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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