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This table must not be manually created. Users should skip this, and all other tables marked "Built by script" in this summary, preparing only the rest of their datapackage's TSV files (those marked "Prepared by submitter") for submission. Once the "Prepared by submitter" tables are ready, users should then use the C2M2 submission prep script to automatically generate this table (and the other "Built by script" tables) using the information in the "Prepared by submitter" tables.
The sample_prep_method.tsv table will have as many rows as the number of unique OBI terms appearing in the sample_prep_method column of biosample.tsv.
Terms for populating sample_prep_method should describe the process by which the biosample was generated and should come from the planned process branch of Ontology for Biomedical Investigations (OBI), with the exclusion of things from the assay branch. Assays result in data, not in biosamples (as defined by OBI), so, the field assay_type is in the file.tsv table. Some nodes of interest in planned process are: material processing, specimen collection process, and material component separation.
| Field | Field Description | Required? | Field Value Type | Extra Info |
|---|---|---|---|---|
| id | A valid OBI planned process term | Required | string | OBI lookup service Example: OBI:0000094 (material processing) |
| name | A short, human-readable, machine-read-friendly label for this OBI term | Required | string | |
| description | A human-readable description of this OBI term | Optional | string | |
| synonyms | A list of synonyms for this term as identified by the OBI metadata | Optional | JSON array of strings | provide empty JSON array [] if value is null |