International Society for Biocuration
Published July 26, 2019 | Version v1
Report Open

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

Creators

  • 1. European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
  • 2. Renaissance Computing Institute, University of North Carolina at Chapel Hill
  • 3. The Jackson Laboratory, Bar Harbor, ME, USA
  • 4. University of Oregon, Institute of Neuroscience
  • 5. The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA
  • 6. Department of Botany and Plant Pathology, Oregon State University
  • 7. CNRS, Institut Jacques Monod
  • 8. Rothamsted Research
  • 9. University of South Dakota
  • 10. Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo
  • 11. Xenbase, Cincinnati Children's Hospital Medical Center
  • 12. California Institute of Technology
  • 13. Linus Pauling institute, Oregon State University, Corvallis OR, USA
  • 14. PomBase, Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge
  • 15. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
  • 16. Charité Centrum für Therapieforschung, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany
  • 17. Bioversity International
  • 18. University of Cambridge
  • 19. FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK
  • 20. Stowers Institute for Medical Research, Kansas City, MO
  • 21. Institute of Ecology and Evolution, University of Oregon, Eugene, OR
  • 22. ZFIN
  • 23. Oregon Health & Science University, Portland, OR 97217

Description

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).

Notes

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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Additional details

Related works

References
10.5281/zenodo.2382757 (DOI)