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Contents

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 History of the Disease Ontology.
  • The Disease Ontology is organized into seven high level bins.
  • The Disease 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.

The Disease Ontology is currently under review as part of the OBO Foundry review process.

Definition

A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [[1]]

Meetings

Curation

Current activities

svn snapshot

DO Style Guides

  • Style Guide: documented curation guiding principles.
  • Relations_in_DO: list of OBO-Edit relations included in the Disease Ontology.

Workshops

Download DO

Link to how to Download DO

DO Statistics

Latest statistics in a pdf

Publications

  • Northwestern technical publication highlighting the creation of DO version 3 using UMLS and MMTx [2]
  • Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. Annotating the human genome with Disease Ontology. BMC Genomics (2009) 10 S1:S6. Pubmed id 1959488 [3]
  • Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics (2009) 25:i63-8. Pubmed id 19478018
  • Osborne JD, Lin SM, Zhu LJ, Kibbe WA. Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods Mol Biol. (2007) 408:153-69. Pubmed id 18314582

DO Links

DO Project Resources and DO Related Links: DO_Links

DO web browser [4]

DO scripts: DO_scripts

Follow DO on Twitter

Join our DO LinkedIn Group

Become a member of the DO Facebook group

Funding

The PIs would like to gratefully recognize the NCRR for funding this activity. The Disease Ontology has been funded by the National Institutes of Health - National Center for Research Resources, NCRR, R01RR025342 under the ARRA mechanism. Please cite R01RR025342 in any publications in which Disease Ontology contributed to your work.

About Us

Link to more information about the Disease Ontology and people involved About Us

License

This work is licensed under a Creative Commons Attribution 3.0 Unported License.

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