Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions

Journal of Biomedical Semantics
Junguk HurYongqun He

Abstract

Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorporates interaction terms from the PSI Molecular Interactions (PSI-MI) and Gene Ontology (GO). Using INO-based literature mining results, a modified Fisher's exact test was established to analyze significantly over- and under-represented enriched gene-gene interaction types within a specific area. Such a strategy was applied to study the vaccine-mediated gene-gene interactions using all PubMed abstracts. The Vaccine Ontology (VO) and INO were used to support the retrieval of vaccine terms and interaction keywords from the literature. INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies. Current INO includes 540 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms with 'INO_' prefix. A new annotation property, '...Continue Reading

References

May 1, 1994·Vaccine·R T ChenS G Wassilak
Jul 12, 2003·Bioinformatics·J-D KimJ Tsujii
Oct 2, 2003·Genome Biology·Douglas A HosackRichard A Lempicki
Dec 17, 2009·Bioinformatics·Maureen A SartorGilbert S Omenn
Jun 24, 2010·BMC Research Notes·Zuoshuang XiangYongqun He
Jul 14, 2010·Journal of Biomedicine & Biotechnology·Arzucan OzgürYongqun He
Jun 1, 2011·Journal of Biomedical Semantics·Arzucan OzgürYongqun He
Nov 28, 2012·Nucleic Acids Research·Janna HastingsChristoph Steinbeck

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Citations

Dec 24, 2015·Frontiers in Microbiology·İlknur KaradenizArzucan Özgür
Jan 20, 2018·Journal of Biomedical Semantics·Nicolas MatentzogluRobert Stevens
Nov 22, 2017·The Plant Journal : for Cell and Molecular Biology·Ryan F McCormickJohn E Mullet
Dec 24, 2019·BMC Bioinformatics·Junguk HurYongqun He
Feb 27, 2016·Journal of Biomedical Semantics·Cui TaoSivaram Arabandi
Jan 13, 2017·Database : the Journal of Biological Databases and Curation·Ferhat AydınArzucan Özgür
Mar 16, 2017·Journal of Biomedical Semantics·Junguk HurYongqun He

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Software Mentioned

INO Foundry
VO
Ngram Statistics Package
PSI
Perl
Protégé
INO
MI
OntoFox
SPARQL

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