Ontological annotation of problematic fossils

[evo-palaeo]

Identification of homology in fossil taxa requires an a priori hypothesis of relationships. Most fossil taxa can be unambiguously assigned to a broad taxonomic group, providing a comparative model for establishing homology. However, for some problematic fossils, this initial step is very challenging. Problematic fossils have frequently been interpreted using different comparative models by different researchers, resulting in radically different hypotheses of homology for the same set of morphological traits (see Donoghue & Purnell 2009). Such taxa pose a challenge to ontological annotation: Integrating information from character-taxon matrices that have used different comparative models to interpret the same fossil taxon will likely result in illogical annotations.

[wdahdul]

If I understand the issue correctly, it might be of interest for you to see how phenoscape represents conflicting hypotheses of homology, and whether this approach would work for problematic fossil taxa: Mabee, P.M., Balhoff, J.P., Dahdul, W.M., Lapp, H., Mungall, C.J., and T.J. Vision. (2020) A logical model of homology for comparative biology. Systematic Biology. 69(2):345–362, https://doi.org/10.1093/sysbio/syz067