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Turn ontology into TSV that can be used to create seperate NTRs

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Nico Matentzoglu edited this page Feb 21, 2020 · 1 revision

This pipeline documents the process of how to turn an input ontology, for example, an extension to HPO (recent example, seizures ontology), into a TSV file that can then be turned into GitHub issues using the HPO Workbench.

An example NTR generated this way is here: https://github.com/obophenotype/human-phenotype-ontology/issues/5486

These are the steps you need to do to generate the TSV:

  1. Edit src/scripts/hpo_field_mappings.yaml to fit your use case.
  2. Navigate to ontology dir as usual: cd src/ontology
  3. Run the make command: sh run.sh make INPUT=../relative/path/to/ontology.owl tmp/ntr_tsv.tsv -B. For example: `sh run.sh make INPUT=../../scratch/HPOSeizures_OWL_v11_20191205.owl tmp/ntr_tsv.tsv -B

This should generate the TSV src/ontology/tmp/ntr_tsv.tsv with the NTRs.

Technical side note: The pipeline is realised as as series of make goals and this scripts: src/scripts/ntr_tsv.py.

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