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hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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Build new CSV files using Alan's script #145

Closed ChuckKollar closed 1 year ago

ChuckKollar commented 2 years ago

We will use the old UMLS-CSVs-2020AB that Jonathan provided as seed CSVs for this process. We will build a new set of CSVs that include processing from Alan's new code.

./build_csv.sh -v PATO UBERON CL DOID CCFASCTB OBI EDAM HSAPDV SBO MI CHEBI MP ORDO PR UNIPROTKB BAO SWO CHMO

AlanSimmons commented 2 years ago

The build script needs the parameter HUBMAP--i.e.,

./build_csv.sh -v PATO UBERON CL DOID CCFASCTB OBI EDAM HSAPDV SBO MI CHEBI MP ORDO PR UNIPROTKB BAO SWO CHMO HUBMAP

AlanSimmons commented 2 years ago

New script and input spreadsheet available in:

https://github.com/hubmapconsortium/ontology-api/tree/main/scripts/skowlnets

Execution triggered by entries in ontologies.json.

AlanSimmons commented 2 years ago

All components to complete this task appear to be ready for testing.

  1. New script to convert application ontology data for HuBMAP (via a SimpleKnowledge spreadsheet).
  2. New script to generate UMLS CSVs. CSVs for the UMLS2022AB have been generated.
  3. The ontologies.json file has been updated to account for HuBMAP.
AlanSimmons commented 1 year ago

This is completed.