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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

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@article{elixirbiovalida-2022/4,
  title={ELIXIR biovalidator for semantic validation of life science metadata.},
  author={Liyanage I, Burdett T, Droesbeke B, Erdos K, Fernandez R et al.},
  journal={Bioinformatics (Oxford, England)},
  volume={38},
  pages={btac195},
  year = "2022"
}

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)

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@article{isaapianopenpla-2021/9,
  title={ISA API: An open platform for interoperable life science experimental metadata.},
  author={Johnson D, Batista D, Cochrane K, Davey RP, Etuk A et al.},
  journal={GigaScience},
  volume={10},
  year = "2021"
}

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

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@article{roadtoeffective-2021/3,
  title={Road to effective data curation for translational research.},
  author={Gu W, Hasan S, Rocca-Serra P & Satagopam VP},
  journal={Drug discovery today},
  volume={26},
  pages={626-630},
  year = "2021"
}

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

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@article{enablingreusabi-2020/3,
  title={Enabling reusability of plant phenomic datasets with MIAPPE 1.1.},
  author={Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN et al.},
  journal={New Phytologist },
  publisher={Wiley},
  year = "2020"
}

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)

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@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)

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@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)

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@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

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@article{experimentdesig-2019/12,
  title={Experiment design driven FAIRification of omics data matrices, an exemplar},
  author={Rocca-Serra P & Sansone S},
  journal={Scientific Data},
  volume={6},
  pages={271},
  publisher={Springer Nature},
  year = "2019"
}

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

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@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

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@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

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@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)

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@article{platformtmastan-2019/8,
  title={PlatformTM, a standards-based data custodianship platform for translational medicine research},
  author={Emam I, Elyasigomari V, Matthews A, Pavlidis S, Rocca-Serra P et al.},
  journal={Scientific Data},
  volume={6},
  number={149},
  year = "2019"
}

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)

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@article{adatacitationro-2019/4,
  title={A data citation roadmap for scholarly data repositories},
  author={Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H et al.},
  journal={Scientific Data},
  volume={6},
  number={28},
  publisher={Nature Research},
  year = "2019"
}

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

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@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

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@article{mztabmadatastan-2019/3,
  title={mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.},
  author={Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K et al.},
  journal={Analytical chemistry},
  volume={91},
  pages={3302-3310},
  year = "2019"
}

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

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@article{addendumthefair-2019/3,
  title={Addendum: The FAIR Guiding Principles for scientific data management and stewardship.},
  author={Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M et al.},
  journal={Scientific data},
  volume={6},
  pages={6-6},
  year = "2019"
}

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

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@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)

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@article{phenomenalproce-2019/2,
  title={PhenoMeNal: processing and analysis of metabolomics data in the cloud.},
  author={Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M et al.},
  journal={GigaScience},
  volume={8},
  year = "2019"
}

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)

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@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

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@article{nmrmlacommunity-2018/1,
  title={nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.},
  author={Schober D, Jacob D, Wilson M, Cruz JA, Marcu A et al.},
  journal={Analytical chemistry},
  volume={90},
  pages={649-656},
  year = "2018"
}

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

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@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)

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@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

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@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)

BibTeX View PDF
@article{interoperablean-2017/11,
  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={},
  publisher={Cold Spring Harbor Laboratory},
  year = "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

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@article{thefutureofmeta-2017/10,
  title={The future of metabolomics in ELIXIR.},
  author={van Rijswijk M, van Rijswijk M, Beirnaert C, Beirnaert C, Caron C et al.},
  journal={F1000Research},
  volume={6},
  pages={1649-1649},
  publisher={F1000},
  year = "2017"
}

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

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@article{datsthedatatags-2017/6,
  title={DATS: the data tag suite to enable discoverability of datasets},
  author={Sansone S-A, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS et al.},
  journal={Scientific Data},
  publisher={Nature Publishing Group},
  year = "2017"
}

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)

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@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

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@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

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@article{biosharingharne-2017/5,
  title={BioSharing: harnessing metadata standards for the data commons},
  author={Sansone S-A, Gonzalez-Beltran A, Rocca-Serra P, McQuilton P, Izzo M et al.},
  journal={bioRxiv},
  publisher={Cold Spring Harbor Laboratory},
  year = "2017"
}

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

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@article{mzmlisanmrmlisa-2017/4,
  title={mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.},
  author={Larralde M, Lawson TN, Weber RJ, Moreno P, Haug K et al.},
  journal={Bioinformatics},
  year = "2017"
}

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)

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@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

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@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

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@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

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@article{theontologyforb-2016/4,
  title={The ontology for biomedical investigations.},
  author={Lin Y, Lister AL, Lord P, Malone J, Manduchi E et al.},
  journal={PLoS One},
  volume={11},
  pages={e0154556},
  publisher={Public Library of Science},
  year = "2016"
}

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

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@article{metabolightsano-2016/3,
  title={MetaboLights: An Open-Access Database Repository for Metabolomics Data.},
  author={Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P et al.},
  journal={Current protocols in bioinformatics},
  volume={53},
  pages={14.13.1-14.13.18},
  year = "2016"
}

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

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@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

BibTeX View PDF
@article{thefairguidingp-2016/1,
  title={The FAIR Guiding Principles for scientific data management and stewardship.},
  author={Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A et al.},
  journal={Scientific data},
  publisher={Nature Publishing Group},
  year = "2016"
}

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 View PDF
@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

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@article{embeddingstanda-2015/8,
  title={Embedding standards in metabolomics: the Metabolomics Society data standards task group},
  author={Salek RM, Arita M, Dayalan S, Ebbels T, Jones AR et al.},
  journal={METABOLOMICS},
  volume={11},
  pages={782-783},
  year = "2015"
}

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 View PDF
@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

BibTeX View PDF
@article{specialissueonb-2015/1,
  title={Special issue on bio-ontologies and phenotypes.},
  author={Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K et al.},
  journal={Journal of biomedical semantics},
  volume={6},
  pages={40},
  year = "2015"
}

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

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@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 View PDF
@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 View PDF
@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)

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@article{meetingreportad-2014/12,
  title={Meeting report: advancing practical applications of biodiversity ontologies},
  author={Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL et al.},
  journal={STANDARDS IN GENOMIC SCIENCES},
  volume={9},
  number={ARTN 17},
  year = "2014"
}

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

BibTeX View PDF
@article{acomprehensivea-2014/9,
  title={A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.},
  author={SEQC/MAQC-III Consortium },
  journal={Nature biotechnology},
  volume={32},
  pages={903-914},
  year = "2014"
}

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

BibTeX View PDF
@article{selectedpapersf-2014/6,
  title={Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting},
  author={Soldatova LN, Rocca-Serra P, Dumontier M & Shah NH},
  journal={JOURNAL OF BIOMEDICAL SEMANTICS},
  volume={5},
  number={ARTN I1},
  year = "2014"
}

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 View PDF
@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

BibTeX View PDF
@article{ebimetagenomics-2014/1,
  title={EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.},
  author={Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A et al.},
  journal={Nucleic acids research},
  volume={42},
  pages={D600-D606},
  year = "2014"
}

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 View PDF
@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

BibTeX View PDF
@article{linkedisasemant-2014/1,
  title={linkedISA: semantic representation of ISA-Tab experimental metadata.},
  author={González-Beltrán A, Maguire E, Sansone S-A & Rocca-Serra P},
  journal={BMC bioinformatics},
  volume={15 Suppl 14},
  pages={S4},
  year = "2014"
}

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 View PDF
@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

BibTeX View PDF
@article{standardizingda-2013/2,
  title={Standardizing data.},
  author={Baker NA, Klemm JD, Harper SL, Gaheen S, Heiskanen M et al.},
  journal={Nature nanotechnology},
  volume={8},
  pages={73-74},
  year = "2013"
}

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

BibTeX View PDF
@article{ontomatonabiopo-2013/2,
  title={OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.},
  author={Maguire E, González-Beltrán A, Whetzel PL, Sansone S-A & Rocca-Serra P},
  journal={Bioinformatics (Oxford, England)},
  volume={29},
  pages={525-527},
  year = "2013"
}

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 View PDF
@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 View PDF
@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 View PDF
@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 View PDF
@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

BibTeX View PDF
@article{translatingstan-2012/8,
  title={Translating standards into practice - one Semantic Web API for Gene Expression.},
  author={Deus HF, Prud'hommeaux E, Miller M, Zhao J, Malone J et al.},
  journal={Journal of biomedical informatics},
  volume={45},
  pages={782-794},
  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

BibTeX View PDF
@article{translatingstan-2012/8,
  title={Translating standards into practice - One Semantic Web API for Gene Expression},
  author={Deus HF, Prud'hommeaux E, Miller M, Zhao J, Malone J et al.},
  journal={Journal of Biomedical Informatics},
  volume={45},
  pages={782-794},
  year = "2012"
}

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

BibTeX View PDF
@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},
  pages={5},
  year = "2012"
}

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 View PDF
@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

BibTeX View PDF
@article{ontheevolvingpo-2012/7,
  title={On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities.},
  author={Sansone S-A & Rocca-Serra P},
  journal={GigaScience},
  volume={1},
  pages={10},
  year = "2012"
}

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

BibTeX View PDF
@article{graphtabalibrar-2012/6,
  title={graph2tab, a library to convert experimental workflow graphs into tabular formats.},
  author={Brandizi M, Kurbatova N, Sarkans U & Rocca-Serra P},
  journal={Bioinformatics (Oxford, England)},
  volume={28},
  pages={1665-1667},
  year = "2012"
}

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

BibTeX View PDF
@inproceedings{translatingstan-2012/4,
  title={Translating standards into practice - One Semantic Web API for Gene Expression},
  author={Deus HF, Zhao J, McCusker J, Fox R, Prud'hommeaux E et al.},
  pages={6-7},
  year = "2012"
}

Toward interoperable bioscience data

Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C et al. (2012), Nature Genetics, 44(2), 121-126

BibTeX View PDF
@article{towardinteroper-2012/2,
  title={Toward interoperable bioscience data},
  author={Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C et al.},
  journal={Nature Genetics},
  volume={44},
  pages={121-126},
  year = "2012"
}

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

BibTeX View PDF
@article{towardinteroper-2012/1,
  title={Toward interoperable bioscience data.},
  author={Sansone S-A, Rocca-Serra P, Field D, Maguire E, Taylor C et al.},
  journal={Nature genetics},
  volume={44},
  pages={121-126},
  publisher={Nature Publishing Group},
  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), 444-453

BibTeX View PDF
@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

BibTeX View PDF
@article{sharingandarchi-2011/7,
  title={Sharing and archiving nucleic acid structure mapping data.},
  author={Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P et al.},
  journal={RNA (New York, N.Y.)},
  volume={17},
  pages={1204-1212},
  year = "2011"
}

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 View PDF
@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 View PDF
@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

BibTeX View PDF
@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={Nucleic acids research},
  volume={39},
  pages={D7-10},
  year = "2011"
}

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

BibTeX View PDF
@article{datastandardsfo-2011/1,
  title={Data standards for Omics data: the basis of data sharing and reuse.},
  author={Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J et al.},
  journal={Methods in molecular biology (Clifton, N.J.)},
  volume={719},
  pages={31-69},
  year = "2011"
}

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

BibTeX View PDF
@article{overcomingtheon-2011/,
  title={Overcoming the ontology enrichment bottleneck with Quick Term Templates},
  author={Rocca-Serra P, Ruttenberg A, O'Connor MJ, Whetzel PL, Schober D et al.},
  journal={APPLIED ONTOLOGY},
  volume={6},
  pages={13-22},
  year = "2011"
}

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 View PDF
@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

BibTeX View PDF
@article{meetingreportbi-2010/12,
  title={Meeting Report: BioSharing at ISMB 2010.},
  author={Field D, Sansone S, Delong EF, Sterk P, Friedberg I et al.},
  journal={Standards in genomic sciences},
  volume={3},
  pages={254-258},
  year = "2010"
}

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 View PDF
@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 View PDF
@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)

BibTeX View PDF
@inproceedings{modelingbiomedi-2010/6,
  title={Modeling biomedical experimental processes with OBI},
  author={Brinkman RR, Courtot M, Derom D, Fostel JM, He Y et al.},
  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 Suppl 1, S7

BibTeX View PDF
@article{modelingbiomedi-2010/6,
  title={Modeling biomedical experimental processes with OBI.},
  author={Brinkman RR, Courtot M, Derom D, Fostel JM, He Y et al.},
  journal={Journal of biomedical semantics},
  volume={1 Suppl 1},
  pages={S7},
  year = "2010"
}

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

BibTeX View PDF
@article{megascienceomic-2009/10,
  title={Megascience. 'Omics data sharing.},
  author={Field D, Sansone S-A, Collis A, Booth T, Dukes P et al.},
  journal={Science (New York, N.Y.)},
  volume={326},
  pages={234-236},
  year = "2009"
}

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

BibTeX View PDF
@article{ownercontrolled-2009/6,
  title={Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network.},
  author={Harttig U, Travis AJ, Rocca-Serra P, Renkema M, van Ommen B et al.},
  journal={Genes & nutrition},
  volume={4},
  pages={113-122},
  year = "2009"
}

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

BibTeX View PDF
@article{surveybasednami-2009/4,
  title={Survey-based naming conventions for use in OBO Foundry ontology development.},
  author={Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J et al.},
  journal={BMC bioinformatics},
  volume={10},
  pages={125},
  year = "2009"
}

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

BibTeX View PDF
@article{usingpathwaysig-2009/1,
  title={Using pathway signatures as means of identifying similarities among microarray experiments.},
  author={Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L et al.},
  journal={PloS one},
  volume={4},
  pages={e4128},
  year = "2009"
}

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 View PDF
@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"
}

Standards for Functional Genomics

Chervitz SA, Parkinson H, Fostel JM, Causton HC, Sanson S-A et al. (2009), 293-329

BibTeX View PDF
@misc{standardsforfun-2009/,
  title={Standards for Functional Genomics},
  author={Chervitz SA, Parkinson H, Fostel JM, Causton HC, Sanson S-A et al.},
  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 View PDF
@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 View PDF
@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

BibTeX View PDF
@inproceedings{thefirstrsbiisa-2008/6,
  title={The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".},
  author={Sansone S-A, Rocca-Serra P, Brandizi M, Brazma A, Field D et al.},
  pages={143-149},
  year = "2008"
}

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

BibTeX View PDF
@article{theobofoundryco-2007/11,
  title={The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.},
  author={Smith B, Ashburner M, Rosse C, Bard J, Bug W et al.},
  journal={Nature biotechnology},
  volume={25},
  pages={1251-1255},
  year = "2007"
}

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 View PDF
@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

BibTeX View PDF
@article{metabolomicssta-2007/9,
  title={Metabolomics standards initiative: ontology working group work in progress},
  author={Sansone S-A, Schober D, Atherton HJ, Fiehn O, Jenkins H et al.},
  journal={METABOLOMICS},
  volume={3},
  pages={249-256},
  year = "2007"
}

ArrayExpress: A Public Repository for Microarray Data

Parkinson H, Sansone SA, Sarkans U, Rocca-Serra P & Brazma A (2006), 4, 95-102

BibTeX View PDF
@misc{arrayexpressapu-2006/12,
  title={ArrayExpress: A Public Repository for Microarray Data},
  author={Parkinson H, Sansone SA, Sarkans U, Rocca-Serra P & Brazma A},
  year = "2006"
}

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

BibTeX View PDF
@article{asimplespreadsh-2006/11,
  title={A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.},
  author={Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A et al.},
  journal={BMC bioinformatics},
  volume={7},
  pages={489},
  year = "2006"
}

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

BibTeX View PDF
@article{datastoragebrin-2006/6,
  title={Data storage: bringing us a step closer to data sharing?},
  author={Rocca-Serra P & Elliott RM},
  journal={The British journal of nutrition},
  volume={95},
  pages={1237-1239},
  year = "2006"
}

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 View PDF
@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

BibTeX View PDF
@article{themgedontology-2006/4,
  title={The MGED Ontology: a resource for semantics-based description of microarray experiments.},
  author={Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J et al.},
  journal={Bioinformatics (Oxford, England)},
  volume={22},
  pages={866-873},
  year = "2006"
}

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

BibTeX View PDF
@article{developmentoffu-2006/1,
  title={Development of FuGO: an ontology for functional genomics investigations.},
  author={Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D et al.},
  journal={Omics : a journal of integrative biology},
  volume={10},
  pages={199-204},
  year = "2006"
}

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

BibTeX View PDF
@article{annotationofenv-2006/1,
  title={Annotation of environmental OMICS data: application to the transcriptomics domain.},
  author={Morrison N, Wood AJ, Hancock D, Shah S, Hakes L et al.},
  journal={Omics : a journal of integrative biology},
  volume={10},
  pages={172-178},
  year = "2006"
}

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 View PDF
@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

BibTeX View PDF
@article{wrestlingwithsu-2006/1,
  title={Wrestling with SUMO and bio-ontologies.},
  author={Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H et al.},
  journal={Nature biotechnology},
  volume={24},
  pages={21-22},
  year = "2006"
}

Wrestling with SUMO and bio-ontologies.

Musen MA, Lewis S & Smith B (2006), Nature biotechnology, 24(1), 21

BibTeX View PDF
@article{wrestlingwithsu-2006/1,
  title={Wrestling with SUMO and bio-ontologies.},
  author={Musen MA, Lewis S & Smith B},
  journal={Nature biotechnology},
  volume={24},
  pages={21},
  year = "2006"
}

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 View PDF
@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

BibTeX View PDF
@article{definingbestpra-2005/4,
  title={Defining best practice for microarray analyses in nutrigenomic studies.},
  author={Garosi P, De Filippo C, van Erk M, Rocca-Serra P, Sansone S-A et al.},
  journal={The British journal of nutrition},
  volume={93},
  pages={425-432},
  year = "2005"
}

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 View PDF
@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

BibTeX View PDF
@article{arrayexpressapu-2005/1,
  title={ArrayExpress--a public repository for microarray gene expression data at the EBI.},
  author={Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S et al.},
  journal={Nucleic acids research},
  volume={33},
  pages={D553-D555},
  year = "2005"
}

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

BibTeX View PDF
@article{ensmartageneric-2004/1,
  title={EnsMart: a generic system for fast and flexible access to biological data.},
  author={Kasprzyk A, Keefe D, Smedley D, London D, Spooner W et al.},
  journal={Genome research},
  volume={14},
  pages={160-169},
  year = "2004"
}

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

BibTeX View PDF
@article{standardization-2004/1,
  title={Standardization Initiatives in the (eco)toxicogenomics domain: a review.},
  author={Sansone SA, Morrison N, Rocca-Serra P & Fostel J},
  journal={Comparative and functional genomics},
  volume={5},
  pages={633-641},
  year = "2004"
}

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

BibTeX View PDF
@article{arrayexpressapu-2003/10,
  title={ArrayExpress: a public database of gene expression data at EBI.},
  author={Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M et al.},
  journal={Comptes rendus biologies},
  volume={326},
  pages={1075-1078},
  year = "2003"
}

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 View PDF
@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

BibTeX View PDF
@article{arrayexpressapu-2003/1,
  title={ArrayExpress--a public repository for microarray gene expression data at the EBI.},
  author={Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J et al.},
  journal={Nucleic acids research},
  volume={31},
  pages={68-71},
  year = "2003"
}

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

BibTeX View PDF
@article{arrayexpressapu-2003/,
  title={ArrayExpress: a public database of gene expression data at EBI},
  author={Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M et al.},
  journal={COMPTES RENDUS BIOLOGIES},
  volume={326},
  pages={1075-1078},
  year = "2003"
}

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

BibTeX View PDF
@article{standardsformic-2002/10,
  title={Standards for microarray data.},
  author={Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C et al.},
  journal={Science (New York, N.Y.)},
  volume={298},
  pages={539},
  year = "2002"
}

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 View PDF
@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

BibTeX View PDF
@article{phenomenalproce-/,
  title={PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud},
  author={Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M et al.},
  journal={GigaScience},
  publisher={Oxford University Press (OUP)}
}