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Metadata integration - bio_characteristics and location, mostly #875
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This commit reflects the results of the BioCharacteristics discussions at the Vancouver metadata breakout session (e.g. negation).
This unifies BioSample to "camelCode". This is to provide temporary consistency, although generally ist should be changed to Biosample throughout the schema.
Metadata bio-characteristics
# Conflicts: # doc/source/api/biometadata.rst # src/main/proto/ga4gh/bio_metadata.proto # src/main/proto/ga4gh/rna_quantification.proto
# Conflicts: # doc/source/api/biometadata.rst # src/main/proto/ga4gh/bio_metadata.proto # src/main/proto/ga4gh/rna_quantification.proto
# Conflicts: # doc/source/appendix/ontologies.rst # src/main/proto/ga4gh/bio_metadata.proto
Integrating external identifiers
…istics # Conflicts: # src/main/proto/ga4gh/bio_metadata.proto
See e.g. * #771 * https://docs.google.com/document/d/1PBIlNtxJAXe2K1wwTlPMNO4N0e03uejl8Da1 4RtEjJg/edit# * https://github.com/ga4gh/ga4gh-schemas/blob/metadata/src/main/resources/ avro/metadata.avdl#L47
* geodata object and implementations See e.g. * #771 * https://docs.google.com/document/d/1PBIlNtxJAXe2K1wwTlPMNO4N0e03uejl8Da1 4RtEjJg/edit# * https://github.com/ga4gh/ga4gh-schemas/blob/metadata/src/main/resources/ avro/metadata.avdl#L47 * attribute type fix * fixing example address
Metadata geoobjects
refactoring BioCharacteristics
bio_characteristics => characteristics
Metadata modify characteristics
This had been bit back-and-forth between characteristics and bio_characteristics. Settling here now to bio_characteristics.
Adding example for Biosample.individual_age_at_collection
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This PR follows previous discussions in the Metadata Task Team (e.g. @mcourtot, @helenp ...), last on 2017-04-27; as well as general agreement about this objects with the schema integration team (@kozbo, @david4096, @ejacox).
Please check for technical inconsistencies, and correct/vote.
Thanks! Michael.