Building an ontology of logic definitions for groups of biological organisms to enable data integration Gaurav Vaidya1, Hilmar Lapp2, Nico Cellinese1 1 University of Florida and Florida Museum of Natural History 2 Duke University All organisms are related to each other: an example with alligators Biologists visualize hypotheses of how organisms are related to each other using phylogenetic trees. For example, the following phylogenetic tree includes the hypothesis that alligators (Alligatoroidea) and crocodiles (Crocodylidae) are more closely related to each other than either are to gavials (Gavialis gangeticus). Fig 3. Lineages on the Open Tree of Life synthetic phylogenetic tree as visualized in [6]. Acknowledgments The Phyloreferencing project is funded by the US NSF through collaborative grants DBI- 1458484 (HL) and DBI-1458604 (NC). GV’s attendance of US2TS was funded by the US2TS Travel Grant. References 1.Brochu (2003) Ann Rev Earth Plan Sci 2003 31:1, 357-397. https://doi.org/10.1146/annurev.earth.31.100901.141308 2.Prosdocimi et al. (2009) Evol Bioinform Online. 5:47–66. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747124/ 3.de Queiroz and Gauthier (1990) Syst Biol 39(4):307–322. https://doi.org/10.2307/2992353 4.Carral et al. (2017) Arxiv 1710.05096 https://arxiv.org/abs/1710.05096 5.Musen, M.A.ACM SIG AI 1(4) http://dx.doi.org/10.1145/2557001.25757003 6.Hinchliff et al. (2015) Proc Nat Acad Sci 112.41 (2015): 12764-12769. https://doi.org/10.1073/pnas.1423041112 Finding a clade on the Open Tree of Life The Open Tree of Life [6] synthesizes information from 987 phylogenies and several taxonomic resources to provide a draft hypothesis of evolutionary relationships between 2,640,941 taxa. Resolving clade definitions on the Open Tree of Life would facilitate navigation. Phylogenetic clade definitions identify groups of organisms unambiguously Phylogenetic clade definitions [3] define groups in terms of their ancestral relationships by specifying biological groups that must be either included in or excluded from the clade on a particular phylogenetic tree: Fig 1. Phylogenetic tree of alligators, crocodiles and caimans from Brochu 2003 [1]. Alligatorinae Alligator mississippiensis and all crocodylians closer to it than to Caiman crocodilus. Brevirostres Last common ancestor of Alligator mississippiensis and Crocodylus niloticus and all of its descendents. How can we translate a definition based on ancestral relationships into an OWL restriction expression? We can use OWL Property Chains as used in [4] to create clade definitions in OWL to traverse phylogenetic trees: - includes TU: has Descendant o represents TU - excludes TU: has Sibling o has Descendant o represents TU Node Alligator mississippiensis represents TU some (Has Name some (Zoological name and Has Scientific Name value "Alligator mississippiensis")) Node Crocodylus niloticus represents TU some (Has Name some (Zoological name and Has Scientific Name value "Crocodylus niloticus")) Phylogenetic trees can be represented in OWL using CDAO The Comparative Data Analysis Ontology (CDAO) [2] allows phylogenetic trees to be represented as an ontology in the Web Ontology Language (OWL). Alligator mississippiensis Caiman crocodilus Crocodylus niloticus Gavialis gangeticus Alligatoridae Brevirostres Crocodylia has Child Transitive as has Descendant has Sibling Symmetrical Note that nodes on this phylogenetic tree represent biological groups (taxa). We can relate these nodes to taxonomic names using the represents TU property from CDAO [2]. Name OWL restriction Nodes matched Alligatorinae includes TU some Alligator mississippiensis Alligator mississippiensis, Alligatoridae, Brevirostres, Crocodylia and excludes TU some Caiman crocodilus Alligator mississippiensis, Crocodylus niloticus, Gavialis gangeticus Name OWL restriction Nodes matched Brevirostres has Child some Brevirostres (includes TU some Alligator mississippiensis Alligator mississippiensis, Alligatoridae, Breviro