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A web services choreography scenario for interoperating bioinformatics applications.

de Knikker R, Guo Y, Li JL, Kwan AK, Yip KY, Cheung DW, Cheung KH - BMC Bioinformatics (2004)

Bottom Line: 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.We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench.For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Medical Informatics, Department of Anesthesiology, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520, USA. remkodeknikker@hotmail.com

ABSTRACT

Background: 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.

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Related in: MedlinePlus

HAPI, the High-density Array Pattern Interpreter. Step 2 of 3 when using HAPI utility's web-based (HTML) interface provided by UCSD
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Related In: Results  -  Collection


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Figure 1: HAPI, the High-density Array Pattern Interpreter. Step 2 of 3 when using HAPI utility's web-based (HTML) interface provided by UCSD

Mentions: Figure 1 shows step 2 of HAPI in which the user needs to select a column that contains the GenBank IDs and can enter a name for the HTML summary page. In step 3 the result file is being generated and the user has to click the link to view the HTML summary page.


A web services choreography scenario for interoperating bioinformatics applications.

de Knikker R, Guo Y, Li JL, Kwan AK, Yip KY, Cheung DW, Cheung KH - BMC Bioinformatics (2004)

HAPI, the High-density Array Pattern Interpreter. Step 2 of 3 when using HAPI utility's web-based (HTML) interface provided by UCSD
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC394315&req=5

Figure 1: HAPI, the High-density Array Pattern Interpreter. Step 2 of 3 when using HAPI utility's web-based (HTML) interface provided by UCSD
Mentions: Figure 1 shows step 2 of HAPI in which the user needs to select a column that contains the GenBank IDs and can enter a name for the HTML summary page. In step 3 the result file is being generated and the user has to click the link to view the HTML summary page.

Bottom Line: 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.We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench.For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Medical Informatics, Department of Anesthesiology, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520, USA. remkodeknikker@hotmail.com

ABSTRACT

Background: 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.

Show MeSH
Related in: MedlinePlus