Awesome
This repository contains the source for the top-level importer for the Monarch ontology
Components
The top-level ontology is found in the file monarch.owl
This imports a number of other ontologies. These will be imported over the web. The ontologies are managed in separate github repositories:
- Phenotypes: obophenotype/upheno
- mammalian-phenotype-ontology
- human-phenotype-ontology
- worm, fly, zebrafish, yeast, ...
- Diseases: monarch-initiative/monarch-disease-ontology
Computational Usage
The ontology can be inspected directly using Protege or used computationally using the OWLAPI. The follow instructions are for developers of the ontology
See the Makefile for details. You will need owltools.
For local development, you can create a cache of all dependent ontologies:
make catalog-v001.xml
This creates:
cache/
- a directory containing a mirrored copy of each imported ontologycatalog-v001.xml
- an index connecting the ontology URIs in the import to files incache
After this is completed, you can work with monarch.owl in a more efficient way, or work off-line.
For example:
owltools --use-catalog monarch.owl MY-STUFF-HERE
Alternatively, if you open monarch.owl in Protege, it should automatically use the catalog