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Article: Biosphere: The interoperation of web services in microarray cluster analysis

TitleBiosphere: The interoperation of web services in microarray cluster analysis
Authors
Issue Date2004
PublisherAdis International Ltd. The Journal's web site is located at http://bioinformatics.adisonline.com/
Citation
Applied Bioinformatics, 2004, v. 3 n. 4, p. 253-256 How to Cite?
AbstractThe growing use of DNA microarrays in biomedical research has led to the proliferation of analysis tools. These software programs address different aspects of analysis (e.g. normalisation and clustering within and across individual arrays) as well as extended analysis methods (e.g. clustering, annotation and mining of multiple datasets). Therefore, microarray data analysis typically requires the interoperability of multiple software programs involving different analysis types and methods. Such interoperation is often hampered by the heterogeneity inherent in the software tools (which may function by implementing different interfaces and using different programming languages). To address this problem, we employed the simple object access protocol (SOAP)-based web service approach that provides a uniform programmatic interface to these heterogeneous software components. To demonstrate this approach in the microarray context, we created a web server application, Biosphere, which interoperates a number of web services that are geographically widely distributed. These web services include a clustering web service, which is a suite of different clustering algorithms for analysing microarray data; XEMBL, developed at the European Bioinformatics Institute (EBI) for retrieving EMBL Nucleotide Sequence Database sequence data; and three gene annotation web services: GetGO, GetHAPI and GetUMLS. GetGO allows retrieval of Gene Ontology™ (GO) annotation, and the other two web services retrieve annotation from the biomedical literature that is indexed based on the Medical Subject Headings (MeSH®) terms. With these web services, Biosphere allows the users to do the following: (i) cluster gene expression data using seven different algorithms; (ii) visualise the clustering results that are grouped statistically in colour; and (iii) retrieve sequence, annotation and citation data for the genes of interest. Availability: Biosphere and its web services described in Web Service Description Language (WSDL) can be accessed at http://rook.cecid.hku.hk:8280/BiosphereServer. Contact: Kei-Hoi Cheung (kei.cheung@yale.edu). © 2004 Adis Data Information BV. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/89076
ISSN
2009 SCImago Journal Rankings: 0.660
References

 

DC FieldValueLanguage
dc.contributor.authorCheung, KHen_HK
dc.contributor.authorDe Knikker, Ren_HK
dc.contributor.authorGuo, Yen_HK
dc.contributor.authorZhong, Gen_HK
dc.contributor.authorHager, Jen_HK
dc.contributor.authorYip, KYen_HK
dc.contributor.authorKwan, AKHen_HK
dc.contributor.authorLi, Pen_HK
dc.contributor.authorCheung, DWen_HK
dc.date.accessioned2010-09-06T09:52:05Z-
dc.date.available2010-09-06T09:52:05Z-
dc.date.issued2004en_HK
dc.identifier.citationApplied Bioinformatics, 2004, v. 3 n. 4, p. 253-256en_HK
dc.identifier.issn1175-5636en_HK
dc.identifier.urihttp://hdl.handle.net/10722/89076-
dc.description.abstractThe growing use of DNA microarrays in biomedical research has led to the proliferation of analysis tools. These software programs address different aspects of analysis (e.g. normalisation and clustering within and across individual arrays) as well as extended analysis methods (e.g. clustering, annotation and mining of multiple datasets). Therefore, microarray data analysis typically requires the interoperability of multiple software programs involving different analysis types and methods. Such interoperation is often hampered by the heterogeneity inherent in the software tools (which may function by implementing different interfaces and using different programming languages). To address this problem, we employed the simple object access protocol (SOAP)-based web service approach that provides a uniform programmatic interface to these heterogeneous software components. To demonstrate this approach in the microarray context, we created a web server application, Biosphere, which interoperates a number of web services that are geographically widely distributed. These web services include a clustering web service, which is a suite of different clustering algorithms for analysing microarray data; XEMBL, developed at the European Bioinformatics Institute (EBI) for retrieving EMBL Nucleotide Sequence Database sequence data; and three gene annotation web services: GetGO, GetHAPI and GetUMLS. GetGO allows retrieval of Gene Ontology™ (GO) annotation, and the other two web services retrieve annotation from the biomedical literature that is indexed based on the Medical Subject Headings (MeSH®) terms. With these web services, Biosphere allows the users to do the following: (i) cluster gene expression data using seven different algorithms; (ii) visualise the clustering results that are grouped statistically in colour; and (iii) retrieve sequence, annotation and citation data for the genes of interest. Availability: Biosphere and its web services described in Web Service Description Language (WSDL) can be accessed at http://rook.cecid.hku.hk:8280/BiosphereServer. Contact: Kei-Hoi Cheung (kei.cheung@yale.edu). © 2004 Adis Data Information BV. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherAdis International Ltd. The Journal's web site is located at http://bioinformatics.adisonline.com/en_HK
dc.relation.ispartofApplied Bioinformaticsen_HK
dc.subject.meshCluster Analysisen_HK
dc.subject.meshDatabase Management Systemsen_HK
dc.subject.meshDatabases, Proteinen_HK
dc.subject.meshGene Expression Profiling - methodsen_HK
dc.subject.meshInformation Storage and Retrieval - methodsen_HK
dc.subject.meshInterneten_HK
dc.subject.meshNatural Language Processingen_HK
dc.subject.meshOligonucleotide Array Sequence Analysis - methodsen_HK
dc.subject.meshSystems Integrationen_HK
dc.subject.meshUser-Computer Interfaceen_HK
dc.titleBiosphere: The interoperation of web services in microarray cluster analysisen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1175-5636&volume=3&issue=4&spage=253&epage=256&date=2004&atitle=Biosphere:+The+Interoperation+of+Web+Services+in+Microarray+Cluster+Analysisen_HK
dc.identifier.emailKwan, AKH:khkwan@hkucc.hku.hken_HK
dc.identifier.emailCheung, DW:dcheung@cs.hku.hken_HK
dc.identifier.authorityKwan, AKH=rp00127en_HK
dc.identifier.authorityCheung, DW=rp00101en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.2165/00822942-200403040-00007en_HK
dc.identifier.pmid15702956-
dc.identifier.scopuseid_2-s2.0-21344453433en_HK
dc.identifier.hkuros103202en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-21344453433&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume3en_HK
dc.identifier.issue4en_HK
dc.identifier.spage253en_HK
dc.identifier.epage256en_HK
dc.publisher.placeNew Zealanden_HK
dc.identifier.scopusauthoridCheung, KH=7402406608en_HK
dc.identifier.scopusauthoridDe Knikker, R=8711173200en_HK
dc.identifier.scopusauthoridGuo, Y=7406311192en_HK
dc.identifier.scopusauthoridZhong, G=8711173400en_HK
dc.identifier.scopusauthoridHager, J=7101717879en_HK
dc.identifier.scopusauthoridYip, KY=7101909946en_HK
dc.identifier.scopusauthoridKwan, AKH=7101738204en_HK
dc.identifier.scopusauthoridLi, P=7404772870en_HK
dc.identifier.scopusauthoridCheung, DW=34567902600en_HK

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