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. 2008 Nov;9(6):493-505.
doi: 10.1093/bib/bbn029. Epub 2008 Jul 11.

Experience using web services for biological sequence analysis

Heinz Stockinger  1 , Teresa Attwood, Shahid Nadeem Chohan, Richard Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro Fernandes, Robert D Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurelie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman
Affiliations

Experience using web services for biological sequence analysis

Heinz Stockinger et al. Brief Bioinform. 2008 Nov.

Abstract

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.

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Figures

Figure 1:
Figure 1:
A simplification of required design and implementation steps to provide a service over the Internet. The focus in this article is on the programmatic interface.
Figure 2:
Figure 2:
ELM workflow. The diagram provides information about data flow, which services are used and where additional algorithms are deployed rather than web services.
Figure 3:
Figure 3:
A Federated Database System using a centralised mediator and a global schema to integrate various sources.
Figure 4:
Figure 4:
A PDMS taking advantage of a network of pair-wise schema mappings to propagate a query from one database to the others.
See this image and copyright information in PMC

References

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    1. EMBRACE Consortium. Workshop: Deploying Web Services for Biological Sequence Annotation (Geneva, Switzerland, from 30 May to 1 June 2007) [(December 2007, date last accessed).]. Deliverable D5.2.10, June 2007. Available at http://www.embracegrid.info.
    1. EMBRACE. Network of Excellence. [(October 2007, date last accessed).]. http://www.embracegrid.info.
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    1. UniProt Consortium. The Universal Protein Resource (UniProt) Nucleic Acids Res. 2007;35(Database issue):D193–7. - PMC - PubMed

Publication types