The representation of heart development in the gene ontology

An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the...

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Published in	Developmental biology Vol. 354; no. 1; pp. 9 - 17
Main Authors	Khodiyar, Varsha K., Hill, David P., Howe, Doug, Berardini, Tanya Z., Tweedie, Susan, Talmud, Philippa J., Breckenridge, Ross, Bhattarcharya, Shoumo, Riley, Paul, Scambler, Peter, Lovering, Ruth C.
Format	Journal Article
Language	English
Published	United States Elsevier Inc 01.06.2011
Subjects	Animals Annotation Cardiovascular cardiovascular diseases Cell Differentiation - genetics community development Computational Biology - methods data collection Databases, Genetic Development Gene Expression Profiling Gene Expression Regulation, Developmental Gene Ontology genes Genetic Predisposition to Disease Heart Heart - embryology Heart - growth & development Heart Diseases - genetics Heart Diseases - pathology Humans information retrieval microarray technology morphogenesis Myocardium - cytology Myocardium - metabolism proteomics research and development signal transduction Signal Transduction - genetics stem cells Vocabulary, Controlled Heart Development Cardiovascular Annotation Gene Ontology
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Abstract	An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development. This work also aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. ► The usefulness of high-throughput data depends on the ability to interpret it. ► Gene Ontology (GO) annotations are used to interpret high-throughput data. ► Understanding heart development is important in understanding heart disease. ► We have expanded the available GO terms for heart development from 12 to over 280. ► This dataset could improve interpretation of cardiovascular high-throughput data.
AbstractList	An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development and aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development. This work also aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development. This work also aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. ► The usefulness of high-throughput data depends on the ability to interpret it. ► Gene Ontology (GO) annotations are used to interpret high-throughput data. ► Understanding heart development is important in understanding heart disease. ► We have expanded the available GO terms for heart development from 12 to over 280. ► This dataset could improve interpretation of cardiovascular high-throughput data.
Author	Tweedie, Susan Riley, Paul Scambler, Peter Lovering, Ruth C. Breckenridge, Ross Hill, David P. Talmud, Philippa J. Bhattarcharya, Shoumo Howe, Doug Berardini, Tanya Z. Khodiyar, Varsha K.
AuthorAffiliation	c The Zebrafish Information Network, 5291 University of Oregon, Eugene, Oregon, USA ( dhowe@zfin.org ) d The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institute for Science, Stanford, California, USA ( tberardi@acoma.stanford.edu ) e FlyBase, Department of Genetics, University of Cambridge, UK ( sart2@gen.cam.ac.uk ) b Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine, USA ( dph@informatics.jax.org ) f Centre for Metabolism and Experimental Therapeutics, Rayne Institute, University College London, London, UK ( r.breckenridge@ucl.ac.uk ) a Cardiovascular GO Annotation Initiative, Centre for Cardiovascular Genetics, Rayne Institute, University College London, London, UK ( v.khodiyar@ucl.ac.uk ; p.talmud@ucl.ac.uk , r.lovering@ucl.ac.uk ) i Gene Ontology Consortium ( www.geneontology.org ) g Department of Cardiovascular Medicine & Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK ( shoumo@me.com ) h Universi
AuthorAffiliation_xml	– name: c The Zebrafish Information Network, 5291 University of Oregon, Eugene, Oregon, USA ( dhowe@zfin.org ) – name: g Department of Cardiovascular Medicine & Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK ( shoumo@me.com ) – name: h University College London-Institute of Child Health, Guilford St, London, UK ( p.riley@ich.ucl.ac.uk , p.scambler@ich.ucl.ac.uk ) – name: e FlyBase, Department of Genetics, University of Cambridge, UK ( sart2@gen.cam.ac.uk ) – name: a Cardiovascular GO Annotation Initiative, Centre for Cardiovascular Genetics, Rayne Institute, University College London, London, UK ( v.khodiyar@ucl.ac.uk ; p.talmud@ucl.ac.uk , r.lovering@ucl.ac.uk ) – name: b Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine, USA ( dph@informatics.jax.org ) – name: i Gene Ontology Consortium ( www.geneontology.org ) – name: f Centre for Metabolism and Experimental Therapeutics, Rayne Institute, University College London, London, UK ( r.breckenridge@ucl.ac.uk ) – name: d The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institute for Science, Stanford, California, USA ( tberardi@acoma.stanford.edu )
Author_xml	– sequence: 1 givenname: Varsha K. surname: Khodiyar fullname: Khodiyar, Varsha K. email: v.khodiyar@ucl.ac.uk organization: Cardiovascular GO Annotation Initiative, Centre for Cardiovascular Genetics, Rayne Institute, University College London, London, UK – sequence: 2 givenname: David P. surname: Hill fullname: Hill, David P. email: dph@informatics.jax.org organization: Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA – sequence: 3 givenname: Doug surname: Howe fullname: Howe, Doug email: dhowe@zfin.org organization: The Zebrafish Information Network, 5291 University of Oregon, Eugene, OR, USA – sequence: 4 givenname: Tanya Z. surname: Berardini fullname: Berardini, Tanya Z. email: tberardi@acoma.stanford.edu organization: The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, USA – sequence: 5 givenname: Susan surname: Tweedie fullname: Tweedie, Susan email: sart2@gen.cam.ac.uk organization: FlyBase, Department of Genetics, University of Cambridge, UK – sequence: 6 givenname: Philippa J. surname: Talmud fullname: Talmud, Philippa J. email: p.talmud@ucl.ac.uk organization: Cardiovascular GO Annotation Initiative, Centre for Cardiovascular Genetics, Rayne Institute, University College London, London, UK – sequence: 7 givenname: Ross surname: Breckenridge fullname: Breckenridge, Ross email: r.breckenridge@ucl.ac.uk organization: Centre for Metabolism and Experimental Therapeutics, Rayne Institute, University College London, London, UK – sequence: 8 givenname: Shoumo surname: Bhattarcharya fullname: Bhattarcharya, Shoumo email: shoumo@me.com organization: Department of Cardiovascular Medicine & Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK – sequence: 9 givenname: Paul surname: Riley fullname: Riley, Paul email: p.riley@ich.ucl.ac.uk organization: University College London-Institute of Child Health, Guilford St, London, UK – sequence: 10 givenname: Peter surname: Scambler fullname: Scambler, Peter email: p.scambler@ich.ucl.ac.uk organization: University College London-Institute of Child Health, Guilford St, London, UK – sequence: 11 givenname: Ruth C. surname: Lovering fullname: Lovering, Ruth C. email: r.lovering@ucl.ac.uk organization: Cardiovascular GO Annotation Initiative, Centre for Cardiovascular Genetics, Rayne Institute, University College London, London, UK
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Snippet	An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from...
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SubjectTerms	Animals Annotation Cardiovascular cardiovascular diseases Cell Differentiation - genetics community development Computational Biology - methods data collection Databases, Genetic Development Gene Expression Profiling Gene Expression Regulation, Developmental Gene Ontology genes Genetic Predisposition to Disease Heart Heart - embryology Heart - growth & development Heart Diseases - genetics Heart Diseases - pathology Humans information retrieval microarray technology morphogenesis Myocardium - cytology Myocardium - metabolism proteomics research and development signal transduction Signal Transduction - genetics stem cells Vocabulary, Controlled
Title	The representation of heart development in the gene ontology
URI	https://dx.doi.org/10.1016/j.ydbio.2011.03.011 https://www.ncbi.nlm.nih.gov/pubmed/21419760 https://search.proquest.com/docview/865694958 https://search.proquest.com/docview/904469588 https://pubmed.ncbi.nlm.nih.gov/PMC3302178
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