Open Biomedical Ontologies
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The Open Biomedical and Biological Ontologies (OBO; formerly Open Biomedical Ontologies) is an effort to create ontologies (controlled vocabularies) for use across biological and medical domains. OBO forms part of the resources of the U.S. National Center for Biomedical Ontology and a central element of the NCBO's BioPortal.
OBO Foundry
The OBO ontology library forms the basis of the OBO Foundry,[1] 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.
The OBO file format
The OBO file format is a biology-oriented language for building ontologies. It is based on the principles of Web Ontology Language (OWL).
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.[2]
See also
- Ontology Lookup Service
- The Ontology Lookup Service[3] is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.
- Gene Ontology Consortium
- Sequence Ontology
- Generic Model Organism Databases
- Functional Genomics Data (FGED)
- Ontology for Biomedical Investigations
- Plant ontology
- Phenoscape
References
- ^ Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; Goldberg, L. J.; Eilbeck, K.; Ireland, A.; Mungall, C. J.; Leontis, N.; Rocca-Serra, P.; Ruttenberg, A.; Sansone, S. A.; Scheuermann, R. H.; Shah, N.; Whetzel, P. L.; Lewis, S. (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.
- ^ Antezana, E.; Egana, M.; De Baets, B.; Kuiper, M.; Mironov, V. (2008). "ONTO-PERL: An API for supporting the development and analysis of bio-ontologies". Bioinformatics. 24 (6): 885–887. doi:10.1093/bioinformatics/btn042. PMID 18245124.
- ^ Ontology Lookup Service
External links
- Open Biomedical Ontologies (OBO)
- Ontology browser for most of the Open Biological Ontologies at BRENDA website
- PubOnto: OBO-based literature search tool
- ONTO-PERL
- 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
- Morphster Project by University of Austin, Texax. On archive.org