Sansone Group

Susanna-Assunta Sansone - Principal Investigator, Leader

Philippe Rocca-Serra - Technical Leader

Eamonn Maguire - Developer, D.Phil student

Alejandra Gonzalez-Beltran - Developer (joining June 2012)

Open position - Biocurator

we have also projects for international trainees and students. Interested? Contact us

Our research and service activities

We develop and applying new methods and tools for improving representation and visualization, but also management and sharing of experiments in life science. Our activities are around and in support of the biocuration activity and its pivotal role in enabling reproducible research, driving science and discoveries. 

We collaborate with data producers and service providers,  grass-root standards initiatives, pre-competitive informatics initiatives, journals and funding agencies to build and promote the uptake of community-driven ontology, reporting standards and semantic web technologies to facilitate curation and data sharing.

Our projects

• The Investigation / Study / Assay (ISA) metadata tracking framework
• tool kit to facilitate standards compliant collection, curation and local management of experiments used by an increasingly diverse set of life science groups world-wide.
• BioSharing: policy, standards and communication
• a web-based catalogue to centralize bioscience data policies, reporting standards and links to other related portals, including MIBBI; also a communication forum to maintain linkages between funders, journals and leaders of the standardization efforts.
• Ontology for BioMedical Investigation (OBI)
•  an international, collaborative effort to build an integrated ontology for the description of biological and clinical investigations.
• MGportal (new, more soon)
• a global metagenomics portal (based at the EMBL-EBI) to handle next-generation sequencing data and associated metadata.
• COSMOS (new, more soon)
• e-infrastructure, standards and data-flow for metabolomics and its interface to biomedical and life science in Europe and world-wide.
• China partnering (new, more soon)
• exchange programme to establish common standards and practices for annotating and sharing bioscience data, starting with genomics.

Selected publications

1. Sansone*, Rocca-Serra* et al., Towards interoperable bioscience data, Nat Genet, 2012 [PDF]

2. Ho Sui et al., The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons, Nucleic Acids Res, 2012 [PDF] 

3. Deua et al., Translating standards into practice - One Semantic Web API for Gene Expression, J Biomed Inform, 2012 [PDF] 

4. Harland et al., Empowering industrial research with shared biomedical vocabularies, Drug Discov Today, 2011 [PDF]

5. Rocca-Serra et al., Sharing and archiving nucleic acid structure mapping data, RNA 2011 [PDF]

6. Yilmaz et al., Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications, Nat Biotechnol, 2011 [PDF]

7. Gaudet et al., Towards BioDBcore: a community-defined information specification for biological database, Nucleic Acids Res, 2011 [PDF]

8. Rocca-Serra et al., ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level, Bioinformatics, 2010 [PDF]

9. Brinkman et al., Modeling biomedical experimental processes with OBI, J Biomed Semantics, 2010 [PDF]

10. Field*, Sansone* et al., Megascience. 'Omics data sharing, Science, 2009 [PDF]

11. Taylor*, Field*, Sansone*, et al., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project, Nat Biotechnol, 2008 [PDF]

12. Smith et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nat Biotechnol, 2007 [PDF]

Funding sources

 BBSRC, NERC, EU