What's in a genotype?

An ontological characterization for integration of genetic variation data

Matthew H. Brush, Chris Mungall, Nicole Washington, Melissa Haendel

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

4 Citations (Scopus)

Abstract

Exploration of the mechanistic basis of biology and disease has long leveraged the concept of a genotype, which represents the genetic composition associated with a physical trait. Translational research efforts rely increasingly on the ability to integrate genotype-phenotype data across systems and organism communities, but are hindered by the lack of a shared, computable model of the information coded into genotype representations. Here, we present the efforts of the Monarch Initiative to build GENO, an ontological model of genotype information. The Monarch Initiative is a collaborative effort to integrate data from diverse resources to leverage model systems for disease research based on their phenotypes. The genotype model we have developed is based on decomposing the different types of information represented in a genotype, is interoperable with existing OBO Foundry ontologies, and utilizes modeling from orthogonal ontologies to describe a broad range of attributes of these sequences. We describe the features and utility of such an approach toward the integration of diverse genotype data with a broad spectrum of related biomedical data. Copyright

Original languageEnglish (US)
Title of host publicationICBO 2013 - Proceedings of the 4th International Conference on Biomedical Ontology 2013
PublisherCEUR-WS
Pages105-108
Number of pages4
Volume1060
StatePublished - 2013
Event4th International Conference on Biomedical Ontology, ICBO 2013 - Montreal, Canada
Duration: Jul 7 2013Jul 12 2013

Other

Other4th International Conference on Biomedical Ontology, ICBO 2013
CountryCanada
CityMontreal
Period7/7/137/12/13

Fingerprint

Ontology
Foundries
Computer simulation
Chemical analysis

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Brush, M. H., Mungall, C., Washington, N., & Haendel, M. (2013). What's in a genotype? An ontological characterization for integration of genetic variation data. In ICBO 2013 - Proceedings of the 4th International Conference on Biomedical Ontology 2013 (Vol. 1060, pp. 105-108). CEUR-WS.

What's in a genotype? An ontological characterization for integration of genetic variation data. / Brush, Matthew H.; Mungall, Chris; Washington, Nicole; Haendel, Melissa.

ICBO 2013 - Proceedings of the 4th International Conference on Biomedical Ontology 2013. Vol. 1060 CEUR-WS, 2013. p. 105-108.

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

Brush, MH, Mungall, C, Washington, N & Haendel, M 2013, What's in a genotype? An ontological characterization for integration of genetic variation data. in ICBO 2013 - Proceedings of the 4th International Conference on Biomedical Ontology 2013. vol. 1060, CEUR-WS, pp. 105-108, 4th International Conference on Biomedical Ontology, ICBO 2013, Montreal, Canada, 7/7/13.
Brush MH, Mungall C, Washington N, Haendel M. What's in a genotype? An ontological characterization for integration of genetic variation data. In ICBO 2013 - Proceedings of the 4th International Conference on Biomedical Ontology 2013. Vol. 1060. CEUR-WS. 2013. p. 105-108
Brush, Matthew H. ; Mungall, Chris ; Washington, Nicole ; Haendel, Melissa. / What's in a genotype? An ontological characterization for integration of genetic variation data. ICBO 2013 - Proceedings of the 4th International Conference on Biomedical Ontology 2013. Vol. 1060 CEUR-WS, 2013. pp. 105-108
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