Homology in anatomy ontologies: Report from a Phenotype RCN meeting

At the end of October 2012, the working groups of the Phenotype Research Coordination Network (RCN) all met at the Asilomar Conference Center, in Pacific Grove, CA. One of the groups, the Vertebrate working group, made it their goal to discuss methods of representing phylogenetic and serial homology in anatomy ontologies, an issue that is central to Phenoscape as well. Though common ancestry is implicit in the semantics of many classes and subclass relationships (see for example the ‘homology_notes’ for digit in Uberon), most multispecies anatomy ontologies, including Uberon, VSAO, and TAO, do not assert homology relationships between anatomical entities.  Nonetheless, homology is central to comparative biology, and therefore to enriching computations across data types, species, and evolutionary change.

The working group used ontological relationships, phenotypes, and homology assertions across a small set of skeletal elements from vertebrate fins and limbs as a test case to identify requirements for making and reasoning over homology assertions. These included both positive (data expected to be returned) and negative (data expected not to be returned) results for particular queries involving phylogenetic and serial homology.  The group developed a number of such queries across subtype (is_a) and partonomy (part_of) relationships.  One example is that without homology assertions a query for phenotypes involving the ‘humerus’ would not retrieve phenotypes for ‘femur’.  Asserting that the ‘forelimb skeleton’ is serially homologous to the ‘hindlimb skeleton’ would not remedy this, because doing so would not imply that their parts (humerus and femur, respectively) would be homologous as well.  Instead, serial homology must be directly asserted between entities, even when they are parts of other already homologous structures (i.e., in this case humerus and femur have to also be directly asserted to be serial homologues).  Conversely, it was determined that homology relations, both serial and phylogenetic, should propagate to subclasses. For example, to return phenotypes for types of both the ‘paired fin skeleton’ and the ‘skeleton of limb’ in a query for either requires asserting phylogenetic homology only for these high-level classes. With this assertion propagating to all their subclasses, such as  ‘pectoral fin skeleton’, ‘hindlimb skeleton’, or ‘autopodial skeleton’, phenotypes for any of their subtypes would then also be returned.  The group also discussed how to define the identity of elements of a series consistently and ideally, universally.  The consensus was to specify subsets of digits for different taxa with different conventions, e.g., a basal tetrapod subset and a bird subset.

In summary, as identified at the workshop the requirements for reasoning over both phylogenetic and serial homology turned out to be fully consistent with standard OWL property semantics. Furthermore, the recommendations that emerged from the workshop for defining elements in a repeated series are fully in line with the goal of defining classes in anatomy ontologies such that they can be applied unambiguously, including in a manner that is not inconsistent with knowledge of developmental and evolutionary origin.

Aside from several Phenoscape personnel (Jim Balhoff,  David Blackburn, Alex Dececchi, Hilmar Lapp, Paula Mabee, Chris Mungall), participants in the meeting included Eric KansaHans Larsson and Karen Sears, who were new to the RCN (and Phenoscape). We are grateful to them for helping us work through the questions in a way that kept it grounded in enabling science.

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