inter anatomy ontology bridge ontologies

Chris Mungall edited this page Aug 22, 2014 · 4 revisions

Inter anatomy ontology bridge module ontologies

Authors and contributors:

  • Melissa Haendel (author)
  • Chris Mungall (author)
  • Carlo Torniai (author)

Date: 2012

Document Type: ontology_usage_article

Abstract

This article describes how connections between species anatomy ontologies are made via formal axioms that connect to Uberon

Problem

Figure 2 from the Uberon paper graphically illustrates how Uberon classes subsume classes in existing anatomy ontologies;

Figure 2

Figure legend: 'Illustration of how Uberon relates anatomical silos into a unified view. Uberon classes are shown in gray and classes from external ontologies are indicated with their respective prefix. Classes in light gray have computable definitions, which are indicated by the relations shown. For example, 'alveolus of lung' is_a 'alveolus' that is part_of some 'lung'. 'Respiration organ' is_a organ that is capable_of GO:respiratory gaseous exchange. The blue circle indicates what would be included in a mammal-restricted subset of Uberon, as swim bladder is not found in mammals. Use of Uberon together with taxon-specific anatomy ontologies enables bridging of the data with full reasoning capabilities. In this example, Uberon 'lung' subsumes the lung classes from the mouse and human anatomy ontologies. Classes in the blue circle plus the blue classes at the bottom would be available in uberon-collected-mammal.owl. Note that some relationships have been trimmed for illustration purposes.'

This article describes how to obtain the axioms that connect these ontologies

Multi-species bridge modules

Links between Uberon and other AOs are stored as bridge ontologies. These all have ontology URIs of the form:

http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ONTOLOGY.owl

Where ONTOLOGY is the official obolibrary ontology ID (i.e. the ontology namespace in lowercase).

Bridge modules fall into different categories, depending on the nature of the relationship between Uberon and the other AO

Equivalent-for-taxon axioms

These are 3-valued relations between a generic structure, a taxon and an anatomy class, represented as an owl equivalence to a taxon-constrained class expression.

Example:

    MA:lung EquivalentTo (UBR:lung AND part_of some NCBITaxon:Mus)

This is stronger than simply saying the mouse lung is a subclass of the generic lung.

This is the preferred pattern for species-specific anatomy ontologies

SubClass axioms

Example:

    EMAPA:lung SubClassOf UBR:lung

These are weaker than taxonomic equivalence. These bridging axioms are made for ontologies such as EMAPA which may have multiple distinct classes for what appears to be the same structure.

Equivalence axioms

Example:

    NIF:forebrain EquivalentTo UBR:forebrain

Bona-fide equivalence axioms are the strongest, and are only made when the external AO is deemed to make the same taxonomic generalizations as Uberon.

OBO unique labels

Because ssAOs and Uberon often share labels, the bridge ontologies include a unique label axiom for every ssAO. This uses http://purl.obolibrary.org/obo/IAO_0000589

If you are using Protege, configure it so that it uses this to render. See this issue for more information.

Alternate strategy: assuming complete equivalence

Sometimes it may be beneficial to assume true equivalence between Uberon classes and species AOs, even in cases where this leads to contradictions due to species variability. This may be the case for doing a phenotype similarity analysis. In this case its necessary to remove disjointness axioms. An example of a contradiction that might arise is inferring that human teeth are part of the throat, based on the an equivalence between zebrafish (ceratobranchial 5) tooth, uberon calcareous tooth, and FMA:tooth (the ceratobranchial teeth are in the pharynx). Note that this situation does NOT arise if the correct bridging ontology, http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl, is used, which has weaker equivalent-for-taxon axioms

Usage in importer modules

See reference_0000027 for a description of how bridge modules are used by multi-species anatomy importer modules.

Future directions

In the future