Incorporation of ontology-driven biological knowledge into cardiovascular genomics

Huiru Zheng, Haiying Wang, Francisco Azuaje

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    This study presents a system that enables the incorporation of similarity knowledge extracted from the Cardiovascular Gene Ontology (CGO) into cardiovascular research. The implementation of the system is based on the combination of biological function annotations provided by the CGO for more than 4000 genes associated with cardiovascular processes and topological features encoded in the Gene Ontology (GO). Using cardiovascular-related annotations provided by CGO, term-term similarity within each of the GO hierarchies, i.e., molecular function, biological process and cellular component, is computed using three GO-driven similarity measures (Resnik's, Lin's and Jiang's metrics). These provide the foundation for the estimation of semantic similarity between cardiovascular-associated genes. The system allows users to retrieve between-gene similarity using a single query or batch query mode. This study contributes to the development of automated methods for supporting annotation tasks, such as the generation of new annotations for partially-characterized genes associated with cardiovascular disease.

    LanguageEnglish
    Title of host publicationComputing in Cardiology 2011, CinC 2011
    Pages565-568
    Number of pages4
    Volume38
    Publication statusPublished - 1 Dec 2011
    EventComputing in Cardiology 2011, CinC 2011 - Hangzhou, China
    Duration: 18 Sep 201121 Sep 2011

    Conference

    ConferenceComputing in Cardiology 2011, CinC 2011
    CountryChina
    CityHangzhou
    Period18/09/1121/09/11

    Fingerprint

    Biological Ontologies
    Gene Ontology
    Genomics
    Ontology
    Genes
    Biological Phenomena
    Semantics
    Cardiovascular Diseases
    Research

    Cite this

    Zheng, H., Wang, H., & Azuaje, F. (2011). Incorporation of ontology-driven biological knowledge into cardiovascular genomics. In Computing in Cardiology 2011, CinC 2011 (Vol. 38, pp. 565-568). [6164628]
    Zheng, Huiru ; Wang, Haiying ; Azuaje, Francisco. / Incorporation of ontology-driven biological knowledge into cardiovascular genomics. Computing in Cardiology 2011, CinC 2011. Vol. 38 2011. pp. 565-568
    @inproceedings{94768971d8134342b5cb1b87d559127c,
    title = "Incorporation of ontology-driven biological knowledge into cardiovascular genomics",
    abstract = "This study presents a system that enables the incorporation of similarity knowledge extracted from the Cardiovascular Gene Ontology (CGO) into cardiovascular research. The implementation of the system is based on the combination of biological function annotations provided by the CGO for more than 4000 genes associated with cardiovascular processes and topological features encoded in the Gene Ontology (GO). Using cardiovascular-related annotations provided by CGO, term-term similarity within each of the GO hierarchies, i.e., molecular function, biological process and cellular component, is computed using three GO-driven similarity measures (Resnik's, Lin's and Jiang's metrics). These provide the foundation for the estimation of semantic similarity between cardiovascular-associated genes. The system allows users to retrieve between-gene similarity using a single query or batch query mode. This study contributes to the development of automated methods for supporting annotation tasks, such as the generation of new annotations for partially-characterized genes associated with cardiovascular disease.",
    author = "Huiru Zheng and Haiying Wang and Francisco Azuaje",
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    day = "1",
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    Zheng, H, Wang, H & Azuaje, F 2011, Incorporation of ontology-driven biological knowledge into cardiovascular genomics. in Computing in Cardiology 2011, CinC 2011. vol. 38, 6164628, pp. 565-568, Computing in Cardiology 2011, CinC 2011, Hangzhou, China, 18/09/11.

    Incorporation of ontology-driven biological knowledge into cardiovascular genomics. / Zheng, Huiru; Wang, Haiying; Azuaje, Francisco.

    Computing in Cardiology 2011, CinC 2011. Vol. 38 2011. p. 565-568 6164628.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

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    Zheng H, Wang H, Azuaje F. Incorporation of ontology-driven biological knowledge into cardiovascular genomics. In Computing in Cardiology 2011, CinC 2011. Vol. 38. 2011. p. 565-568. 6164628