A personalized, integrated system for rice functional genomics - - PowerPoint PPT Presentation

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May 02, 2023 618 likes •750 views

A personalized, integrated system for rice functional genomics Pierre Larmande CIRAD, UMR 1096 DAP, Avenue Agropolis,F-34398 Montpellier 05, France Context Our lab is involved in rice functional genomics. Three plant databases, namely

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A personalized, integrated system for rice functional genomics

Pierre Larmande

CIRAD, UMR 1096 DAP, Avenue Agropolis,F-34398 Montpellier 05, France

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Pierre Larmande - Nettab 2007

Context

 Our lab is involved in rice functional genomics.  Three plant databases, namely OryGenesDB,

OryzaTagLine and GreenPhylDB.

 OryGenesDB : reverse genetics and genomic

DB OryzaTagLine : phenotypic mutant lines DB. Greenphyl : plant comparative genomics platform.

 DB interconnections needed.

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Pierre Larmande - Nettab 2007

Sequence : phenotype Sequence : phenotype Sequence : sequence

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Pierre Larmande - Nettab 2007

Objectives

 Scientists need flexible systems which

reproduce automatically their actions and generate synthetic results.

 Our aim is to design and implement a

modular system that allows transparent complex queries across these databases using web services.

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Pierre Larmande - Nettab 2007

The system architecture

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Pierre Larmande - Nettab 2007

Why using BioMoby ?

 Specific to bioinformatic web services.  Allows access to hundreds of services.  Our services are available for a large community

and can be discovered with ontology features.

 BioMoby has 3 ontologies : service ontology

(e.g. retrieval, analysis) , namespace ontology (e.g. NCBI_gi, ICIS_germplasm), data type

ntology (e.g. Gene, Dnasequence, etc).

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Pierre Larmande - Nettab 2007

Data types ontology

 We have used a sub domain developed by

the Generation Challenge Programme which provides genetic, genomic and germplasm data types. (Bruskiewich et al, 2006)

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Pierre Larmande - Nettab 2007

 Dashboard is a Graphical User

Interface helping Biomoby service providers to develop and deploy their Biomoby

services. However, because of

its extensibility, it may contain also panels that are useful even for pure Biomoby end-users when they wish to call Biomoby services.

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Pierre Larmande - Nettab 2007

Workflows have been designed with the BioMoby plug-in of Taverna.

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Pierre Larmande - Nettab 2007

We developed 10 services
rganized into 4 workflows.
4 data input could be location,

interpro domain, Gene id, plant name.

Each data output participates

in a full record summary.

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Thanks for your attention !

Poster 15

Pierre Larmande – Nettab 07

Acknowledgments: Sébastien Fromentin Gaëtan Droc