OBO Foundry

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The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment involving developers of science-based ontologies. The foundry is concerned with establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.


Introduction

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies. Ideally, such controlled vocabularies take the form of 'ontologies', which means that they are constructed in such a way as to support logical reasoning over the data annotated in their terms.

The success of this general approach in helping to tame the explosive proliferation of data in the biomedical domain has led to the development of principles of good practice in ontology development, which are now being put into practice within the framework of the Open Biomedical Ontologies consortium through its OBO Foundry initiative. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform and new ontologies are being created in a coordinated effort to create a family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality.

Open Biomedical Ontologies (formerly Open Biological Ontologies) is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO ontologies form part of the resources of the National Center for Biomedical Ontology, where they form a central component of the NCBO's BioPortal.

The OBO Foundry is a collaborative experiment, involving a group of OBO ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. The goal is to develop a set of interoperable humanly validated reference ontologies for all major domains of biomedical research. The project is summarized in this article published in Nature Biotechnology.

Custodians

The custodians of the OBO Foundry are:

Principles

(Version as of 24 April 2006.)

1. The ontology is open and available to be used by all without any constraint other than (1) its origin must be acknowledged and (2) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.

2. The ontology is in, or can be expressed in, a common formal language. (A provisional list of languages supported by OBO is provided at http://obo.sf.net/.)

3. The ontology possesses a unique identifier space within OBO.

4. The ontology provider has procedures for identifying distinct successive versions.

5. The ontology has a clearly specified and clearly delineated content.

6. The ontology includes textual definitions for all terms.

7. The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.

8. The ontology is well-documented.

9. The ontology has a plurality of independent users.

10. The ontologies in the OBO Foundry will be developed in a collaborative effort.

Members of the OBO Foundry

Mature Ontologies undergoing reform

  • Cell Ontology (CL)
  • Chemical Entities of Biological Interest (ChEBI)
  • Foundational Model of Anatomy (FMA) Ontology
  • Gene Ontology (GO)
  • Phenotypic Quality Ontology (PaTO)
  • Relation Ontology (RO)
  • Sequence Ontology (SO)

Foundry ontologies being built ab initio

  • Common Anatomy Reference Ontology (CARO)
  • Environment Ontology (EnvO)
  • Fish Multi-Species Anatomy Ontology (NSF funding received)
  • Ixodidae and Argasidae (Tick) Anatomy Ontology
  • Mosquito Anatomy Ontology (MAO)
  • Ontology for Biomedical Investigations (OBI)
  • Protein Ontology (PRO)
  • RNA Ontology (RnaO)
  • Spider Anatomy Ontology (SPD)
  • Subcellular Anatomy Ontology (SAO)
  • Xenopus Anatomy Ontology (XAO)

Ontologies in planning phase

  • Biobank/Biorepository Ontology
  • Food Ontology
  • Infectious Disease Ontology (IDO)
  • Immunology Ontology
  • Vaccine Ontology
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