Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Nat Biotechnol
2007 Nov 01;2511:1251-5. doi: 10.1038/nbt1346.
Show Gene links
Show Anatomy links
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
Smith B
,
Ashburner M
,
Rosse C
,
Bard J
,
Bug W
,
Ceusters W
,
Goldberg LJ
,
Eilbeck K
,
Ireland A
,
Mungall CJ
,
OBI Consortium
,
Leontis N
,
Rocca-Serra P
,
Ruttenberg A
,
Sansone SA
,
Scheuermann RH
,
Shah N
,
Whetzel PL
,
Lewis S
.
???displayArticle.abstract???
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 or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.
Ashburner,
Ontologies for biologists: a community model for the annotation of genomic data.
2003, Pubmed
Ashburner,
Ontologies for biologists: a community model for the annotation of genomic data.
2003,
Pubmed
Bada,
Enrichment of OBO ontologies.
2007,
Pubmed
Bard,
An ontology for cell types.
2005,
Pubmed
Bodenreider,
The Unified Medical Language System (UMLS): integrating biomedical terminology.
2004,
Pubmed
Brazma,
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
2001,
Pubmed
Brinkley,
A framework for using reference ontologies as a foundation for the semantic web.
2006,
Pubmed
Buetow,
Cyberinfrastructure: empowering a "third way" in biomedical research.
2005,
Pubmed
Camon,
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
2004,
Pubmed
Camon,
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
2003,
Pubmed
Campbell,
The Unified Medical Language System: toward a collaborative approach for solving terminologic problems.
1998,
Pubmed
Ceusters,
A terminological and ontological analysis of the NCI Thesaurus.
2005,
Pubmed
Ceusters,
Mistakes in medical ontologies: where do they come from and how can they be detected?
2004,
Pubmed
Gene Ontology Consortium,
The Gene Ontology (GO) project in 2006.
2006,
Pubmed
Grenon,
Biodynamic ontology: applying BFO in the biomedical domain.
2004,
Pubmed
Hill,
Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies.
2002,
Pubmed
Kelso,
eVOC: a controlled vocabulary for unifying gene expression data.
2003,
Pubmed
Kohane,
Building national electronic medical record systems via the World Wide Web.
1996,
Pubmed
Lee,
Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.
2006,
Pubmed
Leontis,
The RNA Ontology Consortium: an open invitation to the RNA community.
2006,
Pubmed
Luo,
Modular organization of protein interaction networks.
2007,
Pubmed
Mabee,
Phenotype ontologies: the bridge between genomics and evolution.
2007,
Pubmed
,
Xenbase
Martone,
E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains.
2004,
Pubmed
Mungall,
Obol: integrating language and meaning in bio-ontologies.
2004,
Pubmed
Natale,
Framework for a protein ontology.
2007,
Pubmed
Ramírez,
Linking of digital images to phylogenetic data matrices using a morphological ontology.
2007,
Pubmed
Rebholz-Schuhmann,
Facts from text--is text mining ready to deliver?
2005,
Pubmed
Rubin,
National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge.
2006,
Pubmed
Sansone,
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group.
2006,
Pubmed
Schulz,
Spatial location and its relevance for terminological inferences in bio-ontologies.
2007,
Pubmed
Sjöblom,
The consensus coding sequences of human breast and colorectal cancers.
2006,
Pubmed
Smith,
HL7 RIM: an incoherent standard.
2006,
Pubmed
Smith,
Relations in biomedical ontologies.
2005,
Pubmed
Taylor,
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
2008,
Pubmed
Whetzel,
Development of FuGO: an ontology for functional genomics investigations.
2006,
Pubmed
Whetzel,
The MGED Ontology: a resource for semantics-based description of microarray experiments.
2006,
Pubmed
Yue,
Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints.
2005,
Pubmed