Siregal
Siregal, the Plant Genetic Resources Information System of the National Institute for Agronomical Research (INRA)
Siregal is an INRA project whose goal is to build and to maintain the Plant Genetic Resources Information System of the National Institute for Agronomical Research (INRA), France. It relies on a database, gathering descriptions on several agronomically interesting plant species. It is fully integrated into URGI Information System GnpIS .
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Siregal, the GnpIS Genetic resource module
Goal / Description
Genetic resources at INRA
INRA manages genetic resource collections for more than 50 plant species: model plants for genome study, crop species (cereals, fodder, oilseed crops, market garden crops and fruit trees) and decorative species (lawn and ornamental plants). These collections represent significant biodiversity in the species concerned and are therefore considered of excellent quality. INRA seeks to give value to its collections and to keep most of its genetic resources widely accessible.Bases of research projects, these patrimonial and scientific genetic resources help to improve crop species and to analyse genes and how they work. Amongst INRA's duties are the collect of new specimens, the conservation, the characterization and the diffusion of this plant material. These steps must be carried out in the respect of information traceability, more especially as INRA wishes to integrate these collections in accredited Biological Resource Centers (BRC). Read more ...
Siregal
That is why a software managing the collections and the associated data is essential. INRA thus decided to set up a Plant Genetic Resource Information System (Siregal) which is universal for all plant species, professional, useful for the INRA staff and its partners, which respects the standards and which integrates the genetic data, existing or to come.Realized in close cooperation with the managers and bioinformaticians of the BRCs , under cover of a steering committee made up of experts of the field, the software promises to be appropriate for the greatest number. Developed by experienced bioinformatics engineers , its quality and its perenniality are guaranteed.The convivial interface of the Web site of Siregal is addressed to several types of Net surfers:
- general public rediscovers biodiversity through genetic resource collections;
- the managers of the resource centers daily ensure the traceability of the samples and the data;
- the researchers connect information of various origins (phenotype, environment, molecular characterization...).
The main stored data are of two types:
- multicrop passport descriptors relate to all plant species: taxonomy, country of origin, biological status (wild, mutant, hybrid...), pedigree...
- specific data can be different for each species group and describe the characterization of a sample, in particular from the morphological, agronomic or resistance to the diseases point of view .
In addition, links towards other databases (internal and external) will allow to cross the various types of information.
Data analysis
Exporting the data contained in Siregal will allow their analysis in many scientific applications: plant identification help, study of the interaction of the genotype and environment on the phenotype, core-collection extraction, diversity analysis, visualization of the geographical distribution of a character, coefficient of parentage computing...
Open to other projects
Siregal is designed to store the data from the INRA Genetic Resource accessions, but is also suitable to host accessions from other projects, especially concerning biodiversity.For example, the genetic resources used in phenotyping experiments are hosted in GnpIS genetic resource module.The Siregal project, through its User Commitee, has developed th GnpIS genetic resource module , which is completely integrated in GnpIS. Beside GnpIS, the Siregal web site relies on the same pages as GnpIS, but displays only accessions managed by INRA Biological Resource Centers.
Duration: 31/08/2005 to 31/12/2015
Coordinator: Anne-Françoise Adam-Blondon, Sophie Durand
Actors
Partners
- Genetic Resource Centers (GRC) from the Plant Biology and Breeding Department (Département Biologie et Amélioration des Plantes - BAP) at INRA :
- IRHS at Angers: apple, pear, rose
- URGAFL at Avignon: tomato, eggplant, pimento, melon, lettuce, apricot, almond
- UREF at Bordeaux: Prunus, chestnut
- UMR GDEC at Clermont-Ferrand: cereals
- SRA in Corsica: citrus fruits
- UMR LEG in Dijon: grain legumes
- URP PPF in Lusignan: forage, turf
- UMR AGAP in Montpellier: maize, Medicago truncatula, grapevine, soy bean
- UMR IGEPP in Rennes : Brassica, potato, Allium
- IJPB in Versailles : Arabidopsis thaliana
Project organization
Here are the main actors of the project:
- Project manager: Sophie Durand, URGI Versailles, manages the bioinformatics part of the project.
- Principal investigator: Anne-Françoise Adam-Blondon, URGI Versailles, coordinates the scientific part the project.
- Steering committee: composed of experts of the fields, gives the strategy
- Scientific user committee: composed of users from all the partners, expresses the user need and tests the software
- Bioinformatician committee: composed of bioinformaticians from some partners, helps the users expressing their needs, submits data for insertion into Siregal, tests software.
- Development team at URGI: Sophie Durand, Erik Kimmel, Cyril Pommier, Nacer Mohellibi, Raphaël Flores, Célia Michotey and non-permanent staff
- URGI Platform coordination: Anne-Françoise Adam-Blondon, Joëlle Amselem
- URGI Platform administration: Claire Guerche, Mikaël Loaec
Communication
A poster has been presented at the 2009 TDWG Conference in Montpellier.
You can contact us at: Siregal project INRA-URGI Route de Saint - Cyr 78000 VERSAILLES FRANCE Don't hesitate to ask us for an account to access private data of your project.
Results
Software
The web interface is currently available. You can browse the different species and display taxon and accession cards. Or you can search for specific information present in the underlying database. The Genetic Resource module is one of the thematics of GnpIS: it's then linked to the other thematics via accession card (genotyping and phenotyping) and via the taxon card to all other thematics.
Data
Several species are represented in Siregal; others will follow. See news for more details.
Perspectives
- New data will be inserted or updated
- A submission tool is under development : it will allow GRC curators to manage their data : insertion, update, ...
- More data will be transfered to international databases such as GBIF and Eurisco .
- The web interface will be completely rewritten in a "unified interface": particularly a new query form, more integrated with other thematics
Creation date: 07 Dec 2009
eZ PublishPublication supervisor: A-F. Adam-Blondon
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