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Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition

Matentzoglu, Nicolas; Balhoff, James P.; Bello, Susan M.; Bradford, Yvonne M.; Carmody, Leigh C.; Cooper, Laurel D.; Courtier-Orgogozo, Virginie; Cuzick, Alayne; Dahdul, Wasila M.; Diehl, Alexander D.; Engel, Stacia; Fey, Petra; Fisher, Malcom; Grove, Christian A.; Haendel, Melissa A.; Harris, Midori A.; Harris, Nomi L.; Köhler, Sebastian; Laporte, Marie-Angélique; McMurray, Eunice Y.; McMurry, Julie A.; Milano, Annalisa; Mungall, Chris; Munoz-Torres, Monica C.; Pilgrim, Clare; Pillai, Ajay; Robb, Sofia MC; Robinson, Peter N.; Schofield, Paul; Segerdell, Erik; Shanmugasundram, Achchuthan; Toro, Sabrina; Vasilevsky, Nicole; Wang, Shur-Jen; Wood, Val; Osumi-Sutherland, David

The Phenotypes Traversing All the Organisms Workshop (POTATO) series brings together phenotype ontology curators and developers to reconcile phenotype ontologies across species. In the first workshop (Oregon, 2018), we introduced methods and tools for community-driven development of logical definitions for phenotypes. Together we resolved some of the logically divergent definitions across organisms. As a result, 14 phenotype ontologies and databases covering all major model organisms joined a common Phenotype Ontology Reconciliation Effort with bi-weekly meetings and focus groups. A report of the first installment of the workshop, including a detailed description outlining the motivation of the workshop series, is available on Zenodo (1). The central purpose of this workshop was to bring together users and developers of phenotype ontologies and to provide them with a forum to share, learn and debate. The second edition of the workshop further aimed to address two of the fundamental bottlenecks identified in the course of these community efforts:

  • The Phenotype And Trait Ontology (PATO), an essential driver of inference in phenotype ontologies, has limitations that can make it hard to understand and use in defining phenotypes. For example, textual definitions need to be added and improved, and hierarchies refined to be more intuitive. 

  • The phenotype ontology community needs efficient ways to directly contribute to anatomical and cell concepts in the species-independent anatomy ontology Uberon and the Cell Ontology (CL).

The workshop was funded by NIH Office of the Director Grant #5R24OD011883, as well as by the phenomics conference grant 5U13CA221044-03. Coffee and other sustenance was kindly provided by the International Society for Biocuration. A big thank you goes to Midori Harris who oversaw the workshop logistics and ensured a surprise-free workshop experience! ERRATA: The funding statement in the PDF is replaced by the one above.
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