Bioclipse and Webservices

Bioclipse and Webservices Embrace Workshop / 2008-11-03 Egon Willighagen Uppsala University http://chemblaics.blogspot.com/

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

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 machine-to- machine interaction over a networkquot;

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/

Web Service? • W3C quot;a software system – SOAP designed to support – WSDL interoperable machine-to- machine interaction • EMBRACE over a networkquot; – + REST

Web Service? • W3C – SOAP – WSDL • EMBRACE – + REST

Web Service? • W3C • Transport Layer – SOAP – HTTP – WSDL – SMTP –… • EMBRACE – + REST • Application Layer – SOAP / BioMoby – REST – ...

Do we care? ... • As scientist we are interested in solving our questions, not in technical solutions... • But ... – commitment – open standards

What about Databases? • If database retrieval is a service too... • Retrieval services have different requirements than computation services...

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

What do we use them for? • Massive computation – workflows (Taverna, ...) – integrate and mine databases But what then? – visualization – feed to R – convert to PDF – ...

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 – ... • Categorization – ...

Workflow as Service

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 ?

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)

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 !

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.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>

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/

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

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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Bioclipse and Webservices

by Egon Willighagen

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