Analysis of vaccine-related networks using semantic medline and the vaccine ontology

Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang D Liu

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

Abstract

A major challenge in the vaccine research has been to identify important vaccine-related networks and logically explain the results. In this paper, we showed that networkbased analysis of vaccine-related networks can discover the underlying structure information consistent with that captured by the Vaccine Ontology and propose new hypotheses for vaccine disease or gene associations. First, a vaccine-vaccine network was inferred using a bipartite network projection strategy on the vaccine-disease network extracted from the Semantic MEDLINE database. In total, 76 vaccines and 573 relationships were identified to construct the vaccine network. The shortest paths between all pairs of vaccines were calculated within the vaccine network. The correlation between the shortest paths of vaccine pairs and their semantic similarities in the Vaccine Ontology was then investigated. Second, a vaccinegene network was also constructed, in which several important vaccine-related genes were identified. This study demonstrated that a combinatorial analysis using literature knowledgebase, semantic technology, and ontology is able to reveal unidentified important knowledge critical to biomedical research and public health and generate testable hypotheses for future experimental verification.

Original languageEnglish (US)
Title of host publicationCEUR Workshop Proceedings
PublisherCEUR-WS
Volume1061
StatePublished - 2013
Event4th International Conference on Biomedical Ontology, ICBO 2013 Workshops on International Workshop on Vaccine and Drug Ontology Studies, VDOS 2013 and International Workshop on Definitions in Ontologies, DO 2013 - Part of the Semantic Trilogy 2013 - Montreal, Canada
Duration: Jul 6 2013Jul 12 2013

Other

Other4th International Conference on Biomedical Ontology, ICBO 2013 Workshops on International Workshop on Vaccine and Drug Ontology Studies, VDOS 2013 and International Workshop on Definitions in Ontologies, DO 2013 - Part of the Semantic Trilogy 2013
CountryCanada
CityMontreal
Period7/6/137/12/13

Fingerprint

Vaccines
Ontology
Semantics
Genes
Public health

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Zhang, Y., Tao, C., He, Y., Kanjamala, P., & Liu, H. D. (2013). Analysis of vaccine-related networks using semantic medline and the vaccine ontology. In CEUR Workshop Proceedings (Vol. 1061). CEUR-WS.

Analysis of vaccine-related networks using semantic medline and the vaccine ontology. / Zhang, Yuji; Tao, Cui; He, Yongqun; Kanjamala, Pradip; Liu, Hongfang D.

CEUR Workshop Proceedings. Vol. 1061 CEUR-WS, 2013.

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

Zhang, Y, Tao, C, He, Y, Kanjamala, P & Liu, HD 2013, Analysis of vaccine-related networks using semantic medline and the vaccine ontology. in CEUR Workshop Proceedings. vol. 1061, CEUR-WS, 4th International Conference on Biomedical Ontology, ICBO 2013 Workshops on International Workshop on Vaccine and Drug Ontology Studies, VDOS 2013 and International Workshop on Definitions in Ontologies, DO 2013 - Part of the Semantic Trilogy 2013, Montreal, Canada, 7/6/13.
Zhang Y, Tao C, He Y, Kanjamala P, Liu HD. Analysis of vaccine-related networks using semantic medline and the vaccine ontology. In CEUR Workshop Proceedings. Vol. 1061. CEUR-WS. 2013
Zhang, Yuji ; Tao, Cui ; He, Yongqun ; Kanjamala, Pradip ; Liu, Hongfang D. / Analysis of vaccine-related networks using semantic medline and the vaccine ontology. CEUR Workshop Proceedings. Vol. 1061 CEUR-WS, 2013.
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