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The Phenotype Ontologies Reconciliation Effort

Phenotype ontologies have emerged in the last decade as a means to curate, organise and query phenotypic content. Representing ontologies in a common language, OWL, facilitated the integration of those ontologies into various tool-chains, such as terminological services (OLS, OntoBee), search engines and more recently sophisticated diagnostic and analytic tools such as Exomiser. The phenotype ontology community has made much progress to date standardising their development practices, in particular by committing to OBO principles. OBO principles encourage, for example, standard practices for representing identifiers, well-documented and open development practices and some shared standard vocabularies such as the Relation Ontology that facilitate integration.

Despite the wealth of shared practices and a well-developed shared ecosystem of tools such as Protege, Robot, owltools, and the OWL API, phenotype ontologies (and their cousins, disease ontologies) are often not very deeply integrated and interoperable. Entity-quality (EQ) patterns co-evolved with large phenotype ontologies such as the Human Phenotype Ontology (HP), Mammalian Phenotype Ontology (MP) and Zebrafish Phenotype Ontology (ZP) as a means to integrate ontologies without having to manually maintain links between them. EQ patterns allow ontologies to logically define phenotypes in terms of an entity (E, also called the 'bearer'), often an anatomical entity or a biological process, and a (modified) phenotypic quality (Q), such as 'abnormal morphology': For example, 'Abnormal eye morphology' could be defined as an 'abnormal morphology' that inheres in the 'eye'. By using standard vocabularies such as GO or UBERON for representing the entities and PATO for representing the phenotypic qualities, ontologies could now be combined and classified together.

While EQ patterns are now widespread in the phenotype community, their development was, up until now, mostly disconnected across the different species. Despite frequent manual efforts to align definitions, large proportions of existing ontologies continued to contain logically incompatible definitions, which precludes smooth integration for cross-species queries and inference. The Phenotype Ontologies Reconciliation Effort is a community effort that attempts to reconcile logical definition across a number of important phenotype ontologies. The effort was formed as part of the POTATO (Phenotype Ontologies Traversing All The Organisms) Workshop, co-located with ICBO 2018. The workshop went into its second iteration in April 2019, co-located with biocuration2019 in Cambridge, UK.

Our whitepaper (and workshop report) outlines our objectives and rationale in more detail.

Current members

Ontology People Involved Groups Status
Ascomycete Phenotype Ontology (APO) Stacia Engel Alliance of Genome Resources, Saccharomyces Genome Database IN
C. elegans Phenotype Ontology (WBPheno) Chris Grove Alliance of Genome Resources, WormBase IN
Cellular Microscopy Phenotype Ontology (CMPO) Simon Jupp Samples, Phenotypes and Ontologies, EMBL-EBI IN
Dictyostelium discoideum phenotype ontology (DDPHENO) Petra Fey dictyBase IN
Drosophila Phenotype Ontology (DPO) David Osumi-Sutherland, Clare Pilgrim FlyBase IN
Fission Yeast Phenotype Ontology (FYPO) Midori A. Harris, Valerie Wood PomBase IN
Human Phenotype Ontology (HP) Peter Robinson, Sebastian Koehler, Leigh Carmody, Nicole Vasilevsky Monarch Initiative IN
Mammalian Phenotype Ontology (MP) Sue Bello, Anna Anagnostopoulos Alliance of Genome Resources, MGI IN
Phenoscape Knowledge Base Jim Balhoff, W. Dahdul Phenoscape IN
PHI-base Phenotype Ontology (PHIPO) Alayne Cuzick PHI-base IN
Planarian Phenotype Ontology (PLANP) Sofia Robb Stowers Institute for Medical Research IN
Plant Trait Ontology (TO) Laurel Cooper*, Marie-Angélique Laporte, Pankaj Jaiswal Planteome, Bioversity IN
FuTRES Ontology of Vertebrate Traits Meghan Balk, Ramona Walls FuTRES IN
Xenopus Phenotype Ontology (XPO) Erik Segerdell XenBase IN
Zebrafish Phenotype Ontology (ZP) Yvonne Bradford Alliance of Genome Resources, ZFIN IN


If you are interested in joining the phenotype ontology community, or need help with setting up your own phenotype ontology development environment, please send an email to the phenotype ontology editors mailing list. Members of the effort communicate in a bi-weekly teleconference and coordinates most aspects of the reconciliation process through a slack space and GitHub issues.