Phenotype Ontologies Traversing All The Organisms (POTATO) Workshop
Dates: August 07, 2018
Location: International Conference on Biological Ontologies (ICBO), Corvallis, Oregon
Workshop Organizers: David Osumi-Sutherland (EBI), Nico Matentzoglu (EBI), Nicole Vasilevsky (OHSU), Chris Mungall (LBNL), Jim Balhoff (RENCI), Melissa Haendel (OHSU/OSU)
Logical definitions, in particular those following the Entity-Quality approach, are increasingly used to drive automated classification of phenotypes and integrate phenotypes across species semantically. Over the years, the lack of consistent and widespread use of common standards resulted in conceptually equivalent or similar phenotypes with logically divergent definitions. Recently, pattern-based approaches such as Dead Simple Ontology Design Patterns (DOSDP) have emerged as a way to reconcile such divergent definitions on a large scale. To facilitate the widespread adoption of DOSDP-based phenotype ontology development and to organise the reconciliation process involving key model organism communities, we have established the Phenotype Ontologies Traversing All The Organisms (POTATO) Workshop Series. These workshops are part of the NIH-funded “Forums for Integrative Phenomics” conference award, which provide a venue for phenotype ontology developers and phenomics informaticians to align their goals and technical approaches. The first POTATO workshop provided training in cutting-edge tools and techniques for developing and releasing ontologies using design patterns and automated imports. This workshop also featured collaborative exercises in reconciling divergent logical definitions drawn from major phenotype ontologies that resulted in a set of general recommendations for how to improve phenotype ontologies and their development as well as a set of reconciled definitions. As a result of the workshop, many of the attendees have joined a phenotype ontology reconciliation effort, aimed at developing and implementing common design patterns across a range of phenotype ontologies.
Dates: April 07, 2019
Location: Biocuration2019, Cambridge, UK
Workshop Organizers: David Osumi-Sutherland (EBI), Nico Matentzoglu (EBI), Nicole Vasilevsky (OHSU), Chris Mungall (LBNL)
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. The central purpose of this second 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.
3rd Unified Phenotype Ontology (uPheno) Workshop
Dates: November 15, 2021
Time: 9am - 12pm PT, 12pm - 3pm ET, 5pm - 8pm BST
- 09:00 - 09:15 am: Welcome & The why, how, who, what of the reconciliation effort
- 09:15 - 09.30 am: A brief tutorial on modelling trait and phenotype classes using OWL logical definitions and the Entity-Quality model
- 09:30 - 09:45 am: Problem statement and rationale of the workshop
- 09:45 - 10:25 am: Breakout 1: “Define a set of grouping classes to organise gene-to-phenotype data I”
- 10:25 - 10:35 am: Break
- 10:35 - 10:50 am: Report breakout 1
- 10:50 - 11:30 am: Breakout 2: “Define a set of grouping classes to organise gene-to-phenotype data II”
- 11:30 - 11:50 am: Report breakout 2
- 11:50 - 12:00 pm: Wrap up
To join the Phenotype Ontology Reconciliation Effort or for any other questions, please contact Nico Matentzoglu: nicolas.matentzoglu (at) gmail.com or Nicole Vasilevsky: nicole(at) tislab.org