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?
\"a software system
designed to support
interoperable
machine-to-
machine interaction
over a network\"

Web Service?
• W3C \"a software system
– SOAP designed to support
– WSDL interoperable
machine-to-
machine interaction
over a network\"
Web Services Glossary, http://www.w3.org/TR/ws-gloss/

Web Service?
• W3C \"a software system
– SOAP designed to support
– WSDL interoperable
machine-to-
machine interaction
• EMBRACE over a network\"
– + 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 ?

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
– 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=\"egonw@ws1.bmc.uu.se/home\"
id=\"JSO-0.12.5-6\" to=\"cdk.ws1.bmc.uu.se\"
type=\"set\">
<command
xmlns=\"http://jabber.org/protocol/commands\"
action=\"execute\" node=\"calculateMass\">
<iodata xmlns=\"urn:xmpp:tmp:io-data\" type=\"input\">
<in>
<smiles xmlns=\"urn:xws:cdk:input\">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)