EMBL-EBI Web Services

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====== Web Service Registries ======

Finding Web Services which provide access to a particular analysis tool or data resource can be difficult. While web search engines (e.g. [[http://www.google.com/|Google]] or [[http://www.bing.com/|Bing]]) can find web interfaces to such services they often fail to find the Web Service documentation. This problem is being addressed by the development of Web Services registries.

===== Life Sciences =====

Many organisations or project provide lists of their Web Services. For example:
  * [[http://www.cbs.dtu.dk/services/ws.php|Web Services at CBS]]
  * [[http://www.xml.nig.ac.jp/index.html|Web API for Biology]] ((Kwon Y., Shigemoto Y., Kuwana Y. and Sugawara H (2009)\\ **Web API for biology with a workflow navigation  system.**\\ Nucleic Acids Res. 37:W11-6; DOI: [[http://dx.doi.org/10.1093/nar/gkp300|10.1093/nar/gkp300]]; PubMed: [[http://europepmc.org/abstract/MED/19417067|19417067]])) at [[http://www.ddbj.nig.ac.jp/|DDBJ]]
  * [[:|EMBL-EBI Web Services]] ((McWilliam H., Valentin F., Goujon M., Li W., Narayanasamy M., Martin J., Miyar T. and Lopez R. (2009)\\ **Web services at the European Bioinformatics Institute - 2009**\\ Nucleic Acids Res. 37:W6-W10; DOI: [[http://dx.doi.org/10.1093/nar/gkp302|10.1093/nar/gkp302]]; PubMed: [[http://europepmc.org/abstract/MED/19435877|19435877]])) from [[http://www.ebi.ac.uk/|EMBL-EBI]]
  * [[http://gbio-pbil.ibcp.fr/ws/|gBIO Web Services]] from [[http://www.ibcp.fr/|Institut de Biologie et Chimie des Protéines]] (IBCP)
  * [[http://www.genome.jp/kegg/soap/|KEGG API]] ((Shuichi Kawashima, Toshiaki Katayama, Yoko Sato and Minoru Kanehisa (2003)\\ **KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System**\\ Genome Informatics 14:673-674; Full text: [[http://hc.ims.u-tokyo.ac.jp/JSBi/journal/GIW03/GIW03P172.pdf|PDF]])) from [[http://www.genome.jp/kegg/|KEGG]]
  * [[http://eutils.ncbi.nlm.nih.gov/|E-Utilities]], [[http://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html|QBlAST URL API]] and [[http://www.ncbi.nlm.nih.gov/books/NBK55699/|SOAP-based BLAST]] from [[http://www.ncbi.nlm.nih.gov/|NCBI]]

While these lists are useful, they do not cover the universe of Web Services, and give a restricted view of the Web Services available. So a number of projects are collecting and annotating Web Services in the life sciences to give a broader view. For example:
  * [[http://www.biocatalogue.org/|BioCatalogue]] ((Bhagat J., Tanoh F., Nzuobontane E., Laurent T., Orlowski J., Roos M., Wolstencroft K., Aleksejevs S., Stevens R., Pettifer S., Lopez R. and Goble C.A. (2010)\\ **BioCatalogue: a universal catalogue of web services for the life sciences.**\\ Nucleic acids research, 38:W689-94; DOI [[http://dx.doi.org/10.1093/nar/gkq394|10.1093/nar/gkq394]]; PubMed [[http://europepmc.org/abstract/MED/20484378|20484378]])) ((Wikipedia: [[http://en.wikipedia.org/wiki/BioCatalogue]])): includes REST, SOAP, DAS and BioMoby services.
  * [[http://www.dasregistry.org/|DAS registry]] ((Prlić A., Down T.A., Kulesha E., Finn R.D., Kähäri A. and Hubbard T.J. (2007)\\ **Integrating sequence and structural biology with DAS.**\\ BMC Bioinformatics 8:333; DOI: [[http://dx.doi.org/10.1186/1471-2105-8-333|10.1186/1471-2105-8-333]]; PubMed: [[http://europepmc.org/abstract/MED/17850653|17850653]])): a registry of [[http://www.biodas.org/|Distributed Annotation System (DAS)]] ((Dowell R.D., Jokerst R.M., Day A., Eddy S.R. and Stein L. (2001)\\ **The distributed annotation system.**\\ BMC Bioinformatics 2:7; DOI: [[http://dx.doi.org/10.1186/1471-2105-2-7|10.1186/1471-2105-2-7]]; PMID: [[http://europepmc.org/abstract/MED/11667947|11667947]])) ((Wikipedia: [[http://en.wikipedia.org/wiki/Distributed_Annotation_System]])) services.
  * [[http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/CentralRegistry.html|MOBY Central]]: a registry of [[http://www.biomoby.org/|BioMoby]] ((The BioMoby Consortium (2008)\\ **Interoperability with Moby 1.0 — It’s better than sharing your toothbrush!**\\ Briefings in Bioinformatics, 9(3):220-231; DOI: [[http://dx.doi.org/10.1093/bib/bbn003|10.1093/bib/bbn003]]; PubMed: [[http://europepmc.org/abstract/MED/18238804|18238804]])) ((Wikipedia: [[http://en.wikipedia.org/wiki/BioMOBY]])) services.
  * [[http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices|myGrid Registry or Biological Web Services]] ((myGrid: http://www.mygrid.org.uk/))
  * [[http://sadiframework.org/registry/services/|SADI registry]]: a registry of [[http://sadiframework.org/content/|SADI (Semantic Automated Discovery and Integration)]] services.
  * [[http://www.embraceregistry.net/|The EMBRACE Service Registry]] ((EMBRACE Network of Excellence: http://www.embracegrid.info/)) ((Pettifer, S., Thorne D., McDermott P., Attwood T., Baran J., Bryne J.C., Hupponen T., Mowbray D. and Vriend G. (2009)\\ **An active registry for bioinformatics web services**\\ Bioinformatics 25(16):2090-2091; DOI: [[http://dx.doi.org/10.1093/bioinformatics/btp329|10.1093/bioinformatics/btp329]]; PubMed: [[http://europepmc.org/abstract/MED/19460889|19460889]]))

===== General =====

As well as domain specific registries there are a number which are collating information about web services in any domain. For example:
  * [[https://www.hpi.uni-potsdam.de/naumann/sites/servicedepot/index.jsp|Depot @ HPI]]
  * [[http://www.service-repository.com/|Membrane Service Registry]]
  * [[http://www.programmableweb.com/apis|ProgrammableWeb]]
  * [[http://webservices.seekda.com/|seekda Web Services portal]]
  * [[http://sswap.info/|Sswap]]
  * [[http://www.wsindex.org/|WSIndex]]
  * [[http://www.xmethods.com/|XMethods]]

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