespace in biosample.tsv for the file that describes this biosample. If your program has not implemented multiple id_namespaces, this will be exactly the same for all rows and in the collection_id_namespace column |
| biosample_local_id | The ID of this biosample | Required if table is populated | If a row has this value, it must have a value for every column Value type is string |
For each row this will be the value of local_id in biosample.tsv for the file that describes this biosample. |
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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_protein.tsv
- biosample_ptm.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_ptm.tsv
- collection_substance.tsv
- collection_taxonomy.tsv
- compound.tsv
- data_type.tsv
- dcc.tsv (formerly
primary_dcc_contact.tsv - disease.tsv
- domain_location.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
- ptm.tsv
- ptm_type.tsv
- ptm_subtype.tsv
- sample_prep_method.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