Optimal Assembly Sequence generation through computational ...
Implementing computational analysis through Web services
description
Transcript of Implementing computational analysis through Web services
![Page 1: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/1.jpg)
Implementing computational analysis
through Web services
Arnaud KerhornouCRG/INBBarcelona
-BioMed Workshop
IRBNovember 2007
![Page 2: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/2.jpg)
Current situation in Bioinformatics
![Page 3: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/3.jpg)
•Discovery
•Service description
•Ontologies
•Data transfert
•Automation
Limits
![Page 4: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/4.jpg)
BioMoby architecture
PublishFind
Bind
Service registry
Service Provider
Service Descriptions
Service Description
Service
WDSL, UDDIWSDL, UDDI
Service Requestor
A web service is an interface that describes a collection of operations that are network accessible through standardized XML messaging
![Page 5: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/5.jpg)
BioMoby
a unifying framework approach
The bioMoby project aims to provide bioinformatics resources through the web. It can be data retrieval resources or analysis resources.
It defines an ontology-based messaging standard The services are registered in a central “yellow pages”
server to facilitate the discovery The services specifications are formalized in a description
language.
![Page 6: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/6.jpg)
It provides:•A Central Registry of services•A set of standards to specify:
•Message formatting,•Error reporting•Asynchronous requests
•An API written in two languages, perl and java •Ontologies to represent
•Types of services,•Data types
The BioMoby framework
![Page 7: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/7.jpg)
Ontology
• Data exchange relies on the use of Ontologies.
• Ontology to represent knowledge in a given domain
• In bioinformatics: – OBO (GO, SO and many many more)
• http://obo.sourceforge.net/cgi-bin/table.cgi
– Biomoby datatypes to classify service input/output– Biomoby service types
![Page 8: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/8.jpg)
Establish Ontologies to formalize the representation of:•Types of services•Types of data
The BioMoby ontologies
![Page 9: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/9.jpg)
Bioinformatics
Sequence
Analysis
MultipleSequence
Alignment
PairwiseSequence
Alignment
Alignment
GeneFinding
is-a
Service
The Service TypeOntology
![Page 10: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/10.jpg)
Object
String
Integer
Virtual
SequenceGeneric
Sequence
DNA
Sequence
AminoAcid
Sequence
text_plain text_formatted GFF
has-a
is-a
is-a
has-a
has-a
The Data TypeOntology
![Page 11: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/11.jpg)
<DNASequence>
<String articleName=”Sequence”>
AAATGTCGCTCGATACGATCAGCTACGA
</String>
<Integer articleName=”Length”>
28
</Integer>
</DNASequence>
Moby DNASequenceObject
![Page 12: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/12.jpg)
BioMobyService specs
• Service name: Free Text
• Service type: Moby service type ontology
• Description: Free text
• One or more inputs: Moby data type ontology
• One or more outputs: Moby data type ontology
• One or more parameters: – name (a string)– value (an ‘primitive’, ie a String or an Integer etc.)
![Page 13: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/13.jpg)
Example
• Service type: GeneFinding
• Description: ab-initio gene finding software
• Input: a DNASequence object
• Output: a GFF object
• Parameters:– Profile (Default is Human)– Strand (Default is both strands)
RunGeneIDGFF service specifications:
![Page 14: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/14.jpg)
Client Side
MobyCentral
ServiceProvider
Internet
ServiceClient
• There are different kind of clients
• Some of them allow the creation of workflows
Programmatic
libraries:
![Page 15: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/15.jpg)
• Java based graphical integrated workbench
• It allows the construction of complex distributed workflows
• It can handle different kind of services (Moby and others)
Client Side: Taverna I
![Page 16: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/16.jpg)
Processors = Webservices
Inputs
Outputs
Client Side: Taverna II
![Page 17: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/17.jpg)
Client Side: Taverna III
Moby Web service Configuration
![Page 18: Implementing computational analysis through Web services](https://reader035.fdocuments.us/reader035/viewer/2022070413/56814ce9550346895db9e760/html5/thumbnails/18.jpg)
• All the info accessible at the Moby homepage at:– http://www.biomoby.org/
• Taverna Web site– http://www.inab.org/MOWServ
• Remora Web interface– http://lipm-bioinfo.toulouse.inra.fr/remora/cgi/remora.cgi
• MowServ Web interface– http://www.inab.org/MOWServ/
• Genome Analysis services page– http://genome.imim.es/webservices
BioMoby on the Web