Open Biomedical Ontologies: Difference between revisions
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#REDIRECT [[OBO Foundry]] {{R from merge}} |
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{{Refimprove|date=January 2012}} |
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{{MOS|reason=Capitalization|date=March 2014}} |
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}} |
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The '''Open Biomedical and Biological Ontologies''' ('''OBO'''; formerly '''Open Biomedical Ontologies''') is an effort to create [[Ontology (information science)|ontologies]] ([[controlled vocabulary|controlled vocabularies)]] for use across biological and medical domains. OBO forms part of the resources of the [[United States|U.S.]] [[National Center for Biomedical Ontology]] and a central element of the NCBO's BioPortal. |
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== OBO Foundry == |
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The OBO ontology library forms the basis of the [[OBO Foundry]],<ref name="pmid17989687">{{Cite journal |
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| last1 = Smith | first1 = B. |
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| authorlink1 = Barry Smith (ontologist) |
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| last2 = Ashburner | first2 = M. |
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| authorlink2 = Michael Ashburner |
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| last3 = Rosse | first3 = C. |
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| last4 = Bard | first4 = J. |
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| last5 = Bug | first5 = W. |
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| last6 = Ceusters | first6 = W. |
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| last7 = Goldberg | first7 = L. J. |
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| last8 = Eilbeck | first8 = K. |
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| last9 = Ireland | first9 = A. |
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| last10 = Mungall |
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| doi = 10.1038/nbt1346 | first10 = C. J. |
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| last11 = Leontis | first11 = N. |
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| last12 = Rocca-Serra | first12 = P. |
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| last13 = Ruttenberg | first13 = A. |
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| last14 = Sansone | first14 = S. A. |
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| last15 = Scheuermann | first15 = R. H. |
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| last16 = Shah | first16 = N. |
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| last17 = Whetzel | first17 = P. L. |
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| last18 = Lewis | first18 = S. | authorlink18 = Suzanna Lewis |
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| title = The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration |
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| journal = [[Nature Biotechnology]] |
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| volume = 25 |
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| issue = 11 |
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| pages = 1251–1255 |
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| year = 2007 |
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| pmid = 17989687 |
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| pmc =2814061 |
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}} {{open access}}</ref> a collaborative experiment involving a group of ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster [[interoperability]] of ontologies within the broader OBO framework and also to ensure a gradual improvement of quality and formal rigor in ontologies. The library operates to design ways to meet the increasing needs of data and information integration in the biomedical domain. |
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==The OBO file format== |
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The OBO file format is a biology-oriented language for building ontologies. It is based on the principles of [[Web Ontology Language|Web Ontology Language (OWL)]]. |
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As a community effort, a standard common mapping has been created for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL. The research contains methodical examination of each of the constructs of OBO and a layer cake for OBO, similar to the Semantic Web stack.<ref name="pmid18245124">{{Cite journal|last1=Antezana|first1=E.|last2=Egana|first2=M.|last3=De Baets|first3=B.|last4=Kuiper|first4=M.|last5=Mironov|first5=V.|year=2008|title=ONTO-PERL: An API for supporting the development and analysis of bio-ontologies|journal=Bioinformatics|volume=24|issue=6|pages=885–887|doi=10.1093/bioinformatics/btn042|pmc=|pmid=18245124}}</ref> |
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== See also == |
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* [[Ontology Lookup Service]] |
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* [[Gene Ontology Consortium]] |
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* [[Sequence Ontology]] |
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* [[Generic Model Organism Database|Generic Model Organism Databases]] |
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* [[FGED Society|Functional Genomics Data]] (FGED) |
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* [[Ontology for Biomedical Investigations]] |
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* [[Plant ontology]] |
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* [[Phenoscape]] |
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==References== |
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{{reflist}} |
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==External links== |
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*[http://obofoundry.org Open Biomedical Ontologies (OBO)] |
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*[https://www.ebi.ac.uk/ols/index Ontology Lookup Service website] |
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*[http://www.brenda-enzymes.org/ontology.php Ontology browser for most of the Open Biological Ontologies at BRENDA website] |
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*[http://brainarray.mbni.med.umich.edu/Brainarray/prototype/PubOnto/ PubOnto: OBO-based literature search tool] |
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*[https://metacpan.org/release/ONTO-PERL ONTO-PERL] |
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*[https://web.archive.org/web/20120828100848/http://tagc.univ-mrs.fr/SimCT/ SimCT] Web-based tool to display relationships between biological objects annotated to an ontology in the form of a tree, based on their annotation similarity. On [[archive.org]] |
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*[https://web.archive.org/web/20080907194111/http://www.morphster.org/ Morphster Project] by University of Austin, Texax. On archive.org |
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[[Category:Bioinformatics]] |
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[[Category:Ontology (information science)]] |
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