Wheat Innovation Workshop - INRA - Événements · PDF fileInternational Wheat...

16th - 17th November 2015

Clermont-Ferrand, FranceInternational

Wheat

Innovation

Workshop

Breedwheat data collection and integration in a user-oriented database

Nathalie Rivière, Biogemma

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

• Breedwheat Information System (BIS): Insure a centralized

repository:

– Access to data for partners

– Combine data from WP

• Specific developments

– Integrate new types of data

– Link data

• Feed the database with BW data

Data management: objectives


• Define user needs

• Develop the database

• Collect data

• Integrate data

Strategy

User Needs Collection


• Breedwheat is a large and long project:

– Huge diversity of data

– Evolution of technologies and volumes to be

anticipated

• Genetic resources: passport data for the whole INRA

collection

• Polymorphisms discovery

– SNP: different approaches, calling tools, formats

– CNV, PAV: new approaches

Which kind of data?


• Genotyping data

– Technologies: Kaspar, Axiom, Sequencing

formats, volumes

• Phenotyping data

– Several partners, locations, traits

format, ontology

• Expression analysis

– Microarrays, RNAseq

• Genomic selection

• Association studies: THE link between all data => major

axis for the development of the database

Which kind of data?


Links between data

varieties

SNP

genotypingphenotyping

QTL/association

Trait

GenomeGenetic map

BREEDWHEAT INFORMATION SYSTEM


• Start with existing tool: GnpIS

• GnpIS: developed by INRA (URGI) and in

collaborative projects

• GnpIS choosen for several large projects– Breedwheat

– Amaizing (maize)

– Peamust (pea)

– Rapsodyn (rapeseed)

– Aker (sugar beet)

• Transversal developments across projects

Use of GnpIS


• GnpIS IS the repository for IWGSC sequences

• Breedwheat data in a global wheat portal with access to

public and private data

GnpIS for wheat


GnpIS for Wheat

http://wheat-urgi.versailles.inra.fr

Search into wheat data in GnpIS

http://wheat-urgi.versailles.inra.fr/


GnpIS for Wheat


• Association studies module is central

– Specifications for the development defined by scientific experts

– Linked to phenotype, genetic resource, genotype, SNP

• Filtering options, graphical displays, export of connected

data

Example of user oriented development


Association data

Link to gbrowse for genomic context

Data filtering (pval, model, chr…)


• Objective: To share data with other projects

• Main issue: phenotypic data

• In the frame of european Transplant project

– WP3: Community standards for the interoperability of

data resources

• Collaborative developments, URGI involved

– ISA-TAB format compliant with GnpIS

• All public data integrated in GnpIS are queryable via

the european Transplant portal

GnpIS interoperability

15


GnpIS interoperability

Direct export to standard format compliant with other european databases

Data Collection


• Identify key contacts

– Scientist: who knows the data and who will centralize data from

the others

– Bioinformaticians

• To format the data

• To integrate the data

Data flow

Data Production

Data check and format

Data InsertionOne Unique Scientific Contact

One Unique WP5 ContactOne Unique WP5 Contact : data

type expert


• Define a standard

– Done in Year 1 with users

– Based on exisiting file (Arvalis)

– Multi-sheet excel file

Format: Phenotyping Example

Also other tabs for :• Variables• ITK• Treatments• Trial Definition• Contacts Description• …


o Share BW measurement protocols among partners

o Add new traits not in the wheat crop ontology (e.g. M-Fus-spk)

o Aggregate multiple ontologies (e.g. wheat crop ontology +

environment ontology + crop research ontology)

Vocabulary: BW Ontology


• Submission forms

• Data formatting

• Data integrity checked

• Data integration

Integration tool kit

Breedwheat data in GnpIS


• BW accessions are available at the INRA BRC

Genetic resources


All field trials from 2011 integrated

Phenotyping data


Several SNP sets:• Developed in BW project• Publicly available and used for

genotyping in BW

SNP data


A single assay (BW Axiom420K) for all the geneticresources of the project

Genotyping data


• Data management critical for efficient use of data by

each partner

• Standardization mandatory

– Formats

– Vocabulary

• Help from bioinformaticians required

• Database must be user-oriented

Conclusions


• 4 years overview:

– Data flow and contacts are identified

– Data available are integrated or in progress

– Developments were made following users feedback

Conclusions

Aknowledgements

URGI team:T. LetellierR. FloresC. PommierG. MerceronD. SteinbachH. QuesnevilleM. Alaux

Biogemma team:F. SapetJ. TeyssierJ. DuarteM. LeveugleN. Rivière

And all users!

Wheat Innovation Workshop - INRA - Événements · PDF fileInternational Wheat...

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