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Turn ontology into TSV that can be used to create seperate NTRs
Nico Matentzoglu edited this page Feb 21, 2020
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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:
- Edit
src/scripts/hpo_field_mappings.yaml
to fit your use case. - Navigate to ontology dir as usual:
cd src/ontology
- 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
.