Convert ontology files in .obo format to tables term.txt, term2term.txt and graph_path.txt
from the GO MySQL Database Schema.
Gene Ontology (GO) will at some point no longer provide their ontology in the GO MySQL Database Schema.
The GO enrichment R-package GOfuncR,
however, needs the old table format as input.
Since GOfuncR, although primarly used with the Gene Ontology, works with any ontology, this conversion can be useful for other ontologies in .obo format too, e.g. the Human Phenotype Ontology.
obo_to_term_tables.py has 2 positional arguments: the .obo file and the target directory for the term tables.
Optional --root_nodes need to be defined for other ontologies than Gene Ontology.
Assuming you saved obo_to_term_tables.py and obo_to_term_functions.py in directory /path/to/script/
- Download and convert Gene Ontology
wget http://current.geneontology.org/ontology/go-basic.obo
/path/to/script/obo_to_term_tables.py go-basic.obo .
- Download and convert Human Phenotype Ontology
wget http://purl.obolibrary.org/obo/hp.obo
/path/to/script/obo_to_term_tables.py hp.obo . --root_nodes "All"