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The Gene Ontology in 2010: extensions and refinements.

Nucleic acids research | Jan 22, 2010

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

Pubmed ID: 19920128 RIS Download

Mesh terms: Animals | Computational Biology | Databases, Genetic | Databases, Nucleic Acid | Databases, Protein | Genomics | Humans | Information Storage and Retrieval | Internet | Software | User-Computer Interface | Vocabulary, Controlled

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Associated grants

  • Agency: NHGRI NIH HHS, Id: #P41HG02273
  • Agency: NHGRI NIH HHS, Id: HG000330
  • Agency: NIGMS NIH HHS, Id: U24 GM088849
  • Agency: NHGRI NIH HHS, Id: U41 HG003751
  • Agency: NHGRI NIH HHS, Id: P41 HG02273
  • Agency: NHGRI NIH HHS, Id: HG02223
  • Agency: NHGRI NIH HHS, Id: U41 HG002273
  • Agency: NHLBI NIH HHS, Id: HL64541
  • Agency: NHGRI NIH HHS, Id: HG002659
  • Agency: NHGRI NIH HHS, Id: P41 HG003751
  • Agency: NHGRI NIH HHS, Id: HG003751
  • Agency: NIGMS NIH HHS, Id: U24GM077905
  • Agency: NHGRI NIH HHS, Id: HG01315
  • Agency: British Heart Foundation, Id: SP/07/007/23671
  • Agency: Medical Research Council, Id: G0500293
  • Agency: NIGMS NIH HHS, Id: U24GM088849
  • Agency: NHGRI NIH HHS, Id: HG004341

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This is a list of tools and resources that we have found mentioned in this publication.


AmiGO

Official Web-based tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally. The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. AmiGO can be used to:
* search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
* perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
* search for GO terms and view the genes or gene products they are annotated to
* browse the GO ontology and view terms
* the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
* term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
* GOOSE is for advanced users who want to run custom SQL queries against the GO database.

tool

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GO

A community-based bioinformatics resource consisting of three structured controlled vocabularies (ontologies) for the annotation of gene products with respect to their molecular function, cellular component, and biological role in a species-independent manner. This initiative to standardize the representation of gene and gene product attributes across species and databases is an effort to address the need for consistent descriptions of gene products in different databases. The Gene Ontology project encourages input from the community into both the content of the GO and annotation using GO. There are three separate aspects to this effort: first, they write and maintain the ontologies themselves; second, they make cross-links between the ontologies and the genes and gene products in the collaborating databases; and third, they develop tools that facilitate the creation, maintenance and use of ontologies. The controlled vocabularies are structured so that users can query them at different levels: for example, uers can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or users can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product.

tool

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SO

A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.

tool

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