Integrating phenotype ontologies across multiple species

Christopher J. Mungall; Georgios V. Gkoutos; Cynthia L. Smith; Melissa A. Haendel; Suzanna E. Lewis; Michael Ashburner

doi:10.1186/gb-2010-11-1-r2

Integrating phenotype ontologies across multiple species

Christopher J. Mungall, Georgios V. Gkoutos, Cynthia L. Smith, Melissa A. Haendel, Suzanna E. Lewis, Michael Ashburner

Research output: Contribution to journal › Article › peer-review

226 Scopus citations

Abstract

Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology.

Original language	English (US)
Article number	r2
Journal	Genome biology
Volume	11
Issue number	1
DOIs	https://doi.org/10.1186/gb-2010-11-1-r2
State	Published - Jan 8 2010
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2010-11-1-r2

Cite this

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abstract = "Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology.",

author = "Mungall, {Christopher J.} and Gkoutos, {Georgios V.} and Smith, {Cynthia L.} and Haendel, {Melissa A.} and Lewis, {Suzanna E.} and Michael Ashburner",

note = "Funding Information: CJM, GG, MAH, MA and SEL were funded by NIH grant U54 HG004028. CJM and SEL were also funded by NIH grant [BIRN number here]. CLS was funded by NHGRI/NIH grant HG000330. GG and MAH were also funded by BBSRC grant [BG/G004358/1]. Many thanks to Nicole Washington for comments on the manuscript. We would also like to thank the two anonymous reviewers who provided helpful comments for improvement.",

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AU - Mungall, Christopher J.

AU - Gkoutos, Georgios V.

AU - Smith, Cynthia L.

AU - Haendel, Melissa A.

AU - Lewis, Suzanna E.

AU - Ashburner, Michael

N1 - Funding Information: CJM, GG, MAH, MA and SEL were funded by NIH grant U54 HG004028. CJM and SEL were also funded by NIH grant [BIRN number here]. CLS was funded by NHGRI/NIH grant HG000330. GG and MAH were also funded by BBSRC grant [BG/G004358/1]. Many thanks to Nicole Washington for comments on the manuscript. We would also like to thank the two anonymous reviewers who provided helpful comments for improvement.

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N2 - Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology.

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Integrating phenotype ontologies across multiple species

Abstract

ASJC Scopus subject areas

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