NET @ EBI
The NET team works to maximize the interactions between Nutrigenomics, Environmental genomics and Toxicogenomics (NET) communities and their collective NETworking capability with EBI groups.
We tackles some of the informatics challenges that these communities face when describing, storing and sharing experiments employing transcriptomics, proteomics and metabolomics (omics) technologies, in combination with conventional biomedical/ environmental methods.
Beyond formal collaborations in funded grants, we have established the following strategic collaborations to maximize data exchange and software interoperability:
NET activities are coordinated by Susanna-Assunta Sansone.
Software developments
-
BioInvIndex - A prototype infrastructure to commonly represent and store experimental metadata of biological, biomedical and environmental studies, commonly ranging from simple one assay-based to complex multi-assay studies
- EU IP CarcinoGenomics (PL 037712)
- ISAcreator -
A standalone application designed to enable users to structure or edit the experimental metadata in ISA-TAB format and package it with the corresponding data files for submission to the BioInvestigation Index
- EU IP CarcinoGenomics (PL 037712)
- Nutri - BASE - A set of generic and nutrition specific plugins for BASE, a widely used LIMS for the annotation of array-based data
Interoperability standards
- MIBBI - A Portal for extant minimum information checklists (e.g. MIAME for microarray, MIAPE for proteomics) and a Foundry to promote gradual integration
- NERC Bioinformatics Center (NEBC-EBI partnership)
- Ontology - Contribution to the collaborative development of OBI, an ontology for the description of
experimental metadata, under the OBO Foundry
- BBSRC e-Science (BB/D524283/1)
- ISA-TAB format - Collaborative development with MGED RSBI working group of a tab-delimited format for representing experimental metadata, that can be rendered in FuGE XML format
- EU IP CarcinoGenomics (PL 037712)
- Workshop series - On omics standards designed to advance the coordinated development of synergistic standards, such as MIBBI, OBI, FuGE and ISA-TAB
- BBSRC Tool and Resources fund (BB/E025080/1)
Members
Coordination: Susanna-Assunta Sansone
Technical Coordination: Philippe Rocca-Serra
MIBBI: Chris Taylor (NEBC Bioinformatician)
BioInvIndex: Nataliya Sklyar (Software Engineer)
BioInvIndex: Marco Brandizi (Software Engineer)
ISAcreator: Eamonn Maguire (Software Engineer)
Trainees:
Manon Delahaye
Richard Evans
Alumni:
Daniel Schober (Post-Doc); Dominic Oyeniran (Software Engineer); Alexander Garcia Castro (Ontology, trainee); Bhuwan Tiwari (Software Engineer, trainee); Catherine Leroy (Software Engineer, trainee); Pierre Marguerite (Software Engineer, trainee).
 |