Molecular Function reaction participants

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Molecular functions with Rhea xrefs are automatically linked to ChEBI terms identifying the chemicals participating in the reaction. The ChEBI participants are extracted from data provided by Rhea.

The generated file is imported into go-edit.obo and merged into the go-plus.owl release. It can be viewed on GitHub here:

The participants links follow this structure:

 id: GO:0000016
 relationship: RO:0000057 CHEBI:15377
 relationship: RO:0000057 CHEBI:17716
 relationship: RO:0000057 CHEBI:27667
 relationship: RO:0000057 CHEBI:4167

Because the OWL formulation for grouping chemicals into two sides of an undirected reaction is overly complex, we simply link all chemicals on either side uniformly, using a 'has participant' relation. This is sufficient to connect the the GO term with relevant chemical entities in knowledge graph applications using GO.

Currently only links to ChEBI terms are included. If a reaction participant is a Rhea generic term rather than a specific ChEBI chemical, it will not be linked.

Regenerating the reaction participants files

The participant relations are generated via a SPARQL query over the Rhea RDF dataset along with a Scala script. For details see the imports/go-catalytic-activities-participants.owl target in the ontology Makefile.

A GitHub action runs on a daily schedule and will automatically open a pull request if there are changes to the participants files. The action can also be triggered manually at any time using the Run workflow button on the action page.

Review Status

Last reviewed: 2023-09-18 Reviewed by: Jim Balhoff