ga4gh / ga4gh-schemas

Models and APIs for Genomic data. RETIRED 2018-01-24
http://ga4gh.org
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Biosample sample characteristics #710

Closed mbaudis closed 8 years ago

mbaudis commented 8 years ago

This PR addresses the need for a different structure and naming of the Biosample.disease attribute:

The renaming to samplecharacteristics is in line with the use e.g. at GEO; however, the `sample` prefix may not be strictly necessary. Alternatives welcome.

david4096 commented 8 years ago

This makes sense: to have a tag-bag field that strictly represents Ontology Terms, although the semantic context of those terms can be lost if no name is provided.

Please also consider the approach of allowing tagging via Ontology Term (and others) in a generic attributes field by upgrading the info field. This would allow a data curator to define named tag bags on a biosample with some more context without adding new named fields to the message. This replaces the info field and both approaches are not exclusive. PR for this feature here.

I'm +1 for this approach as it solves the immediate issue of specifying tissue type for TCGA data.

mbaudis commented 8 years ago

Closed & moved to https://github.com/ga4gh/schemas/issues/711 (clean up).