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Article: A web services choreography scenario for interoperating bioinformatics applications

TitleA web services choreography scenario for interoperating bioinformatics applications
Authors
Issue Date2004
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/
Citation
Bmc Bioinformatics, 2004, v. 5 How to Cite?
AbstractBackground: Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. Results: To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web services choreography language (BPEL4WS). Conclusion: While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow. © 2004 de Knikker et al; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/43671
ISSN
2015 Impact Factor: 2.435
2015 SCImago Journal Rankings: 1.722
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorde Knikker, Ren_HK
dc.contributor.authorGuo, Yen_HK
dc.contributor.authorLi, JLen_HK
dc.contributor.authorKwan, AKHen_HK
dc.contributor.authorYip, KYen_HK
dc.contributor.authorCheung, DWen_HK
dc.contributor.authorCheung, KHen_HK
dc.date.accessioned2007-03-23T04:51:42Z-
dc.date.available2007-03-23T04:51:42Z-
dc.date.issued2004en_HK
dc.identifier.citationBmc Bioinformatics, 2004, v. 5en_HK
dc.identifier.issn1471-2105en_HK
dc.identifier.urihttp://hdl.handle.net/10722/43671-
dc.description.abstractBackground: Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. Results: To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web services choreography language (BPEL4WS). Conclusion: While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow. © 2004 de Knikker et al; licensee BioMed Central Ltd.en_HK
dc.format.extent1136931 bytes-
dc.format.extent26624 bytes-
dc.format.mimetypeapplication/pdf-
dc.format.mimetypeapplication/msword-
dc.languageengen_HK
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/en_HK
dc.relation.ispartofBMC Bioinformaticsen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshInternet - standards - trendsen_HK
dc.subject.meshOligonucleotide array sequence analysis - statistics & numericalen_HK
dc.subject.meshComputational biology - methods - standards - trendsen_HK
dc.subject.meshDatabases, genetic - statistics & numerical dataen_HK
dc.subject.meshGene expression profiling - tatistics & numerical dataen_HK
dc.titleA web services choreography scenario for interoperating bioinformatics applicationsen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2105&volume=5&issue=25&spage=&epage=&date=2004&atitle=A+web+services+choreography+scenario+for+interoperating+bioinformatics+applicationsen_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.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1186/1471-2105-5-25en_HK
dc.identifier.pmid15113410en_HK
dc.identifier.pmcidPMC394315-
dc.identifier.scopuseid_2-s2.0-2942612342en_HK
dc.identifier.hkuros95428-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-2942612342&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume5en_HK
dc.identifier.isiWOS:000221407400001-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridde Knikker, R=8711173200en_HK
dc.identifier.scopusauthoridGuo, Y=7406311192en_HK
dc.identifier.scopusauthoridLi, JL=7410075530en_HK
dc.identifier.scopusauthoridKwan, AKH=7101738204en_HK
dc.identifier.scopusauthoridYip, KY=7101909946en_HK
dc.identifier.scopusauthoridCheung, DW=34567902600en_HK
dc.identifier.scopusauthoridCheung, KH=7402406608en_HK
dc.identifier.citeulike1459388-

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