GSO: A semantic web ontology to capture 3D genome structure

W. Jim Zheng, Jingcheng Du, Jijun Tang, Cui Tao

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

Abstract

More and more evidences indicate that the 3D conformation of eukaryotic genome plays important functional role in the cell. While extensive experimental investigations have been performed to study such structurefunction relationships using techniques such as Hi-C methods, there is no data standard to capture the 3D conformation of the genome. In previous work, we have developed an object-oriented framework, Genome3D, to integrate, model and visualize human genome in 3-dimension. We report here about a high level ontology, Genome Structure Ontology (GSO), to capture the 3D conformation of eukaryotic genome. GSO captures the structural organization of eukaryotic genome at levels ranging from chromosome, to 30nm fiber, to nucleosome and then to the atomic level of DNA. We believe such ontology could play a significant role in annotating, analyzing and describing molecular data for the 3D conformation of eukaryotic genome.

Original languageEnglish (US)
Title of host publicationCEUR Workshop Proceedings
PublisherCEUR-WS
Volume1320
StatePublished - 2014
Externally publishedYes
Event7th International Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2014 - Berlin, Germany
Duration: Dec 9 2014Dec 11 2014

Other

Other7th International Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2014
CountryGermany
CityBerlin
Period12/9/1412/11/14

Fingerprint

Semantic Web
Ontology
Genes
Conformations
Chromosomes
DNA
Fibers

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Zheng, W. J., Du, J., Tang, J., & Tao, C. (2014). GSO: A semantic web ontology to capture 3D genome structure. In CEUR Workshop Proceedings (Vol. 1320). CEUR-WS.

GSO : A semantic web ontology to capture 3D genome structure. / Zheng, W. Jim; Du, Jingcheng; Tang, Jijun; Tao, Cui.

CEUR Workshop Proceedings. Vol. 1320 CEUR-WS, 2014.

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

Zheng, WJ, Du, J, Tang, J & Tao, C 2014, GSO: A semantic web ontology to capture 3D genome structure. in CEUR Workshop Proceedings. vol. 1320, CEUR-WS, 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2014, Berlin, Germany, 12/9/14.
Zheng WJ, Du J, Tang J, Tao C. GSO: A semantic web ontology to capture 3D genome structure. In CEUR Workshop Proceedings. Vol. 1320. CEUR-WS. 2014
Zheng, W. Jim ; Du, Jingcheng ; Tang, Jijun ; Tao, Cui. / GSO : A semantic web ontology to capture 3D genome structure. CEUR Workshop Proceedings. Vol. 1320 CEUR-WS, 2014.
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