search

x-atlas-consortia / ubkg-etl

A framework that combines data from the UMLS with assertions from other data sources into a set of CSV files that can be imported into neo4j to build a Unified Biomedical Knowledge Graph (UBKG)
MIT License
3 stars 0 forks source link

sex and weight_unit metadata values #142

Closed AlanSimmons closed 3 months ago

AlanSimmons commented 5 months ago

Statement of problem

The descriptions for the sex and weight_unit ingest metadata fields are incorrect.

The metadata fields are defined in the legacy field-*.yaml files.

Solution options

  1. Correct in the legacy field-*.yaml files, which were supposed to be deprecated.
  2. Add fields to the CEDAR templates.
ngehlenborg commented 5 months ago

@AlanSimmons Looks like there are other mouse specific descriptions for things that maybe should not be mouse specific (date_of_death -- although unlikely to appear in human context but still possible to apply to a different model organism).

CC @bhonick @maxsibilla

jpuerto-psc commented 5 months ago

Fields have been adjusted in HuBMAP's IVT: https://github.com/hubmapconsortium/ingest-validation-tools/pull/1329

murine-source fields should be available via CEDAR, so this should not cause any conflicts on their end.