Open Biomedical Ontologies: Difference between revisions
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'''[[Ontology Lookup Service]]''' |
'''[[Ontology Lookup Service]]''' |
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The [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service] 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. |
The Ontology Lookup Service<ref>[http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service]</ref> 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. |
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'''Gene Ontology Consortium''' |
'''Gene Ontology Consortium''' |
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The goal of the [[Gene |
The goal of the [[Gene Ontology]] (GO) consortium is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes. |
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'''[[Sequence Ontology]]''' |
'''[[Sequence Ontology]]''' |
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The [http://song.sourceforge.net/ Sequence Ontology] |
The Sequence Ontology (SO)<ref>[http://song.sourceforge.net/ Sequence Ontology]</ref> is a part of the Gene Ontology project and the aim is to develop an ontology suitable for describing biological sequences. It is a joint effort by genome annotation centres, including WormBase, the Berkeley Drosophila Genome Project, FlyBase, the Mouse Genome Informatics group, and the Sanger Institute. |
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'''Generic Model Organism Databases''' |
'''Generic Model Organism Databases''' |
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'''Standards and Ontologies for Functional Genomics''' |
'''Standards and Ontologies for Functional Genomics''' |
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[http://www.sofg.org/ SOFG] is both a meeting and a website; it aims to bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments. |
SOFG<ref>[http://www.sofg.org/ SOFG]</ref> is both a meeting and a website; it aims to bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments. |
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'''FGED''' |
'''FGED''' |
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'''[[Plant ontology]]''' |
'''[[Plant ontology]]''' |
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The [http://www.plantontology.org/ Plant Ontology Consortium] |
The Plant Ontology Consortium (POC)<ref>[http://www.plantontology.org/ Plant Ontology Consortium]</ref> aims to develop, curate and share structured controlled vocabularies (ontologies) that describe plant structures and growth/developmental stages. Through this effort, the project aims to facilitate cross database querying by fostering consistent use of these vocabularies in the annotation of tissue and/or growth stage specific expression of genes, proteins and phenotypes. |
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'''Phenoscape''' |
'''Phenoscape''' |
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[http://phenoscape.org/ Phenoscape] is a project to develop a database of phenotype data for species across the Osteriophysi, a large group of |
Phenoscape<ref>[http://phenoscape.org/ Phenoscape]</ref> is a project to develop a database of phenotype data for species across the Osteriophysi, a large group of teleost fish. The data is captured using annotations that combine terms from an anatomy ontology,<ref>[http://bioportal.bioontology.org/ontologies/39892/ anatomy ontology]</ref> an accompanying taxonomic ontology,<ref>[http://bioportal.bioontology.org/ontologies/39905/ taxonomic ontology]</ref> and quality terms from the PATO ontology of phenotype qualities.<ref>[http://bioportal.bioontology.org/ontologies/39886/ PATO ontology of phenotype qualities]</ref> Several other OBO ontologies are also used. The anatomy ontology was developed from the zebrafish anatomy ontology developed by the Zebrafish Information Network.<ref>[http://www.zfin.org/ Zebrafish Information Network]</ref> |
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==Semantic Web== |
==Semantic Web== |
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===OBO |
===OBO and OWL Roundtrip Transformations=== |
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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 |
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 |
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Revision as of 04:22, 7 December 2016
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Open Biomedical Ontologies (abbreviated OBO; formerly Open Biological Ontologies) is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S. National Center for Biomedical Ontology where it will form 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.
Related projects
The Ontology Lookup Service[2] 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
The goal of the Gene Ontology (GO) consortium is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes.
The Sequence Ontology (SO)[3] is a part of the Gene Ontology project and the aim is to develop an ontology suitable for describing biological sequences. It is a joint effort by genome annotation centres, including WormBase, the Berkeley Drosophila Genome Project, FlyBase, the Mouse Genome Informatics group, and the Sanger Institute.
Generic Model Organism Databases
The Generic Model Organism Project (GMOD) is a joint effort by the model organism system databases WormBase, FlyBase, MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to develop reusable components suitable for creating new community databases of biology.
Standards and Ontologies for Functional Genomics
SOFG[4] is both a meeting and a website; it aims to bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments.
FGED
The Functional Genomics Data (FGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics experiments.
Ontology for Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) is an open access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL).
The Plant Ontology Consortium (POC)[5] aims to develop, curate and share structured controlled vocabularies (ontologies) that describe plant structures and growth/developmental stages. Through this effort, the project aims to facilitate cross database querying by fostering consistent use of these vocabularies in the annotation of tissue and/or growth stage specific expression of genes, proteins and phenotypes.
Phenoscape
Phenoscape[6] is a project to develop a database of phenotype data for species across the Osteriophysi, a large group of teleost fish. The data is captured using annotations that combine terms from an anatomy ontology,[7] an accompanying taxonomic ontology,[8] and quality terms from the PATO ontology of phenotype qualities.[9] Several other OBO ontologies are also used. The anatomy ontology was developed from the zebrafish anatomy ontology developed by the Zebrafish Information Network.[10]
Semantic Web
OBO and OWL Roundtrip Transformations
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.[11]
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.
- ^ Ontology Lookup Service
- ^ Sequence Ontology
- ^ SOFG
- ^ Plant Ontology Consortium
- ^ Phenoscape
- ^ anatomy ontology
- ^ taxonomic ontology
- ^ PATO ontology of phenotype qualities
- ^ Zebrafish Information Network
- ^ 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.
External links
- Open Biomedical Ontologies (OBO)
- Ontology browser for most of the Open Biological Ontologies at BRENDA website
- PubOnto: OBO-based literature search tool
- Project Page
- Morphster Project
- 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.