This repository contains common files ontologies and workflows shared between multiple phenotype ontologies.
See (docs/)[docs] for details
For more background, please see:
- Sebastian Köhler, Sandra C Doelken, Barbara J Ruef, Sebastian Bauer, Nicole Washington, Monte Westerfield, George Gkoutos, Paul Schofield, Damian Smedley, Suzanna E Lewis, Peter N Robinson, Christopher J Mungall (2013) Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research F1000Research
- C J Mungall, Georgios Gkoutos, Cynthia Smith, Melissa Haendel, Suzanna Lewis, Michael Ashburner (2010) Integrating phenotype ontologies across multiple species Genome Biology 11 (1)
Please see [GettingStarted] for details on how to work with the OWL files
The [OWLAxiomatization] page describes how we represent phenotypes in OWL, and how we reason with the resulting structures
The [Applications] page describes how the OWL axiomatization is used in applications such as OWLSim. This also describes the [CrossSpeciesPhenotypeOntology].
The primary focus of this repository is on phenotypes, which we consider distinct from diseases. However the [DiseaseIntegration] page contains preliminary information on integrating and axiomatization of disease ontologies.
See [TraitsAndPhenotypes].
See the build-pheno-ontologies job on the Berkeley jenkins server