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Disease Ontology Wiki

Welcome to the Disease Ontology Community Wiki. The Disease Ontology was initially developed as part of the NUgene project starting in 2003 at Northwestern. Work continues on the NUgene project at Northwestern.

  • The Disease Ontology is organized into five high level bins.
  • The Diease Ontology in August 2006 was submitted for inclusion and review to the OBO Foundry.
  • This project is open to collaborative development. Please contact the project PIs, Lynn Schriml at lynn.schriml_at_gmail.com or Warren Kibbe at wakibbe_at_gmail.com

Mission

The mission the Disease Ontology (DO) is to provide an open source ontology for the integration of biomedical data that is associated with human disease. DO will have a formally correct (in the ontology sense), semantically computable structure. Terms in DO will be well defined, using standard references. These terms will be linked to well-established, well-adopted terminologies that contain disease and disease-related concepts such as SNOMED (we are working with SNOMED to see if we can release SNOMED codes linked via UMLS to the community), ICD-9 and ICD-10, MeSH, and UMLS. The combination of a semantically computable structure and the external references to these terminologies will enable useful inference between disparate datasets using one or more of these standard terminologies to code disease. The Disease Ontology will be, at the end of this project, a community-driven, community-accepted ontology of diseases for clinical research and medicine inclusive of genetic, environmental and infectious diseases. The Disease Ontology will encapsulate, therefore, a comprehensive theory of disease. The design of the disease ontology will enable greater understanding of disease states by placing heritable disorders in the context of other infectious diseases and related diseases. The structure of Disease Ontology and the external references to other terminologies will enable the integration of disparate datasets through the concept of disease.

Scope

The Disease Ontology is a community driven, open source ontology that is designed to link disparate datasets through disease concepts. We will provide a computable structure of inheritable, environmental and infectious origins of human disease to facilitate the connection of genetic data, clinical data, and symptoms through the lens of human disease. We hope and anticipate that this will be useful for coupling disease concepts in model organisms to human disease concepts.

The Disease Ontology should enable the cross-walk between disease concepts, genes contributing to disease, and the 'cloud' of associated symptoms, findings and signs. The use of the disease ontology requires these connections to be done through evidence-based associations. Our understanding of disease, and the association of disease with phenotype, environment, and genetics is dynamic and a reflection of current knowledge.

Meetings

Ongoing Development

To get the latest version, choose one of the following methods:

  • To download the Disease Ontology using the subversion command line: 
svn checkout https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/ diseaseontology
  • Get it from the disease ontology subversion web interface
http://gemina.svn.sourceforge.net/viewvc/gemina/trunk/Gemina/ontologies/gemina_symptom.obo?view=log
  • Download it from the OBO Foundry. This version may lag from the current sourceforge release.
http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease_ontology
  • The Disease Ontology is currently under review as part of the OBO Foundry review process.
  • The current focus of the Disease Ontology is to improve the ontological soundness of the ontology,such as removal of plural terms and removal of upper case terms. Additionally, we will be working to add a significant number of definitions to the Disease Ontology.

PIs

Advisory Board

  • Rex Chisholm, Northwestern University
  • Michael Ashburner, University of Cambridge
  • Suzi Lewis, University of California, Berkeley
  • Barry Smith, University of Buffalo, NY
  • Chris Mungall, University of California, Berkeley
  • Maryann Martone, University of California, San Diego
  • Richard Scheuermann, UT Southwestern

Collaborators and Contributors

  • John Osborne, University of Alabama at Birmingham
  • Wendy Wolf, Northwestern
  • Maureen Smith, Northwestern
  • Abel Kho, Northwestern
  • Simon Lin, Northwestern
  • Suvarna Nadendla, University of Maryland, Institute for Genome Sciences
  • Marcus Chibucos, University of Maryland, Institute for Genome Sciences
  • Bernard de Bono, European Bioinformatics Institute
  • Peter Robinson, Humboldt-Universität, Berlin
  • Judy Blake, The Jackson Laboratories
  • Janan Eppig, The Jackson Laboratories

Project Links

Related Links

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