Showing 123 publications by Philippe Rocca-Serra
ELIXIR biovalidator for semantic validation of life science metadata.
Liyanage I, Burdett T, Droesbeke B, Erdos K, Fernandez R et al. (2022), Bioinformatics (Oxford, England), 38(11), btac195
ISA API: An open platform for interoperable life science experimental metadata.
Johnson D, Batista D, Cochrane K, Davey RP, Etuk A et al. (2021), GigaScience, 10(9)
Road to effective data curation for translational research.
Gu W, Hasan S, Rocca-Serra P & Satagopam VP (2021), Drug discovery today, 26(3), 626-630
Enabling reusability of plant phenomic datasets with MIAPPE 1.1.
Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN et al. (2020), New Phytologist
Semantic concept schema of the linear mixed model of experimental observations
Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, Rocca-Serra P, Gonzalez-Beltran AN et al. (2020), Scientific Data, 7(1)
BibTeX
@article{semanticconcept-2020/2,
title={Semantic concept schema of the linear mixed model of experimental observations},
author={Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, Rocca-Serra P, Gonzalez-Beltran AN et al.},
journal={Scientific Data},
volume={7},
number={70},
publisher={Nature Research },
year = "2020"
}
The Data Tags Suite (DATS) model for discovering data access and use requirements
Alter G, Gonzalez-Beltran A, Ohno-Machado L & Rocca-Serra P (2020), GigaScience, 9(2)
BibTeX
@article{thedatatagssuit-2020/2,
title={The Data Tags Suite (DATS) model for discovering data access and use requirements},
author={Alter G, Gonzalez-Beltran A, Ohno-Machado L & Rocca-Serra P},
journal={GigaScience},
volume={9},
number={giz165},
publisher={Oxford University Press},
year = "2020"
}
Use cases, best practice and reporting standards for metabolomics in regulatory toxicology
Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT et al. (2019), Nature Communications, 10(1)
BibTeX
@article{usecasesbestpra-2019/12,
title={Use cases, best practice and reporting standards for metabolomics in regulatory toxicology},
author={Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT et al.},
journal={Nature Communications},
volume={10},
number={3041},
publisher={Springer Science and Business Media LLC},
year = "2019"
}
Experiment design driven FAIRification of omics data matrices, an exemplar
Rocca-Serra P & Sansone S (2019), Scientific Data, 6, 271
Evaluating FAIR maturity through a scalable, automated, community-governed framework
Dumontier M, Sansone S, Bonino Da Silva Santos LO, Prieto M, Batista D et al. (2019), Scientific Data, 6
BibTeX
@article{evaluatingfairm-2019/9,
title={Evaluating FAIR maturity through a scalable, automated, community-governed framework},
author={Dumontier M, Sansone S, Bonino Da Silva Santos LO, Prieto M, Batista D et al.},
journal={Scientific Data},
volume={6},
number={174},
publisher={Springer Nature},
year = "2019"
}
Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework.
Dumontier M, Sansone S, Bonino Da Silva Santos LO, Prieto M, Batista D et al. (2019), Scientific Data, 6
BibTeX
@article{authorcorrectio-2019/9,
title={Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework.},
author={Dumontier M, Sansone S, Bonino Da Silva Santos LO, Prieto M, Batista D et al.},
journal={Scientific Data},
volume={6},
number={230},
publisher={Nature Research},
year = "2019"
}
Evaluating FAIR maturity through a scalable, automated, community-governed framework
Wilkinson M, Dumontier M, Sansone S, Da Silva Santos LOB, Prieto M et al. (2019), Scientific Data, 6
BibTeX
@article{evaluatingfairm-2019/9,
title={Evaluating FAIR maturity through a scalable, automated, community-governed framework},
author={Wilkinson M, Dumontier M, Sansone S, Da Silva Santos LOB, Prieto M et al.},
journal={Scientific Data},
volume={6},
number={174},
publisher={Nature Research},
year = "2019"
}
PlatformTM, a standards-based data custodianship platform for translational medicine research
Emam I, Elyasigomari V, Matthews A, Pavlidis S, Rocca-Serra P et al. (2019), Scientific Data, 6(1)
A data citation roadmap for scholarly data repositories
Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H et al. (2019), Scientific Data, 6(1)
FAIRsharing as a community approach to standards, repositories and policies
Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M et al. (2019), Nature Biotechnology, 37(4), 358-367
BibTeX
@article{fairsharingasac-2019/4,
title={FAIRsharing as a community approach to standards, repositories and policies},
author={Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M et al.},
journal={Nature Biotechnology},
volume={37},
pages={358-367},
publisher={Springer Nature},
year = "2019"
}
mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.
Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K et al. (2019), Analytical chemistry, 91(5), 3302-3310
Addendum: The FAIR Guiding Principles for scientific data management and stewardship.
Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M et al. (2019), Scientific data, 6(1), 6-6
Interoperable and scalable data analysis with microservices: applications in metabolomics
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M et al. (2019), Bioinformatics, 35(9), 3752-3760
BibTeX
@article{interoperablean-2019/3,
title={Interoperable and scalable data analysis with microservices: applications in metabolomics},
author={Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M et al.},
journal={Bioinformatics},
volume={35},
pages={3752-3760},
publisher={Oxford University Press},
year = "2019"
}
PhenoMeNal: processing and analysis of metabolomics data in the cloud.
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M et al. (2019), GigaScience, 8(2)
A computational framework for complex disease stratification from multiple large-scale datasets.
De Meulder B, Lefaudeux D, Mazein A, Chaiboonchoe A, Ahmed H et al. (2018), BMC Systems Biology, 12(60)
BibTeX
@article{acomputationalf-2018/5,
title={A computational framework for complex disease stratification from multiple large-scale datasets.},
author={De Meulder B, Lefaudeux D, Mazein A, Chaiboonchoe A, Ahmed H et al.},
journal={BMC Systems Biology},
volume={12},
publisher={BioMed Central},
year = "2018"
}
nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A et al. (2018), Analytical chemistry, 90(1), 649-656
DataMed - an open source discovery index for finding biomedical datasets
Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E et al. (2018), Journal of the American Medical Informatics Association, 25(3), 300-308
BibTeX
@article{datamedanopenso-2018/1,
title={DataMed - an open source discovery index for finding biomedical datasets},
author={Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E et al.},
journal={Journal of the American Medical Informatics Association},
volume={25},
pages={300-308},
publisher={Oxford University Press},
year = "2018"
}
FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies
Sansone S-A, McQuilton PETER, Rocca-Serra PHILIPPE, Gonzalez-Beltran ALEJANDRA, Izzo MASSIMILIANO et al. (2018), NATURE BIOTECHNOLOGY(4)
BibTeX
@article{fairsharingacoh-2018/1,
title={FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies},
author={Sansone S-A, McQuilton PETER, Rocca-Serra PHILIPPE, Gonzalez-Beltran ALEJANDRA, Izzo MASSIMILIANO et al.},
journal={NATURE BIOTECHNOLOGY},
publisher={Cold Spring Harbor Laboratory},
year = "2018"
}
Data discovery with DATS: exemplar adoptions and lessons learned
Gonzalez-Beltran A, Campbell J, Dunn P, Guijarro D, Ionescu S et al. (2017), Journal of the American Medical Informatics Association, 25(1), 13-16
BibTeX
@article{datadiscoverywi-2017/12,
title={Data discovery with DATS: exemplar adoptions and lessons learned},
author={Gonzalez-Beltran A, Campbell J, Dunn P, Guijarro D, Ionescu S et al.},
journal={Journal of the American Medical Informatics Association},
volume={25},
pages={13-16},
publisher={Oxford University Press},
year = "2017"
}
Interoperable and scalable data analysis with microservices: Applications in Metabolomics
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M et al. (2017)
The future of metabolomics in ELIXIR.
van Rijswijk M, van Rijswijk M, Beirnaert C, Beirnaert C, Caron C et al. (2017), F1000Research, 6, 1649-1649
DATS: the data tag suite to enable discoverability of datasets
Sansone S-A, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS et al. (2017), Scientific Data
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
McMurry JA, Juty N, Blomberg N, Gonzalez-Beltran A, Rocca-Serra P et al. (2017), PLoS Biology, 15(6)
BibTeX
@article{identifiersfort-2017/6,
title={Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data},
author={McMurry JA, Juty N, Blomberg N, Gonzalez-Beltran A, Rocca-Serra P et al.},
journal={PLoS Biology},
volume={15},
number={e2001414},
publisher={Public Library of Science},
year = "2017"
}
Finding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S-A, Alter G, Fore I, Grethe JS et al. (2017), Nature Genetics, 49(6), 816-819
BibTeX
@article{findingusefulda-2017/5,
title={Finding useful data across multiple biomedical data repositories using DataMed},
author={Ohno-Machado L, Sansone S-A, Alter G, Fore I, Grethe JS et al.},
journal={Nature Genetics},
volume={49},
pages={816-819},
publisher={Nature Publishing Group},
year = "2017"
}
BioSharing: harnessing metadata standards for the data commons
Sansone S-A, Gonzalez-Beltran A, Rocca-Serra P, McQuilton P, Izzo M et al. (2017), bioRxiv
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Larralde M, Lawson TN, Weber RJ, Moreno P, Haug K et al. (2017), Bioinformatics
Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop
Verspoor K, Oellrich A, Collier N, Groza T, Rocca-Serra P et al. (2016), Journal of Biomedical Semantics, 7(1)
BibTeX
@article{thematicissueof-2016/12,
title={Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop},
author={Verspoor K, Oellrich A, Collier N, Groza T, Rocca-Serra P et al.},
journal={Journal of Biomedical Semantics},
volume={7},
number={66},
publisher={BioMed Central},
year = "2016"
}
Measures for interoperability of phenotypic data: minimum information requirements and formatting.
Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D et al. (2016), Plant Methods, 12(1), 44
BibTeX
@article{measuresforinte-2016/11,
title={Measures for interoperability of phenotypic data: minimum information requirements and formatting.},
author={Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D et al.},
journal={Plant Methods},
volume={12},
pages={44},
publisher={BioMed Central},
year = "2016"
}
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.
McQuilton P, Gonzalez-Beltran A, Rocca-Serra P, Thurston M, Lister A et al. (2016), Database, 2016
BibTeX
@article{biosharingcurat-2016/5,
title={BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.},
author={McQuilton P, Gonzalez-Beltran A, Rocca-Serra P, Thurston M, Lister A et al.},
journal={Database},
volume={2016},
publisher={Oxford University Press},
year = "2016"
}
The ontology for biomedical investigations.
Lin Y, Lister AL, Lord P, Malone J, Manduchi E et al. (2016), PLoS One, 11(4), e0154556
MetaboLights: An Open-Access Database Repository for Metabolomics Data.
Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P et al. (2016), Current protocols in bioinformatics, 53, 14.13.1-14.13.18
Data standards can boost metabolomics research, and if there is a will, there is a way.
Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S et al. (2016), Metabolomics : Official journal of the Metabolomic Society, 12(1), 14
BibTeX
@article{datastandardsca-2016/1,
title={Data standards can boost metabolomics research, and if there is a will, there is a way.},
author={Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S et al.},
journal={Metabolomics : Official journal of the Metabolomic Society},
volume={12},
pages={14},
publisher={Springer US},
year = "2016"
}
The FAIR Guiding Principles for scientific data management and stewardship.
Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A et al. (2016), Scientific data
Coordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
Salek RM, Neumann S, Schober D, Hummel J, Billiau K et al. (2015), Metabolomics, 11(6), 1598-1599
BibTeX
@article{coordinationofs-2015/12,
title={Coordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access},
author={Salek RM, Neumann S, Schober D, Hummel J, Billiau K et al.},
journal={Metabolomics},
volume={11},
pages={1598-1599},
publisher={Springer},
year = "2015"
}
Embedding standards in metabolomics: the Metabolomics Society data standards task group
Salek RM, Arita M, Dayalan S, Ebbels T, Jones AR et al. (2015), METABOLOMICS, 11(4), 782-783
The center for expanded data annotation and retrieval.
Musen MA, Bean CA, Cheung K-H, Dumontier M, Durante KA et al. (2015), Journal of the American Medical Informatics Association : JAMIA, 22(6), 1148-1152
BibTeX
@article{thecenterforexp-2015/6,
title={The center for expanded data annotation and retrieval.},
author={Musen MA, Bean CA, Cheung K-H, Dumontier M, Durante KA et al.},
journal={Journal of the American Medical Informatics Association : JAMIA},
volume={22},
pages={1148-1152},
publisher={Oxford University Press},
year = "2015"
}
Special issue on bio-ontologies and phenotypes.
Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K et al. (2015), Journal of biomedical semantics, 6, 40
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.
Rocca-Serra P, Walls R, Parnell J, Gallery R, Zheng J et al. (2015), Database : the journal of biological databases and curation, 2015
BibTeX
@article{modelingamicrob-2015/1,
title={Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.},
author={Rocca-Serra P, Walls R, Parnell J, Gallery R, Zheng J et al.},
journal={Database : the journal of biological databases and curation},
volume={2015},
year = "2015"
}
COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.
Salek RM, Neumann S, Schober D, Hummel J, Billiau K et al. (2015), Metabolomics : Official journal of the Metabolomic Society, 11(6), 1587-1597
BibTeX
@article{coordinationofs-2015/1,
title={COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.},
author={Salek RM, Neumann S, Schober D, Hummel J, Billiau K et al.},
journal={Metabolomics : Official journal of the Metabolomic Society},
volume={11},
pages={1587-1597},
year = "2015"
}
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.
González-Beltrán A, Li P, Zhao J, Avila-Garcia MS, Roos M et al. (2015), PloS one, 10(7), e0127612
BibTeX
@article{frompeerreviewe-2015/1,
title={From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.},
author={González-Beltrán A, Li P, Zhao J, Avila-Garcia MS, Roos M et al.},
journal={PloS one},
volume={10},
pages={e0127612},
year = "2015"
}
COPO - Linked open infrastructure for plant data
Shaw F, Etuk A, Gonzalez-Beltran A, Rocca-Serra P, Johnson D et al. (2015), CEUR Workshop Proceedings, 1546, 181-182
BibTeX
@inproceedings{copolinkedopeni-2015/1,
title={COPO - Linked open infrastructure for plant data},
author={Shaw F, Etuk A, Gonzalez-Beltran A, Rocca-Serra P, Johnson D et al.},
pages={181-182},
year = "2015"
}
Meeting report: advancing practical applications of biodiversity ontologies
Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL et al. (2014), STANDARDS IN GENOMIC SCIENCES, 9(1)
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium (2014), Nature biotechnology, 32(9), 903-914
Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting
Soldatova LN, Rocca-Serra P, Dumontier M & Shah NH (2014), JOURNAL OF BIOMEDICAL SEMANTICS, 5
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y et al. (2014), Journal of biomedical semantics, 5(1), 5
BibTeX
@article{biohackathonser-2014/2,
title={BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.},
author={Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y et al.},
journal={Journal of biomedical semantics},
volume={5},
pages={5},
year = "2014"
}
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A et al. (2014), Nucleic acids research, 42(Database issue), D600-D606
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.
González-Beltrán A, Neumann S, Maguire E, Sansone S-A & Rocca-Serra P (2014), BMC bioinformatics, 15 Suppl 1, S11
BibTeX
@article{therisarbiocond-2014/1,
title={The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.},
author={González-Beltrán A, Neumann S, Maguire E, Sansone S-A & Rocca-Serra P},
journal={BMC bioinformatics},
volume={15 Suppl 1},
pages={S11},
year = "2014"
}
linkedISA: semantic representation of ISA-Tab experimental metadata.
González-Beltrán A, Maguire E, Sansone S-A & Rocca-Serra P (2014), BMC bioinformatics, 15 Suppl 14, S4
Visual compression of workflow visualizations with automated detection of macro motifs.
Maguire E, Rocca-Serra P, Sansone S-A, Davies J & Chen M (2013), IEEE transactions on visualization and computer graphics, 19(12), 2576-2585
BibTeX
@article{visualcompressi-2013/12,
title={Visual compression of workflow visualizations with automated detection of macro motifs.},
author={Maguire E, Rocca-Serra P, Sansone S-A, Davies J & Chen M},
journal={IEEE transactions on visualization and computer graphics},
volume={19},
pages={2576-2585},
year = "2013"
}
Standardizing data.
Baker NA, Klemm JD, Harper SL, Gaheen S, Heiskanen M et al. (2013), Nature nanotechnology, 8(2), 73-74
OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.
Maguire E, González-Beltrán A, Whetzel PL, Sansone S-A & Rocca-Serra P (2013), Bioinformatics (Oxford, England), 29(4), 525-527
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P et al. (2013), Nucleic acids research, 41(Database issue), D781-D786
BibTeX
@article{metabolightsano-2013/1,
title={MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.},
author={Haug K, Salek RM, Conesa P, Hastings J, de Matos P et al.},
journal={Nucleic acids research},
volume={41},
pages={D781-D786},
year = "2013"
}
The MetaboLights repository: curation challenges in metabolomics.
Salek RM, Haug K, Conesa P, Hastings J, Williams M et al. (2013), Database : the journal of biological databases and curation, 2013, bat029
BibTeX
@article{themetabolights-2013/1,
title={The MetaboLights repository: curation challenges in metabolomics.},
author={Salek RM, Haug K, Conesa P, Hastings J, Williams M et al.},
journal={Database : the journal of biological databases and curation},
volume={2013},
pages={bat029},
year = "2013"
}
The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework.
Ho Sui S, Merrill E, Gehlenborg N, Haseley P, Sytchev I et al. (2013), AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2013, 70
BibTeX
@article{thestemcellcomm-2013/1,
title={The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework.},
author={Ho Sui S, Merrill E, Gehlenborg N, Haseley P, Sytchev I et al.},
journal={AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science},
volume={2013},
pages={70},
year = "2013"
}
Taxonomy-Based Glyph Design—with a Case Study on Visualizing Workflows of Biological Experiments.
Maguire E, Rocca-Serra P, Sansone S-A, Davies J & Chen M (2012), IEEE transactions on visualization and computer graphics, 18(12), 2603-2612
BibTeX
@article{taxonomybasedgl-2012/12,
title={Taxonomy-Based Glyph Design—with a Case Study on Visualizing Workflows of Biological Experiments.},
author={Maguire E, Rocca-Serra P, Sansone S-A, Davies J & Chen M},
journal={IEEE transactions on visualization and computer graphics},
volume={18},
pages={2603-2612},
year = "2012"
}
MetaboLights: towards a new COSMOS of metabolomics data management.
Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M et al. (2012), Metabolomics : Official journal of the Metabolomic Society, 8(5), 757-760
BibTeX
@article{metabolightstow-2012/10,
title={MetaboLights: towards a new COSMOS of metabolomics data management.},
author={Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M et al.},
journal={Metabolomics : Official journal of the Metabolomic Society},
volume={8},
pages={757-760},
year = "2012"
}
Translating standards into practice - one Semantic Web API for Gene Expression.
Deus HF, Prud'hommeaux E, Miller M, Zhao J, Malone J et al. (2012), Journal of biomedical informatics, 45(4), 782-794
Translating standards into practice - One Semantic Web API for Gene Expression
Deus HF, Prud'hommeaux E, Miller M, Zhao J, Malone J et al. (2012), Journal of Biomedical Informatics, 45(4), 782-794
A call for an international network of genomic observatories (GOs).
Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J et al. (2012), GigaScience, 1(1), 5
A call for an international network of genomic observatories (GOs)
Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J et al. (2012), GigaScience, 1(5)
BibTeX
@article{acallforaninter-2012/7,
title={A call for an international network of genomic observatories (GOs)},
author={Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J et al.},
journal={GigaScience},
volume={1},
year = "2012"
}
The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness.
Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B et al. (2012), Standards in genomic sciences, 6(3), 438-447
BibTeX
@article{themetadatacove-2012/7,
title={The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness.},
author={Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B et al.},
journal={Standards in genomic sciences},
volume={6},
pages={438-447},
year = "2012"
}
On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities.
Sansone S-A & Rocca-Serra P (2012), GigaScience, 1(1), 10
graph2tab, a library to convert experimental workflow graphs into tabular formats.
Brandizi M, Kurbatova N, Sarkans U & Rocca-Serra P (2012), Bioinformatics (Oxford, England), 28(12), 1665-1667
Translating standards into practice - One Semantic Web API for Gene Expression
Deus HF, Zhao J, McCusker J, Fox R, Prud'hommeaux E et al. (2012), ACM International Conference Proceeding Series, 6-7
Toward interoperable bioscience data
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C et al. (2012), Nature Genetics, 44(2), 121-126
Toward interoperable bioscience data.
Sansone S-A, Rocca-Serra P, Field D, Maguire E, Taylor C et al. (2012), Nature genetics, 44(2), 121-126
The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness
Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B et al. (2012), STANDARDS IN GENOMIC SCIENCES, 6(3), 444-453
BibTeX
@article{themetadatacove-2012/,
title={The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness},
author={Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B et al.},
journal={STANDARDS IN GENOMIC SCIENCES},
volume={6},
pages={444-453},
year = "2012"
}
Investigation-Study-Assay, a toolkit for standardizing data capture and sharing
Rocca-Serra P, Maguire E, Taylor C, Field D, Wittenberger T et al. (2012)(16), 173-188
BibTeX
@misc{investigationst-2012/,
title={Investigation-Study-Assay, a toolkit for standardizing data capture and sharing},
author={Rocca-Serra P, Maguire E, Taylor C, Field D, Wittenberger T et al.},
year = "2012"
}
Sharing and archiving nucleic acid structure mapping data.
Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P et al. (2011), RNA (New York, N.Y.), 17(7), 1204-1212
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR et al. (2011), Nature biotechnology, 29(5), 415-420
BibTeX
@article{minimuminformat-2011/5,
title={Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.},
author={Yilmaz P, Kottmann R, Field D, Knight R, Cole JR et al.},
journal={Nature biotechnology},
volume={29},
pages={415-420},
year = "2011"
}
Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone S-A, Taylor C et al. (2011), Database : the journal of biological databases and curation, 2011, baq027
BibTeX
@article{towardsbiodbcor-2011/1,
title={Towards BioDBcore: a community-defined information specification for biological databases.},
author={Gaudet P, Bairoch A, Field D, Sansone S-A, Taylor C et al.},
journal={Database : the journal of biological databases and curation},
volume={2011},
pages={baq027},
year = "2011"
}
Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone S-A, Taylor C et al. (2011), Nucleic acids research, 39(Database issue), D7-10
Data standards for Omics data: the basis of data sharing and reuse.
Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J et al. (2011), Methods in molecular biology (Clifton, N.J.), 719, 31-69
Overcoming the ontology enrichment bottleneck with Quick Term Templates
Rocca-Serra P, Ruttenberg A, O'Connor MJ, Whetzel PL, Schober D et al. (2011), APPLIED ONTOLOGY, 6(1), 13-22
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.
Kettner C, Field D, Sansone S-A, Taylor C, Aerts J et al. (2010), Standards in genomic sciences, 3(3), 259-266
BibTeX
@article{meetingreportfr-2010/12,
title={Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.},
author={Kettner C, Field D, Sansone S-A, Taylor C, Aerts J et al.},
journal={Standards in genomic sciences},
volume={3},
pages={259-266},
year = "2010"
}
Meeting Report: BioSharing at ISMB 2010.
Field D, Sansone S, Delong EF, Sterk P, Friedberg I et al. (2010), Standards in genomic sciences, 3(3), 254-258
Ontology representation and ANOVA analysis of vaccine protection investigation
He Y, Xiang Z, Todd T, Courtot M, Brinkman R et al. (2010), CEUR Workshop Proceedings, 754
BibTeX
@inproceedings{ontologyreprese-2010/12,
title={Ontology representation and ANOVA analysis of vaccine protection investigation},
author={He Y, Xiang Z, Todd T, Courtot M, Brinkman R et al.},
year = "2010"
}
Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies.
van Ommen B, Bouwman J, Dragsted LO, Drevon CA, Elliott R et al. (2010), Genes & nutrition, 5(3), 189-203
BibTeX
@article{challengesofmol-2010/9,
title={Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies.},
author={van Ommen B, Bouwman J, Dragsted LO, Drevon CA, Elliott R et al.},
journal={Genes & nutrition},
volume={5},
pages={189-203},
year = "2010"
}
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.
Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C et al. (2010), Bioinformatics (Oxford, England), 26(18), 2354-2356
BibTeX
@article{isasoftwaresuit-2010/9,
title={ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.},
author={Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C et al.},
journal={Bioinformatics (Oxford, England)},
volume={26},
pages={2354-2356},
year = "2010"
}
Modeling biomedical experimental processes with OBI
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y et al. (2010), Journal of Biomedical Semantics, 1(1)
Modeling biomedical experimental processes with OBI.
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y et al. (2010), Journal of biomedical semantics, 1 Suppl 1, S7
Megascience. 'Omics data sharing.
Field D, Sansone S-A, Collis A, Booth T, Dukes P et al. (2009), Science (New York, N.Y.), 326(5950), 234-236
Reporting Standards for Omics Data: Instruction for Use
Sansone S-A & Rocca-Serra P (2009), MOLECULAR & CELLULAR TOXICOLOGY, 5(3), 46-46
BibTeX
@inproceedings{reportingstanda-2009/9,
title={Reporting Standards for Omics Data: Instruction for Use},
author={Sansone S-A & Rocca-Serra P},
pages={46-46},
year = "2009"
}
ISA Infrastructure - Assisting Users to Report Experimental Metadata
Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor CF et al. (2009), MOLECULAR & CELLULAR TOXICOLOGY, 5(3), 40-40
BibTeX
@inproceedings{isainfrastructu-2009/9,
title={ISA Infrastructure - Assisting Users to Report Experimental Metadata},
author={Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor CF et al.},
pages={40-40},
year = "2009"
}
Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network.
Harttig U, Travis AJ, Rocca-Serra P, Renkema M, van Ommen B et al. (2009), Genes & nutrition, 4(2), 113-122
Survey-based naming conventions for use in OBO Foundry ontology development.
Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J et al. (2009), BMC bioinformatics, 10, 125
Towards interoperable reporting standards for omics data: hopes and hurdles.
Sansone S-A, Rocca-Serra P, Field D, Taylor CF, Tong W et al. (2009), Summit on translational bioinformatics, 2009, 112-115
BibTeX
@article{towardsinterope-2009/3,
title={Towards interoperable reporting standards for omics data: hopes and hurdles.},
author={Sansone S-A, Rocca-Serra P, Field D, Taylor CF, Tong W et al.},
journal={Summit on translational bioinformatics},
volume={2009},
pages={112-115},
year = "2009"
}
Using pathway signatures as means of identifying similarities among microarray experiments.
Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L et al. (2009), PloS one, 4(1), e4128
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M et al. (2009), Nucleic acids research, 37(Database issue), D868-D872
BibTeX
@article{arrayexpressupd-2009/1,
title={ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.},
author={Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M et al.},
journal={Nucleic acids research},
volume={37},
pages={D868-D872},
year = "2009"
}
The carcinoGENOMICS project: critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays.
Vinken M, Doktorova T, Ellinger-Ziegelbauer H, Ahr H-J, Lock E et al. (2008), Mutation research, 659(3), 202-210
BibTeX
@article{thecarcinogenom-2008/9,
title={The carcinoGENOMICS project: critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays.},
author={Vinken M, Doktorova T, Ellinger-Ziegelbauer H, Ahr H-J, Lock E et al.},
journal={Mutation research},
volume={659},
pages={202-210},
year = "2008"
}
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Taylor CF, Field D, Sansone S-A, Aerts J, Apweiler R et al. (2008), Nature biotechnology, 26(8), 889-896
BibTeX
@article{promotingcohere-2008/8,
title={Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.},
author={Taylor CF, Field D, Sansone S-A, Aerts J, Apweiler R et al.},
journal={Nature biotechnology},
volume={26},
pages={889-896},
year = "2008"
}
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone S-A, Rocca-Serra P, Brandizi M, Brazma A, Field D et al. (2008), Omics : a journal of integrative biology, 12(2), 143-149
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
Smith B, Ashburner M, Rosse C, Bard J, Bug W et al. (2007), Nature biotechnology, 25(11), 1251-1255
Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments
Griffin JL, Nicholls AW, Daykin CA, Heald S, Keun HC et al. (2007), METABOLOMICS, 3(3), 179-188
BibTeX
@article{standardreporti-2007/9,
title={Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments},
author={Griffin JL, Nicholls AW, Daykin CA, Heald S, Keun HC et al.},
journal={METABOLOMICS},
volume={3},
pages={179-188},
year = "2007"
}
Metabolomics standards initiative: ontology working group work in progress
Sansone S-A, Schober D, Atherton HJ, Fiehn O, Jenkins H et al. (2007), METABOLOMICS, 3(3), 249-256
ArrayExpress: A Public Repository for Microarray Data
Parkinson H, Sansone SA, Sarkans U, Rocca-Serra P & Brazma A (2006), 4, 95-102
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A et al. (2006), BMC bioinformatics, 7, 489
Data storage: bringing us a step closer to data sharing?
Rocca-Serra P & Elliott RM (2006), The British journal of nutrition, 95(6), 1237-1239
The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case.
Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K et al. (2006), BMC bioinformatics, 7, 267
BibTeX
@article{theuseofconcept-2006/5,
title={The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case.},
author={Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K et al.},
journal={BMC bioinformatics},
volume={7},
pages={267},
year = "2006"
}
The MGED Ontology: a resource for semantics-based description of microarray experiments.
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J et al. (2006), Bioinformatics (Oxford, England), 22(7), 866-873
Development of FuGO: an ontology for functional genomics investigations.
Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D et al. (2006), Omics : a journal of integrative biology, 10(2), 199-204
Annotation of environmental OMICS data: application to the transcriptomics domain.
Morrison N, Wood AJ, Hancock D, Shah S, Hakes L et al. (2006), Omics : a journal of integrative biology, 10(2), 172-178
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group.
Sansone S-A, Rocca-Serra P, Tong W, Fostel J, Morrison N et al. (2006), Omics : a journal of integrative biology, 10(2), 164-171
BibTeX
@article{astrategycapita-2006/1,
title={A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group.},
author={Sansone S-A, Rocca-Serra P, Tong W, Fostel J, Morrison N et al.},
journal={Omics : a journal of integrative biology},
volume={10},
pages={164-171},
year = "2006"
}
Wrestling with SUMO and bio-ontologies.
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H et al. (2006), Nature biotechnology, 24(1), 21-22
Wrestling with SUMO and bio-ontologies.
Musen MA, Lewis S & Smith B (2006), Nature biotechnology, 24(1), 21
Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.
Fostel J, Choi D, Zwickl C, Morrison N, Rashid A et al. (2005), Toxicological sciences : an official journal of the Society of Toxicology, 88(2), 585-601
BibTeX
@article{chemicaleffects-2005/12,
title={Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.},
author={Fostel J, Choi D, Zwickl C, Morrison N, Rashid A et al.},
journal={Toxicological sciences : an official journal of the Society of Toxicology},
volume={88},
pages={585-601},
year = "2005"
}
Defining best practice for microarray analyses in nutrigenomic studies.
Garosi P, De Filippo C, van Erk M, Rocca-Serra P, Sansone S-A et al. (2005), The British journal of nutrition, 93(4), 425-432
The ArrayExpress gene expression database: a software engineering and implementation perspective.
Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A et al. (2005), Bioinformatics (Oxford, England), 21(8), 1495-1501
BibTeX
@article{thearrayexpress-2005/4,
title={The ArrayExpress gene expression database: a software engineering and implementation perspective.},
author={Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A et al.},
journal={Bioinformatics (Oxford, England)},
volume={21},
pages={1495-1501},
year = "2005"
}
ArrayExpress--a public repository for microarray gene expression data at the EBI.
Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S et al. (2005), Nucleic acids research, 33(Database issue), D553-D555
EnsMart: a generic system for fast and flexible access to biological data.
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W et al. (2004), Genome research, 14(1), 160-169
Standardization Initiatives in the (eco)toxicogenomics domain: a review.
Sansone SA, Morrison N, Rocca-Serra P & Fostel J (2004), Comparative and functional genomics, 5(8), 633-641
ArrayExpress: a public database of gene expression data at EBI.
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M et al. (2003), Comptes rendus biologies, 326(10-11), 1075-1078
The common fragile site FRA16C does not map within the 16q smallest region of overlap number 2 frequently lost in breast carcinoma.
Taine L, Rocca-Serra P, El Moneim AA, Verdier N, Moradkhani K et al. (2003), Cancer genetics and cytogenetics, 144(1), 85-86
BibTeX
@article{thecommonfragil-2003/7,
title={The common fragile site FRA16C does not map within the 16q smallest region of overlap number 2 frequently lost in breast carcinoma.},
author={Taine L, Rocca-Serra P, El Moneim AA, Verdier N, Moradkhani K et al.},
journal={Cancer genetics and cytogenetics},
volume={144},
pages={85-86},
year = "2003"
}
ArrayExpress--a public repository for microarray gene expression data at the EBI.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J et al. (2003), Nucleic acids research, 31(1), 68-71
ArrayExpress: a public database of gene expression data at EBI
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M et al. (2003), COMPTES RENDUS BIOLOGIES, 326(10-11), 1075-1078
Standards for microarray data.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C et al. (2002), Science (New York, N.Y.), 298(5593), 539
High-resolution integrated map encompassing the breast cancer loss of heterozygosity region on human chromosome 16q22.1.
Frengen E, Rocca-Serra P, Shaposhnikov S, Taine L, Thorsen J et al. (2000), Genomics, 70(3), 273-285
BibTeX
@article{highresolutioni-2000/12,
title={High-resolution integrated map encompassing the breast cancer loss of heterozygosity region on human chromosome 16q22.1.},
author={Frengen E, Rocca-Serra P, Shaposhnikov S, Taine L, Thorsen J et al.},
journal={Genomics},
volume={70},
pages={273-285},
year = "2000"
}
PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M et al. (0), GigaScience