The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations

Characterization of the gene content of Coxiella burnetii from different lineages in Europe

National audienc

Characterization of the gene content of Coxiella burnetii from different lineages in Europe

National audienc

Information system for phenotype data: trait, trials and genotypes identification and integration

International audienc

qPCR- and genomic-based determination of IS1111 copy numbers suggests an impact of Coxiella burnetii genotypic diversity on Q fever diagnosis and epidemiological studies in ruminants

International audienc

URGI plant and fungi platform: distributed resources through GMOD tools

International audienceNext Generation Sequencing technologies produce very large amount of data. Indeed, genomes are (re-)sequenced at high pace, and new sequences data are produced (eg. RNA-seq, Chip-seq). To face this challenge, the URGI ( http://urgi.versailles.inra.fr ) platform aims at providing tools for genomics, genetics, transcriptomics and polymorphisms comprising: pipelines, databases and user-friendly interfaces to analyze, browse and query the data. We will present plant and fungal genomic resources distributed through GMOD tools integrated in our Information System GnpIS.- Our genome module database (DB) components rely on the well-known schemas from the GMOD consortium. All annotation features and analysis results are primarily stored in the Chado or Bio::SeqFeature schema according to the need. Data can then be searched through GnpIS QuickSearch based on Apache Lucene™. Indexes are generated to query data stored in same or separate GMOD DBs. Query results are returned according to significance with terms, and linked to other GnpIS modules and/or Genome Report System (GRS). Biomart (GMOD) based datamarts were used as an advance search tool. Results of complex search criteria could be exported in different formats or directly send to our Galaxy server for further bioinformatic analysis.- We provide textual or graphical interfaces over the DBs such as GBrowse or Gbrowse_Syn to display sequence annotations or synteny respectively and Apollo for genes structure curation. The GRS provides comprehensive categories of reports through a user-friendly textual interface over structural and functional genomic data stored in Chado databases. - We also present the pipelines we developed for differential gene expression and polymorphism analysis available through our Galaxy server

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis

Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource

International audienc

URGI genome annotation system:an integrated system for structural and functional genome annotation

The URGI platform (http://urgi.versailles.inra.fr) develops a genome annotation system dedicated to plants and their pathogens. This Integrated System relies on: (i) pipelines for Transposable Elements annotation (REPET) and gene structural and functional predictions (ii) databases and user-friendly interfaces to browse and query the data (URGI Information System GnpIS, Genome Report System GRS), (iii) A distributed annotation system for curation of gene structure