Introduction into Webservices and BioMOBY

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Introduction into Webservices and BioMOBY
Dirk Haase

• PlaNet Workshop
• June 23rd/24th 2005

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Problem

• Scientific work requires
• Data resources
• Genomic sequences, ESTs, Protein Sets, Expression
  data, .
• Computational resources
• Similarity searches, Alignments, Domain
  prediction, Functional classification,
  Clustering,
• Often, these resources are existent and
  available, but
• Hard to find
• Distributed all over the world
• No common format

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PAINFUL research
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Problem ctd.

• Resources on the web are human centric? Frequent
  copy reformat paste
• Webservices make the www application-centric

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What is a Webservice?

• Wikipedia a service provided using XML on the
  basis on internet protocols

?
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What is it NOT?

• Web page
• static document accessible via the WWW, displayed
  in a browser
• Web server
• machine/software capable to make static and/or
  dynamic content visible to others over WWW
• Web application
• Program that can be used over WWW by filling out
  input forms and displays result as web page

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Again what is a Webservice?

• Program
• Accessible over the WWW
• Using common standards for
• Being discovered
• Exchange of messages
• Invocation
• A webservice can be invoked by other programs
  without human intervention!

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Actors

• Service Registry
• index who offers what (Yellow Pages)
• Service Provider
• offers data or computational resource
• Service Requestor
• wants to access the offered resource (customer)

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Stages

• Registration
• Service Provider tells registry what he has to
  offer and where this can be found
• Discovery
• Service Requestor asks registry where to find
  what he needs
• Invocation
• Service Requestor executes provided service over
  WWW

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Basic Architecture
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Common StandardsThe Protocols

• Discovery UDDI universal description,
  discovery, and integration
• Description WSDL web service description
  language
• Messaging SOAP simple object access protocol
• Transport HTTP hyper text transport protocol

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WebservicesSummary

• Provides data or computational resources over the
  WWW
• Can be accessed automatically
• ? application-centric web!
• Works for everyone who has internet access (no
  firewall hassles etc.)
• Independent of programming languages
• Usage of broadly accepted protocols

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The BioMoby Idea

• Initiated in 2001 as collaboration of some model
  organism database providers
• Simple, open source platform for discovery,
  integration, representation and retrieval of
  biological data
• Two branches
• Moby-S follows the webservice paradigm
• S-Moby using semantic web technology (not
  covered here)

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MobyWS vs. General WS

• Registry MobyCentral
• Usage of ontologies
• Moby services operate on moby objects
• Usage of namespaces
• Own messaging structure for registration,
  detection and invocation of services

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Ontologies

• Definition a formally defined system of things
  and relations between these things for
  representation of knowledge
• Usually, an ontology builds a hierarchy of
  objects to describe relations in a certain domain
• Well known examples GO, Plant Ontology, taxonomy
  of species

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Ontologies in Moby

• Service types (like Analysis or Retrieval)
• Objects
• Isa specialization of an existing object
• Has/has-a expansion with other objects
• Flexible and open every service provider can add
  new objects to the ontology just as he needs them

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BioMoby Object Ontology
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there are gt100 services registered !
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with Ontologies
Why BioMOBY?
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Pros Cons

• Services can easily be linked together to
  workflows
• Object ontology adds semantic
• Usage of broadly accepted standards
• Existing APIs in Perl, Java, Python
• Special messaging structure complicates
  implementation of services
• - Object ontology requires experience

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A Moby Service Providers perspective

• Which objects does my service work on?
• Which objects does my service output?
• Register new objects if necessary
• What namespaces use my objects?
• Register namespaces if necessary
• Moby-fy the program
• Register new service at MobyCentral
• Wait for users

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Moby for the users Clients

• Requirements for Moby Clients
• Get user input
• Build moby input object(s)
• Contact moby central
• Send moby request to service
• Receive moby response from service
• Handle output moby objects

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Existing clients

• Gbrowse_moby
• PlaNet clients
• Ahab
• Blue Jay
• Taverna
• Other specialized clients

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Biomoby Principle
phenotype
AGI Codes
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Acknowledgements

• Heiko Schoof
• Rebecca Octave
• PlaNet partners
• Moby developers (esp. Mark Wilkinson)