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Bioclipse and Webservices


 Embrace Workshop / 2008-11-03

        Egon Willighagen
           Uppsala University

     h...
My Background

• Chemist / Cheminformatician / Chemometrician
  – data analysis !
  – small molecules
     • crystallograp...
Metabolomics




MetWare, http://www.metware.org/
Drug Discovery




T. Kuhn, CDK-Taverna, http://cdk-taverna.de/
Web Service?

               quot;a software system
                 designed to support
                 interoperable
  ...
Web Service?

• W3C                            quot;a software system
  – SOAP                           designed to suppo...
Web Service?

• W3C             quot;a software system
  – SOAP            designed to support
  – WSDL            interop...
Web Service?

• W3C
  – SOAP
  – WSDL


• EMBRACE
  – + REST
Web Service?

• W3C             • Transport Layer
  – SOAP            – HTTP
  – WSDL            – SMTP
                  ...
Do we care? ...

• As scientist we are
    interested in solving
    our questions, not in
    technical solutions...

• B...
What about Databases?

• If database retrieval is
     a service too...



• Retrieval services
    have different
    req...
What about Databases?

• Big Downloads
   – BioMart
   – FTP sites
• Exploration ...
   – Browser
      • Userscripts
    ...
What do we use them for?

• Massive computation
  – workflows (Taverna, ...)
  – integrate and mine databases



  But wha...
Human Validation: Bioclipse
Bioclipse and Webservices
• Strong integrated services: MyNMRShiftDB




Kuhn and Steinbeck, http://www.nmrshiftdb.org/
Bioclipse' Service Integration

• Webservices
  –   SOAP
  –   BioMoby
  –   Local
  –   Taverna workflows
  –   REST
  – ...
Workflow as Service
Bioclipse' Wishlist

• Strong Data Types
  – Semantics
  – Like BioMoby


• Service Discovery and Annotation
  – http://bi...
OWL-S: Semantic Markup for
    Web Services




http://www.w3.org/Submission/OWL-S/ Copyright 2004, Various
SOAP over HTTP: Limitations

• Synchronous
  – polling required
• HTTP time-outs
  – caused by routers
• Alternatives
  – ...
XMPP/IO-DATA Services

• XMPP
   Extensible Messaging and Presence Protocol


• IO-DATA
   “This specification defines an ...
Services == Component
XMPP/IO-DATA envelope

<iq from=quot;egonw@ws1.bmc.uu.se/homequot;
   id=quot;JSO-0.12.5-6quot; to=quot;cdk.ws1.bmc.uu.seq...
XMPP/IO-DATA: Advantages

• Asynchronous
   – Long running jobs
• Strong Data Typing
   – via XML Schema provided by servi...
Conclusions

• SOAP / WSDL is a solution of many

• Bioclipse
  – SOAP, BioMoby, XMPP/IO-DATA, REST, …
  – Offer Interacti...
Thanx

• Bioclipse Team
  – Uppsala University (Prof. Wikberg)
  – EBI/Hinxton (dr. Steinbeck)
• MetWare Team
  – PRI/Wage...
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Bioclipse and Webservices

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Transcript of "Bioclipse and Webservices"

  1. 1. Bioclipse and Webservices Embrace Workshop / 2008-11-03 Egon Willighagen Uppsala University http://chem­bla­ics.blogspot.com/
  2. 2. My Background • Chemist / Cheminformatician / Chemometrician – data analysis ! – small molecules • crystallography / metabolomics / QSAR • Open Data / Open Source / Open Standards – Jmol http://www.jmol.org/ – Chemistry Development Kit http://cdk.sf.net/ – Bioclipse http://www.bioclipse.net/ http://citeulike.org/user/egonw/tag/papers
  3. 3. Metabolomics MetWare, http://www.metware.org/
  4. 4. Drug Discovery T. Kuhn, CDK-Taverna, http://cdk-taverna.de/
  5. 5. Web Service? quot;a software system designed to support interoperable machine-to- machine interaction over a networkquot;
  6. 6. Web Service? • W3C quot;a software system – SOAP designed to support – WSDL interoperable machine-to- machine interaction over a networkquot; Web Services Glossary, http://www.w3.org/TR/ws-gloss/
  7. 7. Web Service? • W3C quot;a software system – SOAP designed to support – WSDL interoperable machine-to- machine interaction • EMBRACE over a networkquot; – + REST
  8. 8. Web Service? • W3C – SOAP – WSDL • EMBRACE – + REST
  9. 9. Web Service? • W3C • Transport Layer – SOAP – HTTP – WSDL – SMTP –… • EMBRACE – + REST • Application Layer – SOAP / BioMoby – REST – ...
  10. 10. Do we care? ... • As scientist we are interested in solving our questions, not in technical solutions... • But ... – commitment – open standards
  11. 11. What about Databases? • If database retrieval is a service too... • Retrieval services have different requirements than computation services...
  12. 12. What about Databases? • Big Downloads – BioMart – FTP sites • Exploration ... – Browser • Userscripts • Ubiquity – Semantics • Link to Workflows ! Userscripts for the Life Sciences, doi:10.1186/1471-2105-8-487
  13. 13. What do we use them for? • Massive computation – workflows (Taverna, ...) – integrate and mine databases But what then? – visualization – feed to R – convert to PDF – ...
  14. 14. Human Validation: Bioclipse
  15. 15. Bioclipse and Webservices • Strong integrated services: MyNMRShiftDB Kuhn and Steinbeck, http://www.nmrshiftdb.org/
  16. 16. Bioclipse' Service Integration • Webservices – SOAP – BioMoby – Local – Taverna workflows – REST – ... • Categorization – ...
  17. 17. Workflow as Service
  18. 18. Bioclipse' Wishlist • Strong Data Types – Semantics – Like BioMoby • Service Discovery and Annotation – http://biocatalogue.org/ … but than Open – SAWSDL, Semantic Annotation for WSDL … but then independent, possibly social – BioMoby … but then decentralized – OWL-S ?
  19. 19. OWL-S: Semantic Markup for Web Services http://www.w3.org/Submission/OWL-S/ Copyright 2004, Various
  20. 20. SOAP over HTTP: Limitations • Synchronous – polling required • HTTP time-outs – caused by routers • Alternatives – Other transport layers: SMTP, XMPP • Relatively complex – lead to library incompatibilities – requires additional specs (WS-I)
  21. 21. XMPP/IO-DATA Services • XMPP Extensible Messaging and Presence Protocol • IO-DATA “This specification defines an XMPP protocol extension for handling the input to and output from a remote entity.” – Asynchronous !
  22. 22. Services == Component
  23. 23. XMPP/IO-DATA envelope <iq from=quot;egonw@ws1.bmc.uu.se/homequot; id=quot;JSO-0.12.5-6quot; to=quot;cdk.ws1.bmc.uu.sequot; type=quot;setquot;> <command xmlns=quot;http://jabber.org/protocol/commandsquot; action=quot;executequot; node=quot;calculateMassquot;> <iodata xmlns=quot;urn:xmpp:tmp:io-dataquot; type=quot;inputquot;> <in> <smiles xmlns=quot;urn:xws:cdk:inputquot;>CCC</smiles> </in> </iodata> </command> </iq>
  24. 24. XMPP/IO-DATA: Advantages • Asynchronous – Long running jobs • Strong Data Typing – via XML Schema provided by service itself • XML Library: xws4j – deserialization into XMLDOM • or into domain specific classes – hides XMPP layer – LGPL J. Wagener, http://sf.net/projects/xws4j/
  25. 25. Conclusions • SOAP / WSDL is a solution of many • Bioclipse – SOAP, BioMoby, XMPP/IO-DATA, REST, … – Offer Interactivity • Components Missing – semantic, data type thesaurus – service annotation
  26. 26. Thanx • Bioclipse Team – Uppsala University (Prof. Wikberg) – EBI/Hinxton (dr. Steinbeck) • MetWare Team – PRI/Wageningen (dr. van Ham) – IPB/Halle (dr. Neumann) • Johannes Wagener (XMPP) • Thomas Kuhn (CDK-Taverna)
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