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.
File: ro.obo
python manage.py load_relations_ontology --file ro.obo
2.1.2. Sequence ontology¶
Collect of 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.
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.