Philippe Rocca-Serra

Philippe Rocca-Serra

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Philippe Rocca-Serra

Philippe Rocca-Serra

Publications by authors named "Philippe Rocca-Serra"

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The Data Tags Suite (DATS) model for discovering data access and use requirements.

Gigascience 2020 Feb;9(2)

Oxford e-Research Centre University of Oxford 7 Keble Road, Oxford, OX1 3QG United Kingdom.

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http://dx.doi.org/10.1093/gigascience/giz165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006671PMC
February 2020

Experiment design driven FAIRification of omics data matrices, an exemplar.

Sci Data 2019 12 12;6(1):271. Epub 2019 Dec 12.

Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, United Kingdom.

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http://dx.doi.org/10.1038/s41597-019-0286-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908569PMC
December 2019

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

Bioinformatics 2017 Aug;33(16):2598-2600

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870861PMC
August 2017

MetaboLights: An Open-Access Database Repository for Metabolomics Data.

Curr Protoc Bioinformatics 2016 Mar 24;53:14.13.1-14.13.18. Epub 2016 Mar 24.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, United Kingdom.

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http://dx.doi.org/10.1002/0471250953.bi1413s53DOI Listing
March 2016

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.

Database (Oxford) 2015 28;2015. Epub 2015 Jan 28.

Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/database/bau132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309925PMC
September 2015

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

Nucleic Acids Res 2014 Jan 27;42(Database issue):D600-6. Epub 2013 Oct 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK, Oxford e-Research Centre, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK and NERC Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK.

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http://dx.doi.org/10.1093/nar/gkt961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965009PMC
January 2014

Visual compression of workflow visualizations with automated detection of macro motifs.

IEEE Trans Vis Comput Graph 2013 Dec;19(12):2576-85

University of Oxford.

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http://dx.doi.org/10.1109/TVCG.2013.225DOI Listing
December 2013

The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:70. Epub 2013 Mar 18.

Harvard School of Public Health, Biostatistics, Boston, MA, USA ; Harvard Stem Cell Institute, Cambridge, MA, USA.

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December 2013

The MetaboLights repository: curation challenges in metabolomics.

Database (Oxford) 2013 29;2013:bat029. Epub 2013 Apr 29.

Wellcome Trust Genome Campus, European Bioinformatics Institute, Cheminformatics and Metabolism, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/database/bat029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638156PMC
October 2013

MetaboLights: towards a new COSMOS of metabolomics data management.

Metabolomics 2012 Oct 25;8(5):757-760. Epub 2012 Sep 25.

European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD UK.

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http://dx.doi.org/10.1007/s11306-012-0462-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465651PMC
October 2012

Translating standards into practice - one Semantic Web API for Gene Expression.

J Biomed Inform 2012 Aug 24;45(4):782-94. Epub 2012 Mar 24.

Digital Enterprise Research Institute (DERI), National University of Ireland, Galway, Ireland.

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http://dx.doi.org/10.1016/j.jbi.2012.03.002DOI Listing
August 2012

A call for an international network of genomic observatories (GOs).

Gigascience 2012 Jul 12;1(1). Epub 2012 Jul 12.

Biodiversity Institute, Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK.

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http://dx.doi.org/10.1186/2047-217X-1-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617453PMC
July 2012

On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities.

Gigascience 2012 Jul 12;1(1):10. Epub 2012 Jul 12.

Oxford e-Research Centre, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1186/2047-217X-1-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626509PMC
July 2012

The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness.

Stand Genomic Sci 2012 Jul 20;6(3):438-47. Epub 2012 Jul 20.

Microbial Genomics and Metagenomic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.

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http://dx.doi.org/10.4056/sigs.2675953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558968PMC
July 2012

graph2tab, a library to convert experimental workflow graphs into tabular formats.

Bioinformatics 2012 Jun 3;28(12):1665-7. Epub 2012 May 3.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371871PMC
June 2012

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Authors:
Pelin Yilmaz Renzo Kottmann Dawn Field Rob Knight James R Cole Linda Amaral-Zettler Jack A Gilbert Ilene Karsch-Mizrachi Anjanette Johnston Guy Cochrane Robert Vaughan Christopher Hunter Joonhong Park Norman Morrison Philippe Rocca-Serra Peter Sterk Manimozhiyan Arumugam Mark Bailey Laura Baumgartner Bruce W Birren Martin J Blaser Vivien Bonazzi Tim Booth Peer Bork Frederic D Bushman Pier Luigi Buttigieg Patrick S G Chain Emily Charlson Elizabeth K Costello Heather Huot-Creasy Peter Dawyndt Todd DeSantis Noah Fierer Jed A Fuhrman Rachel E Gallery Dirk Gevers Richard A Gibbs Inigo San Gil Antonio Gonzalez Jeffrey I Gordon Robert Guralnick Wolfgang Hankeln Sarah Highlander Philip Hugenholtz Janet Jansson Andrew L Kau Scott T Kelley Jerry Kennedy Dan Knights Omry Koren Justin Kuczynski Nikos Kyrpides Robert Larsen Christian L Lauber Teresa Legg Ruth E Ley Catherine A Lozupone Wolfgang Ludwig Donna Lyons Eamonn Maguire Barbara A Methé Folker Meyer Brian Muegge Sara Nakielny Karen E Nelson Diana Nemergut Josh D Neufeld Lindsay K Newbold Anna E Oliver Norman R Pace Giriprakash Palanisamy Jörg Peplies Joseph Petrosino Lita Proctor Elmar Pruesse Christian Quast Jeroen Raes Sujeevan Ratnasingham Jacques Ravel David A Relman Susanna Assunta-Sansone Patrick D Schloss Lynn Schriml Rohini Sinha Michelle I Smith Erica Sodergren Aymé Spo Jesse Stombaugh James M Tiedje Doyle V Ward George M Weinstock Doug Wendel Owen White Andrew Whiteley Andreas Wilke Jennifer R Wortman Tanya Yatsunenko Frank Oliver Glöckner

Nat Biotechnol 2011 May;29(5):415-20

Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

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https://darchive.mblwhoilibrary.org/bitstream/handle/1912/46
Web Search
http://www.nature.com/doifinder/10.1038/nbt.1823
Publisher Site
http://dx.doi.org/10.1038/nbt.1823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367316PMC
May 2011

Standardization Initiatives in the (eco)toxicogenomics domain: a review.

Comp Funct Genomics 2004 ;5(8):633-41

EMBL-EBI, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1002/cfg.447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447477PMC
June 2010

Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network.

Genes Nutr 2009 Jun 30;4(2):113-22. Epub 2009 Apr 30.

Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany,

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http://dx.doi.org/10.1007/s12263-009-0123-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690731PMC
June 2009

Towards interoperable reporting standards for omics data: hopes and hurdles.

Summit Transl Bioinform 2009 Mar 1;2009:112-5. Epub 2009 Mar 1.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041584PMC
March 2009

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group.

OMICS 2006 ;10(2):164-71

EMBL-EBI, European Nutrigenomics Organisation (NuGO), Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1089/omi.2006.10.164DOI Listing
November 2007

Data storage: bringing us a step closer to data sharing?

Br J Nutr 2006 Jun;95(6):1237-9

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http://dx.doi.org/10.1079/bjn20061747DOI Listing
June 2006

The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case.

BMC Bioinformatics 2006 May 25;7:267. Epub 2006 May 25.

Microarray Informatics Team, The European Bioinformatics Institute--European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-7-267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524992PMC
May 2006

Defining best practice for microarray analyses in nutrigenomic studies.

Br J Nutr 2005 Apr;93(4):425-32

Institute of Food Research, Norwich Research Park, Norwich NR5 7UA, UK.

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http://dx.doi.org/10.1079/bjn20041385DOI Listing
April 2005

ArrayExpress: a public database of gene expression data at EBI.

C R Biol 2003 Oct-Nov;326(10-11):1075-8

EMBL Outstation-Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1016/j.crvi.2003.09.026DOI Listing
May 2004