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ORCIDPhilippe Rocca-Serra
- > Home > Persons > Philippe Rocca-Serra
Publications
- 2021
[j38]Graham Lee, Sebastian Bacon, Ian Bush, Laura Fortunato, David Gavaghan, Thibault Lestang, Caroline Morton, Martin Robinson, Philippe Rocca-Serra, Susanna-Assunta Sansone, Helena Webb
:
Barely sufficient practices in scientific computing. Patterns 2(2): 100206 (2021)- 2020
- [j37]Annika Jacobsen, Ricardo de Miranda Azevedo, Nick S. Juty, Dominique Batista, Simon J. Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. A. Evelo, Carole A. Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina M. Hettne, Jaap Heringa, Rob W. W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George O. Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes:
FAIR Principles: Interpretations and Implementation Considerations. Data Intell. 2(1-2): 10-29 (2020) - [j36]Peter McQuilton, Dominique Batista, Oya Beyan, Ramón Granell, Simon J. Coles, Massimiliano Izzo, Allyson L. Lister, Robert Pergl, Philippe Rocca-Serra, Ben Schaap, Hugh P. Shanahan, Milo Thurston, Susanna-Assunta Sansone:
Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data. Data Intell. 2(1-2): 151-157 (2020) - 2019
- [j35]Payam Emami Khoonsari, Pablo A. Moreno, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Steffen Neumann, Kristian Peters, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly A. Selivanov, Etienne A. Thévenot, Michael van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima, Ola Spjuth:
Interoperable and scalable data analysis with microservices: applications in metabolomics. Bioinform. 35(19): 3752-3760 (2019) - [i2]Peter Wittenburg, Hana Pergl Sustkova, Annalisa Montesanti, Margreet Bloemers, S. H. de Waard, Mark A. Musen, John Graybeal, Kristina M. Hettne, Annika Jacobsen, Robert Pergl, Rob W. W. Hooft, Christine Staiger, Celia W. G. van Gelder, Sebastiaan L. Knijnenburg, A. C. van Arkel, Bert Meerman, Mark D. Wilkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, Peter McQuilton, Alejandra N. González-Beltrán, G. J. C. Aben, Patrícia Henning, Maria Simone de Menezes Alencar, C. Ribeiro, C. R. L. Silva, Luís Fernando Sayão, Luana Sales, Viviane Veiga, Jefferson Lima, Simone Dib, Paula Xavier dos Santos, R. Murtinho, Jakob Tendel, B. F. Schaap, P. M. Brouwer, A. K. Gavai, Yamine Bouzembrak, Hans J. P. Marvin, Albert Mons, Tobias Kuhn, A. A. Gambardella, Ricardo de Miranda Azevedo, Vesa Muhonen, Mira van der Naald, N. W. Smit, M. J. Buys, Taco F. de Bruin, Fieke Schoots, H. J. E. Goodson, Henry S. Rzepa, Keith G. Jeffery, Hugh P. Shanahan, M. Axton, Veniamin Tkachenko, Anne Deslattes Mays, Natalie Meyers, Michael Conlon, Laurel L. Haak, Erik A. Schultes:
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data. CoRR abs/1902.11162 (2019) - 2018
- [j34]Alejandra N. González-Beltrán, John Campbell, Patrick J. Dunn, Diana Guijarro, Sanda Ionescu, Hyeoneui Kim, Jared Lyle, Jeffrey A. Wiser, Susanna-Assunta Sansone, Philippe Rocca-Serra:
Data discovery with DATS: exemplar adoptions and lessons learned. J. Am. Medical Informatics Assoc. 25(1): 13-16 (2018) - [j33]Xiaoling Chen, Anupama E. Gururaj, Ibrahim Burak Özyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra N. González-Beltrán, Claudiu Farcas, Todd Johnson, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Ian Fore, Lucila Ohno-Machado, Jeffrey S. Grethe, Hua Xu:
DataMed - an open source discovery index for finding biomedical datasets. J. Am. Medical Informatics Assoc. 25(3): 300-308 (2018) - 2017
- [i1]Merlijn N. van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-García, Rafael C. Jiménez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata P. Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck:
The future of metabolomics in ELIXIR. F1000Research 6: 1649- (2017) - 2016
- [j31]Peter McQuilton, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Milo Thurston, Allyson L. Lister, Eamonn Maguire, Susanna-Assunta Sansone:
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. Database J. Biol. Databases Curation 2016 (2016) - [c6]Jeffrey S. Grethe, Ibrahim Burak Özyurt, Hua Xu, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
A Scalable Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System. AMIA 2016 - [c5]Hua Xu, Jeffrey S. Grethe, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Yueling Li, Ibrahim Burak Özyurt, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Groundwork for Biomedical Data Discovery. AMIA 2016 - 2015
- [j29]Philippe Rocca-Serra, Ramona L. Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra N. González-Beltrán:
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. Database J. Biol. Databases Curation 2015 (2015) - [j27]Mark A. Musen, Carol A. Bean, Kei-Hoi Cheung, Michel Dumontier, Kim A. Durante, Olivier Gevaert, Alejandra N. González-Beltrán, Purvesh Khatri, Steven H. Kleinstein, Martin J. O'Connor, Yannick Pouliot, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jeffrey A. Wiser:
The center for expanded data annotation and retrieval. J. Am. Medical Informatics Assoc. 22(6): 1148-1152 (2015) - [c4]Felix Shaw, Anthony Etuk, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Paul J. Kersey, Ruth Bastow, Susanna-Assunta Sansone, Vicky Schneider, Robert P. Davey, David Johnson:
COPO - Linked Open Infrastructure for Plant Data. SWAT4LS 2015: 181-182 - 2014
- [j25]Alejandra N. González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra:
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. BMC Bioinform. 15(S-1): S11 (2014) - [j24]Alejandra N. González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra:
linkedISA: semantic representation of ISA-Tab experimental metadata. BMC Bioinform. 15(S-14): S4 (2014) - [j23]Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra N. González-Beltrán, Christopher I. Hunter, Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Maslen, Alex L. Mitchell, Gift Nuka, Arnaud Oisel, Sebastien Pesseat, Rajesh Radhakrishnan, Philippe Rocca-Serra, Maxim Scheremetjew, Peter Sterk, Daniel Vaughan, Guy Cochrane, Dawn Field, Susanna-Assunta Sansone:
EBI metagenomics - a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 42(Database-Issue): 600-606 (2014) - [c3]Philippe Rocca-Serra, Ramona L. Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra N. González-Beltrán:
Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: the Interoperability Gains of a Modular Approach. ICBO 2014: 64 - [c2]Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone, Min Chen:
Redesigning the Sequence Logo with Glyph-based Approaches to Aid Interpretation. EuroVis (Short Papers) 2014 - 2013
- [j22]Reza M. Salek, Kenneth Haug, Pablo Conesa, Janna Hastings, Mark Williams, Tejasvi Mahendraker, Eamonn Maguire, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Susanna-Assunta Sansone, Christoph Steinbeck:
The MetaboLights repository: curation challenges in metabolomics. Database J. Biol. Databases Curation 2013 (2013) - [j21]Eamonn Maguire, Alejandra N. González-Beltrán, Patricia L. Whetzel, Susanna-Assunta Sansone, Philippe Rocca-Serra:
OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets. Bioinform. 29(4): 525-527 (2013) - [j20]Kenneth Haug, Reza M. Salek, Pablo Conesa, Janna Hastings, Paula de Matos, Mark Rijnbeek, Tejasvi Mahendraker, Mark Williams, Steffen Neumann, Philippe Rocca-Serra, Eamonn Maguire, Alejandra N. González-Beltrán, Susanna-Assunta Sansone, Julian L. Griffin, Christoph Steinbeck:
MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res. 41(Database-Issue): 781-786 (2013) - [j19]Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jim Davies, Min Chen:
Visual Compression of Workflow Visualizations with Automated Detection of Macro Motifs. IEEE Trans. Vis. Comput. Graph. 19(12): 2576-2585 (2013) - 2012
- [j16]Shannan J. Ho Sui, Kimberly Begley, Dorothy Reilly, Brad Chapman, Ray McGovern, Philippe Rocca-Serra, Eamonn Maguire, Gabriel M. Altschuler, Terah A. A. Hansen, Ramakrishna Sompallae, Andrei Krivtsov, Ramesh A. Shivdasani, Scott A. Armstrong, Aedín C. Culhane, Mick Correll, Susanna-Assunta Sansone, Oliver Hofmann, Winston Hide:
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res. 40(Database-Issue): 984-991 (2012) - [j15]Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jim Davies, Min Chen:
Taxonomy-Based Glyph Design - with a Case Study on Visualizing Workflows of Biological Experiments. IEEE Trans. Vis. Comput. Graph. 18(12): 2603-2612 (2012) - 2011
- [j14]Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan Remy Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann, Bjoern Peters:
Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontology 6(1): 13-22 (2011) - [j13]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Database J. Biol. Databases Curation 2011 (2011) - [j12]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 39(Database-Issue): 7-10 (2011) - 2010
- [j11]Philippe Rocca-Serra, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar, Chris F. Taylor, Kimberly Begley, Dawn Field, Stephen C. Harris, Winston Hide, Oliver Hofmann, Steffen Neumann, Peter Sterk, Weida Tong, Susanna-Assunta Sansone:
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinform. 26(18): 2354-2356 (2010) - [j10]Ryan Remy Brinkman, Mélanie Courtot, Dirk Derom, Jennifer Fostel, Yongqun He, Phillip W. Lord, James Malone, Helen E. Parkinson, Björn Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.:
Modeling biomedical experimental processes with OBI. J. Biomed. Semant. 1(S-1): S7 (2010) - 2009
- [j9]Daniel Schober, Barry Smith, Suzanna E. Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F. Taylor, Philippe Rocca-Serra, Susanna-Assunta Sansone:
Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinform. 10 (2009) - [j8]Helen E. Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammadreza Shojatalab, Niran Abeygunawardena, Hugo Bérubé, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Ele Holloway, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Ibne Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, Alvis Brazma:
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 37(Database-Issue): 868-872 (2009) - 2006
- [j7]Patricia L. Whetzel, Helen E. Parkinson, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris F. Taylor, Joseph White, Christian J. Stoeckert Jr.:
The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinform. 22(7): 866-873 (2006) - [j6]Alexander García Castro, Philippe Rocca-Serra, Robert Stevens, Chris F. Taylor, Karim Nashar, Mark A. Ragan, Susanna-Assunta Sansone:
The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case. BMC Bioinform. 7: 267 (2006) - 2005
- [j4]Ugis Sarkans, Helen E. Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna-Assunta Sansone, Anna Farne, Tim F. Rayner, Alvis Brazma:
The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinform. 21(8): 1495-1501 (2005) - [j3]Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, Sergio Contrino, Richard Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, P. Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim F. Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone, Alvis Brazma:
ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 33(Database-Issue): 553-555 (2005) - 2003
- [j2]Alvis Brazma, Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, Susanna-Assunta Sansone:
ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31(1): 68-71 (2003)
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