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OBO Foundry specifications


Unique identifier OMICS_09875
Name OBO Foundry
Alternative names Open Biological and Biomedical Ontologies Foundry, Open Biological Ontology
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes


  • UO (The Units Ontology)


  • person_outline Patricia L. Whetzel
  • person_outline Jonathan Bard

Additional information


Publications for Open Biological and Biomedical Ontologies Foundry

OBO Foundry citations


ONS: an ontology for a standardized description of interventions and observational studies in nutrition

PMCID: 5928560
PMID: 29736190
DOI: 10.1186/s12263-018-0601-y
call_split See protocol

[…] Terms to be included in the ONS were collected among partners of the ENPADASI consortium, as well as from templates for data and metadata upload into the DASH-IN databases. In compliance with the OBO Foundry principles [], the ONS has been developed to be as follows: (i) Interoperable with other ontologies, as it has been formalized using the latest OWL 2 Web Ontology Language [] and RDF speci […]


Cell type discovery using single cell transcriptomics: implications for ontological representation

Hum Mol Genet
PMCID: 5946857
PMID: 29590361
DOI: 10.1093/hmg/ddy100

[…] Biomedical ontologies, as promoted by the Open Biomedical Ontology (OBO) Foundry (), provide for a framework to name and define the types, properties and relationships of entities in the biomedical domain. The CL was established in 2005 to provide a standard reference […]


FAIR principles and the IEDB: short term improvements and a long term vision of OBO foundry mediated machine actionable interoperability

PMCID: 5819722
PMID: 29688354
DOI: 10.1093/database/bax105

[…] s in fact the same. Neither model is necessarily right or wrong, but they would need to be manually coordinated and resolved before automation would be possible.We suggest that the effort involved in OBO Foundry ontology creation is also the best venue to provide guidance on how to model statements using OBO Foundry terms. We are in the process of actively coordinating the modeling of datasets in […]


DMTO: a realistic ontology for standard diabetes mellitus treatment

J Biomed Semantics
PMCID: 5800094
PMID: 29409535
DOI: 10.1186/s13326-018-0176-y
call_split See protocol

[…] OWL. As a result, instead of creating a new ontology from scratch, we had to determine if there is any existing domain ontology or source to extend or refine for the current problem. According to the OBO Foundry principles, reusing existing well-defined ontologies can enhance the new one by avoiding redundancy []. In addition, to support standardization, interoperability, reusability, and integrat […]


The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

J Biomed Semantics
PMCID: 5765662
PMID: 29329592
DOI: 10.1186/s13326-017-0169-2

[…] tities and their relations in a specific domain of the world. Hundreds of biological/ biomedical ontologies have been developed in the last two decades. The Open Biological and Biomedical Ontologies (OBO) Foundry is a collaborative initiative aimed at establishing a set of ontology development principles and incorporating ontologies following these principles in an evolving non-redundant and inter […]


Cells in experimental life sciences challenges and solution to the rapid evolution of knowledge

BMC Bioinformatics
PMCID: 5763506
PMID: 29322916
DOI: 10.1186/s12859-017-1976-2

[…] biologically and processed computationally to build a big picture that can present an integrative view of human body at large in a granular-detailed level. The Open Biological/Biomedical Ontologies (OBO) Foundry has been founded and functional for over a decade [], but it is not uncommon to find that many of us on the experimental side remain unaware of many controlled vocabularies and ontologies […]


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OBO Foundry institution(s)
Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA; Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK; Department of Biological Structure, University of Washington, Seattle, WA, USA; Department of Biomedical Sciences, The University of Edinburgh, Edinburgh, Scotland, UK; Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA; Department of Psychiatry and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA; Department of Oral Biology and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA; Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA; European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA; Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA; Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Stanford Medical Informatics, Stanford University School of Medicine, Stanford, CA, USA; Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
OBO Foundry funding source(s)
Supported by the BISC Gene Ontology Consortium, MGED, NCBO and RNA Ontology grants.

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