Open Biomedical Ontologies: Difference between revisions
Content deleted Content added
→Related Projects: Organization name change: MGED -> FGED |
TiagoLubiana (talk | contribs) ←Redirected page to OBO Foundry Tags: New redirect Visual edit: Switched |
||
| (39 intermediate revisions by 28 users not shown) | |||
| Line 1: | Line 1: | ||
#REDIRECT [[OBO Foundry]] {{R from merge}} |
|||
'''Open Biomedical Ontologies''' (abbreviated '''OBO'''; formerly Open Biological Ontologies) is an effort to create [[controlled vocabulary|controlled vocabularies]] for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the [[United States|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]]<ref name="pmid17989687">{{cite journal| author=Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W et al.| title=The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. | journal=Nat Biotechnol | year= 2007 | volume= 25 | issue= 11 | pages= 1251–5 | pmid=17989687 | url=http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=clinical.uthscsa.edu/cite&email=badgett@uthscdsa.edu&retmode=ref&cmd=prlinks&id=17989687 | doi=10.1038/nbt1346 }} </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, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. |
|||
== Related Projects == |
|||
'''Ontology Lookup Service''' |
|||
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. |
|||
'''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. |
|||
'''Sequence Ontology''' |
|||
The [http://song.sourceforge.net/ Sequence Ontology] (SO) 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 Database|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''' |
|||
[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. |
|||
'''FGED''' |
|||
The [[FGED Society|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). |
|||
'''[[Plant ontology]]''' |
|||
The [http://www.plantontology.org/ Plant Ontology Consortium] (POC) 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''' |
|||
[http://phenoscape.org/ Phenoscape] 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 [http://bioportal.bioontology.org/ontologies/39892/ Anatomy Ontology], an accompanying [http://bioportal.bioontology.org/ontologies/39905/ Taxonomic Ontology], and quality terms from the [http://bioportal.bioontology.org/ontologies/39886/ PATO ontology of phenotype qualities]. Several other OBO ontologies are also used. The anatomy ontology was developed from the zebrafish anatomy ontology developed by the [http://www.zfin.org/ Zebrafish Information Network]. |
|||
==OBO and Semantic Web== |
|||
'''OBO & 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. [http://www.cs.utexas.edu/~hamid/oboowl.html Project Page] [http://www.morphster.org/ Morphster Project] |
|||
==References== |
|||
{{reflist}} |
|||
==External links== |
|||
*[http://obofoundry.org Open Biomedical Ontologies (OBO)] |
|||
*[http://www.brenda-enzymes.info/index.php4?page=ontology/ Ontology browser for most of the Open Biological Ontologies at BRENDA website] |
|||
*[http://brainarray.mbni.med.umich.edu/Brainarray/prototype/PubOnto/ PubOnto: OBO-based literature search tool] |
|||
[[Category:Bioinformatics]] |
|||
[[Category:Ontology (information science)]] |
|||
Latest revision as of 13:23, 3 May 2020
Redirect to:
- From a merge: This is a redirect from a page that was merged into another page. This redirect was kept in order to preserve the edit history of this page after its content was merged into the content of the target page. Please do not remove the tag that generates this text (unless the need to recreate content on this page has been demonstrated) or delete this page.
- For redirects with substantive page histories that did not result from page merges use {{R with history}} instead.