Adds Adipose tier2 fields #1638
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It's already part of the gut pr
amnonkhen
requested changes
Dec 16, 2025
| "user_friendly": "Nutritional state", | ||
| "example": "Should be one of: normal, fasting, or feeding tube removed." | ||
| }, | ||
| "fasting_time": { |
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Why no additional units attribute?
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Because the unit is already declared in the definition. The network expects hours to be a fitting unit for fasting time so we skipped adding a dedicated unit - we did this already for ischemic_time for example
| "biopsy_procedure": { | ||
| "description": "Type of biopsy procedure used in the sample collection.", | ||
| "type": "string", | ||
| "enum": [ |
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I see many biopsy entries in OLS. Should this be an ontology field, or is it not urgent?
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We suggested ontologies where possible but the bionetwork had very specific values for biopsy and we agreed to use an enum - if I remember well there is at least one more bionetwork that will add to this enum
hannes-ucsc
requested changes
Dec 17, 2025
json_schema/type/protocol/sequencing/library_preparation_protocol.json
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Co-authored-by: Hannes Schmidt <[email protected]>
amnonkhen
approved these changes
Jan 13, 2026
ncalvanese5
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Jan 13, 2026
ncalvanese1
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Jan 13, 2026
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Release notes
This PR adds the tier 2 fields requested by the Adipose bionetwork (reference sheet here) - none of the fields added in this PR are required
New optional fields
For
module/biomaterial/reproductive_history.json:For
module/biomaterial/blood_test.json:For
type/protocol/biomaterial_collection/collection_protocol.json:For
type/biomaterial/specimen_from_organism.json:For
type/biomaterial/cell_suspension.json:For
module/biomaterial/medical_history.json:For
module/biomaterial/lifestyle.json:For
type/protocol/sequencing/library_preparation_protocol.json:For
module/biomaterial/human_specific.json:Changes to existing fields
For
module/biomaterial/human_specific.json:Reviews requested
Need 4 Reviewers to approve because this is a major update