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OBO Foundry

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The Open Biomedical Ontologies (OBO) Foundry (now The Open Biological and Biomedical Ontologies (OBO) Foundry) is a collaborative experiment involving developers of science-based ontologies. (Smith et al., 2007) 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. The Foundry approach has been adopted by the Neuroscience Information Framework (NIF) Standard and by the cROP (Common Reference Ontologies for Plants) initiatives.

Introduction

The Foundry initiative rests on the belief that the value 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—most conspicuously through the work of the Gene Ontology Consortium—has led to the development of certain proposed 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.

The Open Biological and Biomedical Ontologies (formerly The Open Biomedical Ontologies as well as The 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 in the sense that it is available to be used by all under the following two constraints (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 (March 2010)

The goal of the OBO Foundry initiative is to create an evolving group of biological and biomedical ontologies which will have the potential to cover a wide range of life science phenomena in a modular fashion. To realize this goal, we have subjected a number of candidate ontologies to a process of review, the first phase of which has now been completed, and the results are reported here. The following six ontologies have satisfied the OBO Foundry principles and are recommended as preferred targets for community convergence.

  • CHEBI: Chemical Entities of Biological Interest
  • GO: Gene Ontology
  • PATO: Phenotypic Quality Ontology
  • PRO: Protein Ontology
  • XAO: Xenopus Anatomy Ontology
  • ZFA: Zebrafish Anatomy Ontology

Candidate Members of the OBO Foundry

The following groups of ontologies can be informally distinguished among current OBO Foundry candidate members:

Mature Ontologies undergoing reform

  • Cell Ontology (CL)
  • Foundational Model of Anatomy (FMA) Ontology
  • Plant growth and developmental stage
  • Plant structure
  • Sequence Ontology (SO)

Ontologies being built ab initio within the Foundry framework

  • Common Anatomy Reference Ontology (CARO)
  • Environment Ontology (EnvO)
  • Fish Multi-Species Anatomy Ontology (NSF funding received)
  • Infectious Disease Ontology (IDO)
  • Malaria Ontology (IDO-MAL)
  • Influenza Ontology
  • Ixodidae and Argasidae (Tick) Anatomy Ontology
  • Mosquito Anatomy Ontology (MAO)
  • Ontology for Biomedical Investigations (OBI)
  • Ontology for General Medical Science
  • RNA Ontology (RnaO)
  • Spider Anatomy Ontology (SPD)
  • Subcellular Anatomy Ontology (SAO)
  • Vaccine Ontology

Other candidate ontologies

  • Disease Ontology
  • Drosophila Development
  • Drosophila Gross Anatomy
  • Human Phenotype Ontology
  • Mammalian Phenotype
  • Mouse Adult Gross Anatomy
  • Mouse Gross Anatomy and Development
  • Mouse Pathology
  • Systems Biology Ontology
  • Teleost Anatomy and Development
  • Teleost Taxonomy
  • Tick Gross Anatomy

References

Brush MH, Vasilevsky N, Torniai C, Johnson T, Shaffer C, Haendel MA. "Developing a Reagent Application Ontology within the OBO Foundry Framework", Proceedings of the International Conference on Biomedical Ontology, Buffalo, NY, 2011.

M Courtot, C Mungall, RR Brinkman, A Ruttenberg, '[ceur-ws.org/Vol-833/paper72.pdf Building the OBO Foundry-One Policy at a Time]", Proceedings of the International Conference on Biomedical Ontology, (CEUR 993), 2011.

Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008;36:D344–D350.

A Ghazvinian, NF Noy, MA Musen","How orthogonal are the OBO Foundry ontologies", J Biomed Semantics 2011; 2(Suppl 2): S2. doi: 10.1186/2041-1480-2-S2-S22011

CJ Mungall, GV Gkoutos, CL Smith, et al., "Integrating phenotype ontologies across multiple species", Genome Biology 2010, 11:R2 doi:10.1186/gb-2010-11-1-r2

SL Santamaria, "Development the Animals in Context ontology", Proceedings of the International Conference on Biomedical Ontology, Graz, 2012.

D Schober, B Smith, SE Lewis, W Kusnierczyk et al. "Survey-based naming conventions for use in OBO Foundry ontology development", BMC Bioinformatics 2009, 10:125 doi:10.1186/1471-2105-10-125

P Seyed, SC Shapiro, "[ceur-ws.org/Vol-833/paper23.pdf Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies]", Proceedings of the International Conference on Biomedical Ontology (CEUR 993), 2011.

Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; et al. (2007). "The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology 25 (11): 1251–1255. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687.

CF Taylor, D Field, S-A Sansone, R Apweiler, M Ashburner, et al. “Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project”, Nature Biotechnology, 26 (2008), 889-896. PMC2771753

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