oboparse.py
Parses the OBO format in python
By default it prints each "stanza" in the JSON format.
For example:
curl http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo | python oboparse.py
Or you can use the jq to create a CSV with the terms:
< gene_ontology_ext.obo python oboparse.py | jq -r '.| select(.["@type"]=="Term")|[.id, .name, .["def"], .is_obsolete//false] | @csv'
or a CSV containing the hierarchy of terms:
< gene_ontology_ext.obo python oboparse.py | jq -r '.| select(.["@type"]=="Term" and .is_a)|{id, parent: .is_a[] }|[.id, .parent]|@csv'