The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis

Judith A. Blake1, Midori A. Harris2

1 The Jackson Laboratory, Bar Harbor, Maine, 2 EMBL‐EBI, Wellcome Trust Genome Campus, Cambridge, United Kingdom
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 7.2
DOI:  10.1002/0471250953.bi0702s23
Online Posting Date:  September, 2008
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Abstract

Scientists wishing to utilize genomic data have quickly come to realize the benefit of standardizing descriptions of experimental procedures and results for computer‐driven information retrieval systems. The focus of the Gene Ontology project is three‐fold. First, the project goal is to compile the Gene Ontologies: structured vocabularies describing domains of molecular biology. Second, the project supports the use of these structured vocabularies in the annotation of gene products. Third, the gene product‐to‐GO annotation sets are provided by participating groups to the public through open access to the GO database and Web resource. This unit describes the current ontologies and what is beyond the scope of the Gene Ontology project. It addresses the issue of how GO vocabularies are constructed and related to genes and gene products. It concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research. Curr. Protoc. Bioinform. 23:7.2.1‐7.2.9. © 2008 by John Wiley & Sons, Inc.

Keywords: Gene Ontology; functional annotation; bioOntology

     
 
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Table of Contents

  • Introduction
  • What are Ontologies and Why do We Need Them?
  • What is the Gene Ontology (GO) Consortium?
  • What are the Objectives of the GO Project?
  • What are the Current Ontologies Supported by the GO Project?
  • Why Does the GO Project Refer to Gene Products?
  • What is Beyond the Scope of the GO Project?
  • How are GO Vocabularies Constructed?
  • How Do GO Vocabularies Relate to Other Resources Such as the InterPro?
  • How are Genes and Gene Products Associated with GO Terms?
  • How Do I Browse GO and Find GO Annotations for “My” Genes?
  • Can I Download GO?
  • Where Can I Access and/or Obtain the Complete Gene Product/GO Association Sets?
  • Where Can I Find GO Annotations for Transcripts and Sequences?
  • How Can GO Be Used in Genome and Expression Analysis?
  • How Can I Suggest Additional Terms or Contribute to the GO Project?
  • Summary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Baker, P.G., Goble, C.A., Bechhofer, S., Paton, N.W., Stevens, R., and Brass, A. 1999. An ontology for bioinformatics applications. Bioinformatics 15: 510‐520.
   Bard, J. and Winter, R. 2001. Ontologies of developmental anatomy: Their current and future roles. Brief. Bioinformatics 2: 289‐299.
   Eilbeck, K., Lewis, S.E., Mungall, C.J., Yandell, M., Stein, L., Durbin, R., and Ashburner, M. 2005. The Sequence Ontology: A tool for the unification of genome annotations. Genome Biol. 6: R44.
   The Gene Ontology Consortium. 2000. Gene Ontology: Tool for the unification of biology. Nat. Genet. 25: 25‐29.
   The Gene Ontology Consortium. 2001. Creating the gene ontology resource: Design and implementation. Genome Res. 11: 1425‐1433.
   The Gene Ontology Consortium. 2008. The Gene Ontology Project in 2008. Nucleic Acids Res. 36 (Database issue): D440‐D444.
   GO. 2004. The OBO Flat File Format Specification. Version 1.2 available at http://www.geneontology.org/GO.format.obo‐1_2.shtml.
   Gruber, T.R. 1993. A translational approach to portable ontologies. Know Acq. 5: 199‐220.
   Horrocks, I., Patel‐Schneider, P.F., and van Harmelen, F. 2003. From SHIQ and RDF to OWL: The Making of a Web Ontology Language.Web Semant. 1: 7‐26.
   Jones, D.M. and Paton, R.C. 1999. Toward principles for the representation of hierarchical knowledge in formal ontologies. Data Knowl. Eng. 31: 102‐105.
   Karp, P.D., Riley, M., Paley, S.M., Pellegrini‐Toole, A., and Krummenacker, M. 1999. Eco Cyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 27: 55‐58.
   Quackenbush, J. 2001. Expression Profiler: A suite of Web‐based tools for the analysis of microarray gene expression data. Brief. Bioinform. 2: 388‐404.
   The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. 2001. Functional annotation of a full‐length mouse cDNA collection. Nature 409: 685‐690.
   Riley, M. 1993. Functions of the gene products of Escherichia coli. Microbiol. Rev. 57: 862‐952.
   Riley, M. 1998. Systems for categorizing functions of gene products. Curr. Opin. Struct. Biol. 8: 388‐392.
   Schulze‐Kremer, S. 1998. Ontologies for molecular biology. Pacific Symp. Biocomput. 3: 695‐706.
   Sklyar, N. 2001. Survey of existing Bio‐ontologies. Technical Report 5/2001, Department of Computer Science, University of Leipzig, Germany.
   Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., and Rosse, C. 2005. Relations in biomedical ontologies. Genome Biol. 6: R46.
   Stevens, R., Goble, C.A., and Bechhofer, S. 2000. Ontology‐based knowledge representation for bioinformatics. Brief. Bioinform. 1: 398‐414.
Internet Resources
  http://www.nlm.nih.gov/research/umls/
  UMLS Unified Medical Language System.
  http://www.geneontology.org/
  The Gene Ontology Web site.
  http://www.mged.sourceforge.net/ontologies/
  The Microarray Gene Expression Data (MGED) Society Ontology Working Group (OWG) Web site.
   http://dol.uni‐leipzig.de/pub/2001‐30/en
  A survey of existing bio‐ontologies (Sklyar, ).
   http://www.w3.org/TR/owl‐guide
  OWL Web Ontology Language Guide.
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