Experience using web services for biological sequence analysis

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.

[1]  W. Nejdl,et al.  A Network of Excellence ... , 2005 .

[2]  Sébastien Carrère,et al.  The ProDom database of protein domain families: more emphasis on 3D , 2004, Nucleic Acids Res..

[3]  Mark D. Wilkinson,et al.  BioMOBY: An Open Source Biological Web Services Proposal , 2002, Briefings Bioinform..

[4]  Liisa Holm,et al.  PairsDB atlas of protein sequence space , 2007, Nucleic Acids Res..

[5]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[6]  Rodrigo Lopez,et al.  A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences , 2008, BMC Bioinformatics.

[7]  Rodrigo Lopez,et al.  Web Services at the European Bioinformatics Institute , 2007, Nucleic Acids Res..

[8]  George Coulouris,et al.  Distributed systems - concepts and design , 1988 .

[9]  Cesare Pautasso,et al.  Restful web services vs. "big"' web services: making the right architectural decision , 2008, WWW.

[10]  Anne-Lise Veuthey,et al.  Automated annotation of microbial proteomes in SWISS-PROT , 2003, Comput. Biol. Chem..

[11]  Robert D. Finn,et al.  Integrating sequence and structural biology with DAS , 2007, BMC Bioinformatics.

[12]  Leszek Rychlewski,et al.  ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins , 2003, Nucleic Acids Res..

[13]  Robert D. Finn,et al.  New developments in the InterPro database , 2007, Nucleic Acids Res..

[14]  Michael Muller,et al.  HitKeeper, a generic software package for hit list management , 2007, Source Code for Biology and Medicine.

[15]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[16]  Paul Barry,et al.  The Sequence Retrieval System , 2005 .

[17]  J. Barondess.  On excellence. , 1988, The Pharos of Alpha Omega Alpha-Honor Medical Society. Alpha Omega Alpha.

[18]  Gio Wiederhold,et al.  Mediators in the architecture of future information systems , 1992, Computer.

[19]  Lennart Martens,et al.  The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases , 2007, BMC Bioinformatics.

[20]  S. Salzberg.  Genome re-annotation: a wiki solution? , 2007, Genome Biology.

[21]  Karl Aberer,et al.  GridVine: An Infrastructure for Peer Information Management , 2007, IEEE Internet Computing.

[22]  S. Lacaprara,et al.  Distributed computing grid experiences in CMS , 2005, IEEE Transactions on Nuclear Science.

[23]  Jack A. M. Leunissen,et al.  Evolution of web services in bioinformatics , 2005, Briefings Bioinform..

[24]  Rolf Apweiler,et al.  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries , 2006, BMC Bioinformatics.

[25]  Byron Gallis,et al.  Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains , 2007, Genome Biology.

[26]  Dan Suciu,et al.  Schema mediation for large-scale semantic data sharing , 2005, The VLDB Journal.

[27]  Roy T. Fielding,et al.  Principled design of the modern Web architecture , 2000, Proceedings of the 2000 International Conference on Software Engineering. ICSE 2000 the New Millennium.