Following Daduhl et al. and Vogt et al., our third paper in the phenotype ontologies Weekly Discussion series will dive into an applied example by Balhoff and co-authors (mainly of the Deans Lab) with a clear taxonomic emphasis. Already we have seen that different scientific orientations draw on phenotype ontologies with the expectation of reframing and solving specific problem complexes.
Daduhl et al.‘s focus was firmly within the bounds of evolutionary and phylogenetic analyses of phenotypes across broader and deeper taxonomic scales. Implementation challenges notwithstanding, there was an underlying agreement that the legacy of phenotype-centric systematic work could be appropriated towards the outlined representation and inference goals.
Vogt et al., in turn, emphasized a need for consistent, machine-processable standards with regards to phenotype syntactics, semantics, etc.; including a separation of descriptive and evolutionary/explanatory elements in our morphological terminology. This has the makings of a potentially divergent paradigm in relation to Daduhl et al.‘s program and perspective.
Another interesting development is the Phenoscape team’s exploration of homology relations in ontologies, outlined here: http://phenoscape.org/wiki/Reasoning_over_homology_statements.
In light of these different lines of research, we set ourselves two immediate questions to address:
1. What are actual applications that utilize phenotype ontologies and (optionally) reasoning for (a) multi-taxon studies with (b) an evolutionary/systematic orientation?
2. Suppose we had the “awesome ontology & reasoning” infrastructure on hand, where current technological limits no longer apply. What kinds of questions would we ask this infrastructure to solve for us (that cannot be addressed otherwise)?
The paper for next week applies directly to these questions.
Balhoff, J.P., I. Mikó, M.J. Yoder, P.L. Mullins & A.R. Deans. 2013. A semantic model for species description applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639–659. Available on-line here.