Skip to content

Combined Multispecies Ontologies

Composite (merged) Multispecies Ontologies

See the wiki for more details.

Composite ontologies merge species ontologies into the structure of Uberon, merging in taxonomic equivalents, and relabeling species-specific classes. Note the composite ontologies also merge in all of the Cell Ontology (CL).

name obo owl includes
composite-vertebrate .obo .owl MA, EHDAA2, ZFA, XAO, CL
composite-metazoan .obo .owl MA, EHDAA2, ZFA, XAO, CL, FBbt, WBbt, PORO, CTENO, CEPH
composite-metazoan-basic .obo n/a MA, EHDAA2, ZFA, XAO, CL, FBbt, WBbt, PORO, CTENO, CEPH

Importer (collector) Multispecies Ontologies

See the wiki for more details. See also Fig 3 from the Uberon paper:

The ontology collected-eukaryote.owl imports Uberon plus bridging axioms plus individual species anatomy ontologies. The ontology is constructed recursively, and it is possible to obtain an importer ontology for a variety of taxa.

Sequence of composite build pipeline

Key inputs:

  • $(BRIDGEDIR)/collected-$*.owl - an importer for all metazoan ontologies
  • $(TMPDIR)/ext-weak.owl - a weakened version of ext.owl with disjoints and equivalences to nothing.

  • the catalog.xml: this file really determines which are the files to use for the composite, i.e. all the redirects. Look for issues with weird imports in here

  • merged-composite-%.owl:

    • Opening $(URIBASE)/uberon/$(BRIDGEDIR)/collected-$*.owl while mapping a bunch of things (on top of whats in the catalog):
      • $(URIBASE)/uberon.owl $(TMPDIR)/ext-weak.owl
      • $(URIBASE)/fma.owl $(COMPONENTSDIR)/null.owl
      • $(URIBASE)/uberon/bridge/uberon-bridge-to-fma.owl $(COMPONENTSDIR)/null.owl
    • Merging everything - after this step, no imports left!
    • ext-weak.owl is ext.owl without any of the disjointness axioms, and equivalent to nothing axioms
  • stripped-composite-%.owl: This step removes the logical axioms of a handful of around 5 classes which are unsatisfiable from SSAOs.
  • unreasoned-composite-%.owl: The heavy lifting:
    • Opening (with owltools) stripped-composite
    • Some magic command to merge species ontologies (MERGESPECIES var) into stripped-composite.
    • Merge equivalence sets (see MERGE_EQSETS)
  • composite-%.owl: Run reasoner, relax, reduce, annotate