POTATO workshop aims to ‘root’ out inconsistencies between phenotype ontologies

Monarch Initiative
Sep 17, 2018 · 2 min read
Image for post
Image for post

The Monarch Initiative uses phenotype ontologies to find candidate genes and animal model systems for human diseases. For this to work, similar terms both within and between phenotype ontologies need to be defined using similar logic. Up to now, this has been achieved informally via shared documentation and discussion, but this has been only partially successful. It is not easy to manually keep consistency across terms describing thousands of phenotypes in many different species. In an effort to simplify and standardize the creation of logical definitions, Monarch team members have developed tools for pattern-based development (Dead Simple Ontology Design Patterns (DOSDP) and the Ontology Development Kit (ODK)). These tools allow community-agreed definition pattens to be documented as formal design patterns. A shared repository of design patterns can then be used to generate compatible logical definitions across different phenotype ontologies. Use of such patterns in any given phenotype ontology creates native interoperability across species and domains.

At the International Conference on Biological Ontologies (ICBO) in Corvallis, Oregon this summer, we held a workshop that gathered more than 40 ontology curators, developers, and biomedical experts who study diverse taxa to learn about our updated tool-chain for pattern-based development and to discuss discrepancies between logical definitions across various phenotype ontologies. The Phenotype Ontologies Traversing All The Organisms (POTATO) workshop hosted developers from phenotype ontologies including the Human Phenotype Ontology (HPO), the Mammalian Phenotype Ontology (MP), and phenotype ontologies for C. elegans, Xenopus, Drosophila, plants and Planaria.

As a result of the meeting, representatives of all the phenotypes ontologies have committed to joining an ongoing collaborative community effort to align their respective ontologies by developing and using common sets of design patterns to generate logical definitions for their ontologies. The outcome of these community efforts will be an integrated ecosystem of phenotype ontologies that can be leveraged in HPO-based clinical diagnostics and disease mechanism discovery. More information is available here: https://github.com/obophenotype/upheno/wiki/Phenotype-Ontologies-Reconciliation-Effort#current-members

To join this effort or for any other questions, please contact Nico Matentzoglu: nicolas.matentzoglu@ebi.ac.uk or Nicole Vasilevsky: vasilevs@ohsu.edu

POTATO Organizers: David Osumi-Sutherland (EBI), Nico Matentzoglu (EBI), Nicole Vasilevsky (OHSU), Chris Mungall (LBNL), Jim Balhoff (RENCI), Melissa Haendel (OHSU/OSU)
Funding: This workshop was supported by an NIH conference grant “Forums for Integrative phenomics” to Melissa Haendel and Peter Robinson: 1U13CA221044.

Welcome to a place where words matter. On Medium, smart voices and original ideas take center stage - with no ads in sight. Watch

Follow all the topics you care about, and we’ll deliver the best stories for you to your homepage and inbox. Explore

Get unlimited access to the best stories on Medium — and support writers while you’re at it. Just $5/month. Upgrade

Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store