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TableInfo: biosample.tsv
Amanda Charbonneau edited this page Mar 4, 2021
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The biosample table will contain one row per biosample in your Program
Field | Field Description | Required? | Attributes | Extra Info |
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id_namespace | A CFDE-cleared identifier representing the top-level data space containing this biosample [part 1 of 2-component composite primary key] | Required | Value type is string | If you have not implemented multiple namespaces every row will have the same value |
local_id | An identifier representing this biosample, unique within this id_namespace [part 2 of 2-component composite primary key] | Required | The value in each row must be different for a given namespace Value type is string |
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project_id_namespace | The id_namespace of the primary project within which this biosample was created [part 1 of 2-component composite foreign key] | Required | Value type is string | If you have not implemented multiple namespaces, this will be the same as id_namespace. |
project_local_id | The local_id of the primary project within which this biosample was created [part 2 of 2-component composite foreign key] | Required | Value type is string | For each row (each biosample), this will be the value of 'local_id' in the project table for the project this biosample came from |
persistent_id | A persistent, resolvable (not necessarily retrievable) URI or compact ID permanently attached to this biosample | Non-required: Any number of rows after the header can be filled | The value in each row must be different Value type is string |
Meant to serve as a permanent address to which landing pages (which summarize metadata associated with this file) and other relevant annotations and functions can optionally be attached, including information enabling resolution to a network location from which the file can be downloaded. Actual network locations must not be embedded directly within this identifier: one level of indirection is required in order to protect persistent_id values from changes in network location over time as files are moved around. |
creation_time | An ISO 8601 -- RFC 3339 (subset)-compliant timestamp documenting this biosample's creation time: YYYY-MM-DDTHH:MM:SS±NN:NN | Non-required: Any number of rows after the header can be filled | Value must be datetime | Example valid dates: 2021-01-08 2021-01-08T00:45:40Z 2021-01-08T00:45:40+00:00
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anatomy | An UBERON CV term ID used to locate the origin of this biosample within the physiology of its source or host organism | Non-required: Any number of rows after the header can be filled | Value must be a valid UBERON ID |
UBERON lookup service Example valid UBERON IDs: UBERON:0001988 UBERON:0001052 UBERON:0006956
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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