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TableInfo: biosample.tsv

Amanda Charbonneau edited this page Mar 4, 2021 · 20 revisions

The biosample table will contain one row per biosample in your Program

Field Field Description Required? Attributes Extra Info
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
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
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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