Susanna Assunta Sansone

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
    Irena Spasic
    Manchester Centre for Integrative Systems Biology, The University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK
    BMC Bioinformatics 9:S5. 2008
  2. ncbi The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case
    Alexander Garcia Castro
    Microarray Informatics Team, The European Bioinformatics Institute European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK
    BMC Bioinformatics 7:267. 2006
  3. ncbi The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?"
    Susanna Assunta Sansone
    EMBL EBI The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    OMICS 12:143-9. 2008
  4. ncbi A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group
    Susanna Assunta Sansone
    EMBL EBI, European Nutrigenomics Organisation NuGO, Hinxton, Cambridge, United Kingdom
    OMICS 10:164-71. 2006
  5. ncbi ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 31:68-71. 2003
  6. ncbi The ArrayExpress gene expression database: a software engineering and implementation perspective
    Ugis Sarkans
    EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:1495-501. 2005
  7. ncbi Towards interoperable reporting standards for omics data: hopes and hurdles
    Susanna Assunta Sansone
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Summit on Translat Bioinforma 2009:112-5. 2009
  8. ncbi ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
    Philippe Rocca-Serra
    The European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Bioinformatics 26:2354-6. 2010
  9. ncbi The MetaboLights repository: curation challenges in metabolomics
    Reza M Salek
    Wellcome Trust Genome Campus, European Bioinformatics Institute, Cheminformatics and Metabolism, Hinxton, Cambridgeshire, CB10 1SD, UK
    Database (Oxford) 2013:bat029. 2013
  10. ncbi Survey-based naming conventions for use in OBO Foundry ontology development
    Daniel Schober
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:125. 2009

Detail Information

Publications35

  1. ncbi Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
    Irena Spasic
    Manchester Centre for Integrative Systems Biology, The University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK
    BMC Bioinformatics 9:S5. 2008
    ..However, it is time-consuming and non trivial to construct these resources manually...
  2. ncbi The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case
    Alexander Garcia Castro
    Microarray Informatics Team, The European Bioinformatics Institute European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK
    BMC Bioinformatics 7:267. 2006
    ....
  3. ncbi The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?"
    Susanna Assunta Sansone
    EMBL EBI The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    OMICS 12:143-9. 2008
    ..This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC)...
  4. ncbi A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group
    Susanna Assunta Sansone
    EMBL EBI, European Nutrigenomics Organisation NuGO, Hinxton, Cambridge, United Kingdom
    OMICS 10:164-71. 2006
    ....
  5. ncbi ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 31:68-71. 2003
    ..With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress...
  6. ncbi The ArrayExpress gene expression database: a software engineering and implementation perspective
    Ugis Sarkans
    EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:1495-501. 2005
    ..Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies...
  7. ncbi Towards interoperable reporting standards for omics data: hopes and hurdles
    Susanna Assunta Sansone
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Summit on Translat Bioinforma 2009:112-5. 2009
    ..However, the job of harmonising reporting standards is still very much a work in progress; both software interoperability and the data integration remain challenging as things stand...
  8. ncbi ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
    Philippe Rocca-Serra
    The European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Bioinformatics 26:2354-6. 2010
    ..Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org...
  9. ncbi The MetaboLights repository: curation challenges in metabolomics
    Reza M Salek
    Wellcome Trust Genome Campus, European Bioinformatics Institute, Cheminformatics and Metabolism, Hinxton, Cambridgeshire, CB10 1SD, UK
    Database (Oxford) 2013:bat029. 2013
    ..Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions. Database URL: http://www.ebi.ac.uk/metabolights...
  10. ncbi Survey-based naming conventions for use in OBO Foundry ontology development
    Daniel Schober
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:125. 2009
    ....
  11. ncbi ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
    ..In this update, we describe the ArrayExpress developments over the last two years...
  12. ncbi Summary recommendations for standardization and reporting of metabolic analyses
    John C Lindon
    Biological Chemistry, Biomedical Sciences Division, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
    Nat Biotechnol 23:833-8. 2005
  13. ncbi ArrayExpress: a public database of gene expression data at EBI
    Philippe Rocca-Serra
    EMBL Outstation-Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
    C R Biol 326:1075-8. 2003
    ..Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress)...
  14. ncbi Database development in toxicogenomics: issues and efforts
    William B Mattes
    Pfizer Inc, Groton, Connecticut, USA
    Environ Health Perspect 112:495-505. 2004
    ....
  15. ncbi Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  16. ncbi The carcinoGENOMICS project: critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays
    Mathieu Vinken
    Department of Toxicology, Vrije Universiteit Brussel VUB, Laarbeeklaan 103, B 1090 Brussels, Belgium
    Mutat Res 659:202-10. 2008
    ..Since selecting an appropriate set of chemicals is a frequent impediment in the early stages of similar research projects, the information provided in this paper might be extremely valuable...
  17. ncbi Submission of microarray data to public repositories
    Catherine A Ball
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E317. 2004
  18. ncbi The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Andrew R Jones
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Nat Biotechnol 25:1127-33. 2007
    ..Such advances are important for transparent data management and mining in functional genomics and systems biology...
  19. ncbi An open letter on microarray data from the MGED Society
    Catherine Ball
    Stanford University, USA
    Microbiology 150:3522-4. 2004
  20. ncbi Standards for microarray data: an open letter
    Catherine Ball
    Environ Health Perspect 112:A666-7. 2004
  21. ncbi Wrestling with SUMO and bio-ontologies
    Christian Stoeckert
    Nat Biotechnol 24:21-2; author reply 23. 2006
  22. ncbi The MGED Ontology: a resource for semantics-based description of microarray experiments
    Patricia L Whetzel
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA
    Bioinformatics 22:866-73. 2006
    ..The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). CONTACT: SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  23. ncbi Annotation of environmental OMICS data: application to the transcriptomics domain
    Norman Morrison
    School of Computer Science, University of Manchester, Manchester, United Kingdom
    OMICS 10:172-8. 2006
    ..Finally, we make an open call to the community for participation in the Env Community and its future activities...
  24. ncbi Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use
    Raffaella Corvi
    European Centre for the Validation of Alternative Methods, Institute for Health and Consumer Protection, Joint Research Centre of the European Commission, Ispra, Italy
    Environ Health Perspect 114:420-9. 2006
    ..In this report we summarize the discussions and describe in detail the recommendations for future direction and priorities...
  25. ncbi Defining best practice for microarray analyses in nutrigenomic studies
    Paola Garosi
    Institute of Food Research, Norwich Research Park, Norwich NR5 7UA, UK
    Br J Nutr 93:425-32. 2005
    ..The overall aims are to provide a basic framework of advice for researchers who are new to the use of microarrays and to promote a discussion of standardisation and best practice in the field...
  26. ncbi Establishing reporting standards for metabolomic and metabonomic studies: a call for participation
    Oliver Fiehn
    UC Davis Genome Center, Davis, California 95616, USA
    OMICS 10:158-63. 2006
    ..These include biological study designs, chemical analysis, and data processing, as well as the ontologies that are necessary in this framework...
  27. ncbi Toward a standards-compliant genomic and metagenomic publication record
    George M Garrity
    Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
    OMICS 12:157-60. 2008
    ....
  28. ncbi Meeting report: the fifth Genomic Standards Consortium (GSC) workshop
    Dawn Field
    NERC Center for Ecology and Hydrology, Oxford, United Kingdom
    OMICS 12:109-13. 2008
    ..Further information about the GSC and its range of activities can be found at http://gensc.org...
  29. ncbi The metabolomics standards initiative
    Susanna-Assunta Sansone
    Nat Biotechnol 25:846-8. 2007
  30. ncbi Foreword to the special issue on the Fifth Genomic Standards consortium workshop
    Dawn Field
    NERC Centre for Ecology and Hydrology, Mansfield Rd, Oxford OX1 3SR, United Kingdom
    OMICS 12:99. 2008
  31. ncbi The minimum information about a genome sequence (MIGS) specification
    Dawn Field
    Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
    Nat Biotechnol 26:541-7. 2008
    ..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...
  32. ncbi Meeting report: EU-US Workshop on Molecular Signatures of DNA Damage-Induced Stress Responses. Cortona, Italy, 26-30 September 2003
    Miriam Sander
    Page One Editorial Services, 403 Carolina Circle, Durham, NC 27707-2252, USA
    Mutat Res 550:145-81. 2004
  33. ncbi Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Biotechnol 26:305-12. 2008
    ..This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal...
  34. ncbi The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    Barry Smith
    Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203, USA
    Nat Biotechnol 25:1251-5. 2007
    ..We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved...
  35. ncbi Development of FuGO: an ontology for functional genomics investigations
    Patricia L Whetzel
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    OMICS 10:199-204. 2006
    ....