Skip to content

BEL resources and tools for namespaces, annotations, orthologs, taxonomy, etc and tool

License

Notifications You must be signed in to change notification settings

belbio/bel_resources

Repository files navigation

BEL Resource tools

This repository contains scripts to create standardized load files for BEL Resources for use with the BEL.bio API.

Documentation <http://bel-resources.readthedocs.io/en/latest/>_

Install/setup

Run

bin/

Namespaces

The namespaces prefixes will preferentially use the identifiers derived from the identifiers-org/MIRIAM registry.

Additional biocontexts for these namespaces can be found here: https://github.com/prefixcommons/biocontext

OWL terminologies

We can use OWL terminologies by converting them from OWL to OBOGraph and OBOGraphs Github repo.

Convert OWL to OBO or OBOGraph

http://robot.obolibrary.org/

robot convert --input fma.owl --output fma.obo --format obo --check false

robot convert --input fma.owl --output fma.json --format json  # OBOGraph format

For the OBOGraph (https://github.com/geneontology/obographs/), you can process the nodes and edges as indicated in the overview of OBOGraph above.

If you use robot to convert to OBO format - you'll need to remove the 'owl-axioms' entry. You can use grep -v ^owl-axioms <filename> to do this, but the recommended approach is to use OBOGraph format instead.

Alternatives for OWL processing

About

BEL resources and tools for namespaces, annotations, orthologs, taxonomy, etc and tool

Resources

License

Stars

Watchers

Forks

Packages

No packages published