2.1. Loading ontologies

The ontologies are required and must be loaded first.

2.1.1. Relations ontology

RO is an ontology of relations for use with biological ontologies.

• URL: https://github.com/oborel/obo-relations
• File: ro.obo

python manage.py load_relations_ontology --file ro.obo

2.1.2. Sequence ontology

Collect of SO Ontologies.

• URL: https://github.com/The-Sequence-Ontology/SO-Ontologies
• File: so.obo

python manage.py load_sequence_ontology --file so.obo

2.1.3. Gene ontology

Source ontology files for the Gene Ontology.

• URL: http://current.geneontology.org/ontology/
• File: go.obo

python manage.py load_gene_ontology --file go.obo

• Loading the gene ontology can be faster if you increase the number of threads (–cpu).
• After loading the gene ontology the following records will be created in the Cv table: gene_ontology, external, molecular_function, cellular_component, and biological_process.

2.1.4. Remove ontology

If, by any reason, you need to remove an ontology you should use the command remove_ontology. Most data files you’ll load depend on the ontologies (eg. fasta, gff, blast). You should never delete an ontology after having data files loaded.

python manage.py remove_ontology --help

• This command requires the name of the ontology (Cv.name)
• There are dependencies between the Gene ontology records, therefore you need to delete the entry external first.