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Orthologous features (genes, RNAs, microRNAs, proteins, etc.) by definition share a common ancestor and are separated by a speciation event (see http://en.wikipedia.org/wiki/Homology_%28biology%29#Orthology). Orthologs generally (but not always) share the same function. Orthology relationships enable the use of BEL statements representing observations in one organism for reasoning in a related organism.

The BEL Orthology resource is a BEL document containing orthologous relationships between:

  • HGNC (human) and MGI (mouse) geneAbundances
  • HGNC (human) and RGD (rat) geneAbundances
  • MGI (mouse) and RGD (rat) geneAbundances

This Resource is used by the BEL Compiler (versions 3.0) during Phase III.

Once compiled into a knowledge network (KAM), the geneAbundance orthology relationships can be used by tools/Orthologize.sh to create a network collapsed to human, mouse, or rat nodes. This tool assumes the orthology relationships are 1-to-1 correspondence between nodes in different species. The BEL orthology relationships are not transitive.

The Orthologize tool can collapse the following types of nodes by orthology based on the geneAbundance orthology resource document:

  • geneAbundance
  • proteinAbundance
  • rnaAbundance
  • protein activity (e.g., kinaseActivity) nodes are orthologized only if the activity nodes for both species exist in the KAM

The following types of nodes require additional (user-supplied) orthology information during compilation:

  • composed complexes
  • modified proteins
  • variant proteins
  • translocations (including cellSecretion and cellSurfaceExpression)
  • degradations
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