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The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content.

Pubmed ID: 19578431 RIS Download

Mesh terms: Animals | Cluster Analysis | Database Management Systems | Databases, Genetic | Genomics | Humans | Vocabulary, Controlled

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Associated grants

  • Agency: NHGRI NIH HHS, Id: U41 HG001315
  • Agency: NHGRI NIH HHS, Id: P41 HG002659
  • Agency: NIGMS NIH HHS, Id: U24 GM088849
  • Agency: NHLBI NIH HHS, Id: R01 HL064541
  • Agency: NHGRI NIH HHS, Id: U41 HG002273
  • Agency: NHLBI NIH HHS, Id: HL64541
  • Agency: NHGRI NIH HHS, Id: P41 HG000330
  • Agency: NHGRI NIH HHS, Id: P41 HG001315
  • Agency: NHGRI NIH HHS, Id: P41 HG002223
  • Agency: NICHD NIH HHS, Id: R01 HD033745
  • Agency: NHGRI NIH HHS, Id: U41 HG002223
  • Agency: NHGRI NIH HHS, Id: P41 HG002659-06
  • Agency: NHGRI NIH HHS, Id: U41 HG002659
  • Agency: NIGMS NIH HHS, Id: U24 GM07790
  • Agency: NHGRI NIH HHS, Id: P41 HG02223
  • Agency: British Heart Foundation, Id: SP/07/007/23671
  • Agency: Medical Research Council, Id: G0500293
  • Agency: NHGRI NIH HHS, Id: R01 HG002273
  • Agency: NIGMS NIH HHS, Id: T32 GM007790
  • Agency: NIGMS NIH HHS, Id: R01 GM064426
  • Agency: NICHD NIH HHS, Id: HD033745
  • Agency: NHGRI NIH HHS, Id: HG00022
  • Agency: NIGMS NIH HHS, Id: GM64426
  • Agency: NHGRI NIH HHS, Id: P41 HG002273

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PANTHER

Classification system that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists according to: * Gene families and subfamilies, including annotated phylogenetic trees * Gene Ontology classes: molecular function, biological process, cellular component * PANTHER Protein Classes * Pathways, including diagrams The PANTHER Classifications are the result of human curation as well as sophisticated bioinformatics algorithms. Details of the methods can be found in (Thomas et al., Genome Research 2003; Mi et al. NAR 2005). Version 8.1 contains 7729 protein families, each with a phylogenetic tree relating modern-day genes in 48 organisms.) PANTHER contains the complete sets of protein coding genes for 48 organisms, obtained from definitive sources. PANTHER uses the Gene Ontology for classifications by molecular function, biological process and cellular component. The PANTHER Protein Class ontology was adapted from the PANTHER/X molecular function ontology, and includes commonly used classes of protein functions, many of which are not covered by GO molecular function. You may download the classes and relationship information. PANTHER uses only a subset of GO terms (GO slim) to facilitate browsing. You may download the PANTHER GO slim. You may Score proteins against the PANTHER HMM library and download PANTHER tools and data. PANTHER Pathway consists of over 176, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. Pathways are drawn using CellDesigner software, capturing molecular level events in both signaling and metabolic pathways, and can be exported in SBML format. The SBGN view of the diagram can also be exported. Pathway diagrams are interactive and include tools for visualizing gene expression data in the context of the diagrams.

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