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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

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

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