The Mammalian Phenotype Ontology As a Tool for Annotating, Analyzing and Comparing Phenotypic Information

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2005 Jan 12

PMID 15642099

Citations 226

Authors

Cynthia L Smith

Carroll-Ann W Goldsmith

Janan T Eppig

Affiliations

Soon will be listed here.

Abstract

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data.

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References

Hayamizu T, Mangan M, Corradi J, Kadin J, Ringwald M . The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol. 2005; 6(3):R29. PMC: 1088948. DOI: 10.1186/gb-2005-6-3-r29. View

Bult C, Blake J, Richardson J, Kadin J, Eppig J, Baldarelli R . The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res. 2003; 32(Database issue):D476-81. PMC: 308859. DOI: 10.1093/nar/gkh125. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Eppig J . Algorithms for mutant sorting: the need for phenotype vocabularies. Mamm Genome. 2000; 11(7):584-9. DOI: 10.1007/s003350010111. View

Bard J, Kaufman M, Dubreuil C, Brune R, Burger A, Baldock R . An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech Dev. 1998; 74(1-2):111-20. DOI: 10.1016/s0925-4773(98)00069-0. View

Nadeau J, Balling R, Barsh G, Beier D, Brown S, Bucan M . Sequence interpretation. Functional annotation of mouse genome sequences. Science. 2001; 291(5507):1251-5. DOI: 10.1126/science.1058244. View

Gkoutos G, Green E, Mallon A, Hancock J, Davidson D . Using ontologies to describe mouse phenotypes. Genome Biol. 2005; 6(1):R8. PMC: 549069. DOI: 10.1186/gb-2004-6-1-r8. View

. Creating the gene ontology resource: design and implementation. Genome Res. 2001; 11(8):1425-33. PMC: 311077. DOI: 10.1101/gr.180801. View

Harris M, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R . The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2003; 32(Database issue):D258-61. PMC: 308770. DOI: 10.1093/nar/gkh036. View

10.

Schofield P, Bard J, Booth C, Boniver J, Covelli V, Delvenne P . Pathbase: a database of mutant mouse pathology. Nucleic Acids Res. 2003; 32(Database issue):D512-5. PMC: 308858. DOI: 10.1093/nar/gkh124. View

11.

Hill D, Begley D, Finger J, Hayamizu T, McCright I, Smith C . The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res. 2003; 32(Database issue):D568-71. PMC: 308803. DOI: 10.1093/nar/gkh069. View

12.

Austin C, Battey J, Bradley A, Bucan M, Capecchi M, Collins F . The knockout mouse project. Nat Genet. 2004; 36(9):921-4. PMC: 2716027. DOI: 10.1038/ng0904-921. View

13.

Auwerx J, Avner P, Baldock R, Ballabio A, Balling R, Barbacid M . The European dimension for the mouse genome mutagenesis program. Nat Genet. 2004; 36(9):925-7. PMC: 2716028. DOI: 10.1038/ng0904-925. View

14.

Hill D, Davis A, Richardson J, Corradi J, Ringwald M, Eppig J . Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. Genomics. 2001; 74(1):121-8. DOI: 10.1006/geno.2001.6513. View