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Gene Ontology Consortium And GO Database. Gene Ontology: tool for the unification of biology

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Gene Ontology Consortium And GO Database

Gene Ontology: tool for the unification of biology

M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig, M A Harris, D P Hill, L Issel-Tarver, A Kasarskis, S Lewis, J C Matese, J E Richardson, M Ringwald, G M Rubin & G Sherlock

Nature Genetics 25, 25 - 29 (2000).

http://www.geneontology.org

http://www.godatabase.org

http://www.geneontology.org/GO.contents.doc.shtml

The Open Biomedical Ontology (OBO)

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The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary (GO term) that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.

Go Database: lists of the genes or gene products associated with their particular GO terms, their links to the gene-association files for each of the collaborating databases is available.

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The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in a species-independent manner with three kinds of terms:

  • biological processes
  • cellular components
  • molecular functions
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Data Component of GO Database

http://www.geneontology.org/GO.current.annotations.shtml

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How to Search Genes in GO?

  • Go Terms
  • Gene Symbol or Name
  • FASTA Search
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What The Search Result Includes?

  • Go Terms And GO ID
  • Sequence And Basic Sequence Information
  • Original Database And Detailed Annotation(Evidence)
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Main Resource in GO Website

  • Go Database
  • On Line Query
  • Tools (Consortium and Non-Consortium)
  • Documents and tutorial
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Available Format of Go Database

  • TXT Format
  • XML Format
  • MySQL Format
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What are the possible uses of GO?

* integrating proteomic information from different organisms;

* assigning functions to protein domains;

* finding functional similarities in genes that are overexpressed or underexpressed in diseases and as we age;

* predicting the likelihood that a particular gene is involved in diseases that haven't yet been mapped to specific genes;

* analysing groups of genes that are co-expressed during development;

* developing automated ways of deriving information about gene function from the literature;

* verifying models of genetic, metabolic and product interaction networks.

kegg kyoto encyclopedia of genes and genomes
KEGG(Kyoto Encyclopedia of Genes and Genomes 京都基因与基因组百科全书)

KEGG(Kyoto Encyclopedia of Genes and Genomes)是系统分析基因功能、基因组信息数据库,它有助于研究者把基因及表达信息作为一个整体网络进行研究。基因组信息存储在GENES数据库里,包括完整和部分测序的基因组序列;更高级的功能信息存储在PATHWAY数据库里,包括图解的细胞生化过程如代谢、膜转运、信号传递、细胞周期,还包括同系保守的子通路等信息;KEGG的另一个数据库是LIGAND,包含关于化学物质、酶分子、酶反应等信息。可以免费获取。KEGG提供的整合代谢途径(pathway)查询十分出色,包括碳水化合物、核苷、氨基酸等的代谢及有机物的生物降解,不仅提供了所有可能的代谢途径,而且对催化各步反应的酶进行了全面的注解,包含有氨基酸序列、PDB库的链接等等。KEGG是进行生物体内代谢分析、代谢网络研究的强有力工具。