article

Querying multiple bioinformatics information sources: can semantic web research help?

Authors:

Matthew Coleman,

Terence Critchlow,

Li XiongAuthors Info & Claims

ACM SIGMOD Record, Volume 31, Issue 4

Pages 59 - 64

https://doi.org/10.1145/637411.637421

Published: 01 December 2002 Publication History

Abstract

Advances in Semantic Web and Ontologies have pushed the role of semantics to a new frontier: Semantic Composition of Web Services. A good example of such compositions is the querying of multiple bioinformatics data sources. Supporting effective querying over a large collection of bioinformatics data sources presents a number of unique challenges. First, queries over bioinformatics data sources are often complex associative queries over multiple Web documents. Most associations are defined by string matching of textual fragments in two documents. Second, most of the queries required by Genomics researchers involve complex data extraction, and sophisticated workflows that implement the complex associative access. Third but not the least, complex Genomics-specific queries are often reused many times by Genomics researchers, either directly or through some refinements, and are considered as a part of the research results by Genomics researchers. In this short article we present a list of challenging issues in supporting effective querying over bioinformatics data sources and illustrate them through a selection of representative search scenarios provided by biologists. We end the article with a discussion on how the state-of-art research and technological development in Semantic Web, Ontology, Internet Data Management, and Internet Computing Systems can help addressing these issues.

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Cited By

Djokic-Petrovic MCvjetkovic VYang JZivanovic MWild D(2017)PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasetsJournal of Biomedical Semantics10.1186/s13326-017-0151-z8:1Online publication date: 20-Sep-2017
https://doi.org/10.1186/s13326-017-0151-z
Shaban-Nejad AHaarslev V(2015)Managing changes in distributed biomedical ontologies using hierarchical distributed graph transformationInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2015.06633411:1(53-83)Online publication date: 1-Dec-2015
https://dl.acm.org/doi/10.1504/IJDMB.2015.066334
Dhillon SSidhu ADhillon SSidhu A(2013)IntroductionData Intensive Computing for Biodiversity10.1007/978-3-642-38047-1_1(1-6)Online publication date: 1-Jun-2013
https://doi.org/10.1007/978-3-642-38047-1_1
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Querying multiple bioinformatics information sources: can semantic web research help?
1. Applied computing
  1. Life and medical sciences
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Published In

cover image ACM SIGMOD Record

ACM SIGMOD Record Volume 31, Issue 4

December 2002

104 pages

ISSN:0163-5808

DOI:10.1145/637411

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Copyright © 2002 Authors.

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Association for Computing Machinery

New York, NY, United States

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Published: 01 December 2002

Published in SIGMOD Volume 31, Issue 4

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Cited By

Djokic-Petrovic MCvjetkovic VYang JZivanovic MWild D(2017)PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasetsJournal of Biomedical Semantics10.1186/s13326-017-0151-z8:1Online publication date: 20-Sep-2017
https://doi.org/10.1186/s13326-017-0151-z
Shaban-Nejad AHaarslev V(2015)Managing changes in distributed biomedical ontologies using hierarchical distributed graph transformationInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2015.06633411:1(53-83)Online publication date: 1-Dec-2015
https://dl.acm.org/doi/10.1504/IJDMB.2015.066334
Dhillon SSidhu ADhillon SSidhu A(2013)IntroductionData Intensive Computing for Biodiversity10.1007/978-3-642-38047-1_1(1-6)Online publication date: 1-Jun-2013
https://doi.org/10.1007/978-3-642-38047-1_1
Dhillon SPaunoo BSidhu A(2013)Framework for Biodiversity Information Retrieval in MalaysiaAdvances in Biomedical Infrastructure 201310.1007/978-3-642-37137-0_4(15-24)Online publication date: 2013
https://doi.org/10.1007/978-3-642-37137-0_4
Ram SLaxman Rao N(2012) i BIRA – integrated bioinformatics information resource access Reference Services Review10.1108/0090732121122835440:2(326-343)Online publication date: 11-May-2012
https://doi.org/10.1108/00907321211228354
Marrakchi KBriache AKerzazi ANavas-Delgado IAldana-Montes JEttayebi MLairini KHassani B(2010)A data warehouse approach to semantic integration of pseudomonas dataProceedings of the 7th international conference on Data integration in the life sciences10.5555/1884477.1884488(90-105)Online publication date: 25-Aug-2010
https://dl.acm.org/doi/10.5555/1884477.1884488
Marrakchi KBriache AKerzazi ANavas-Delgado IAldana-Montes JEttayebi MLairini KRossi Hassani B(2010)A Data Warehouse Approach to Semantic Integration of Pseudomonas DataData Integration in the Life Sciences10.1007/978-3-642-15120-0_8(90-105)Online publication date: 2010
https://doi.org/10.1007/978-3-642-15120-0_8
Shaban-Nejad AHaarslev V(2009)Bio-medical Ontologies Maintenance and Change ManagementBiomedical Data and Applications10.1007/978-3-642-02193-0_6(143-168)Online publication date: 2009
https://doi.org/10.1007/978-3-642-02193-0_6
Koutkias VMalousi AMaglaveras N(2007)Engineering agent-mediated integration of bioinformatics analysis toolsMultiagent and Grid Systems10.5555/1375358.13753653:2(245-258)Online publication date: 1-Apr-2007
https://dl.acm.org/doi/10.5555/1375358.1375365
Digiampietri LPerez-Alcazar JMedeiros C(2007)An ontology-based framework for bioinformatics workflowsInternational Journal of Bioinformatics Research and Applications10.1504/IJBRA.2007.0150033:3(268-285)Online publication date: 1-Sep-2007
https://dl.acm.org/doi/10.1504/IJBRA.2007.015003
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