ICBO_2018_62: Reasoning over anatomical homology in the Phenoscape KB

TitleICBO_2018_62: Reasoning over anatomical homology in the Phenoscape KB
Publication TypeConference Paper
Year of Publication2018
AuthorsMabee, P, Balhoff, J, Dahdul, W, Lapp, H, Mungall, C, Vision, T
Conference NameInternational Conference on Biomedical Ontology (ICBO 2018)
Date Published08/06/2018
PublisherInternational Conference on Biological Ontology
Keywordsanatomy ontology, evolution, homology, phenotypes, reasoning

The Phenoscape project (www.phenoscape.org) has semantically annotated the features of species from the comparative literature, enabling links between candidate genes and novel species phenotypes for which they might be responsible. To enable discovery of homologous phenotypes and associated genes, we incorporated machine-reasoning with knowledge about homology into the Phenoscape Knowledgebase (KB). We show that with homology reasoning enabled, the results of database queries can be expanded to incorporate shared evolutionary history. We discuss the challenges in developing a logical model of homology assertions and implications for database queries, as well as theoretical entailment and practical performance tradeoffs between alternative models.