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hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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Spin up an Ontology Neo4j container on DEV using CSVs from a build using Alan's script #146

Closed ChuckKollar closed 1 year ago

ChuckKollar commented 2 years ago

see precondition ontology-api#145

AlanSimmons commented 2 years ago
  1. UMLS CSVs are now generated from a Python script. CSVs for the UMLS2021AB are available.
  2. Script to generate OWLNETS-compatible files for HuBMAP ontology is now available.
  3. ontologies.json file updated to direct build_csv.py to generate nodes and edges for HubMAP ontology.
AlanSimmons commented 1 year ago

Generation architecture (build_csv.sh > build_csv.py > OWLNETS generation scripts > UMLS OWLNETS generation script > CSV files) now includes HuBMAP step.

CSV files, including modifications related to HuBMAP, load successfully into neo4j.

Thus, DEV instance can be instantiated via Docker file, theoretically.

Issues:

  1. The UMLS OWLNETS script overwrites isa assignments for HuBMAP concepts with dbxref code.
  2. Question over whether Docker based neo4j with UMLS node content complies with UMLS licensing.
AlanSimmons commented 1 year ago

@shirey Can we close this?

shirey commented 1 year ago

Finished a while ago under a different issue, yes we'll close. thanks @AlanSimmons