Found: 25

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  • DataMed - an open source discovery index for finding biomedical datasets.

    Published in:
    2018
    By:
    • Xiaoling Chen;
    • Gururaj, Anupama E.;
    • Ozyurt, Burak;
    • Ruiling Liu;
    • Soysal, Ergin;
    • Cohen, Trevor;
    • Tiryaki, Firat;
    • Yueling Li;
    • Nansu Zong;
    • Min Jiang;
    • Rogith, Deevakar;
    • Salimi, Mandana;
    • Hyeon-eui Kim;
    • Rocca-Serra, Philippe;
    • Gonzalez-Beltran, Alejandra;
    • Farcas, Claudiu;
    • Johnson, Todd;
    • Margolis, Ron;
    • Alter, George;
    • Sansone, Susanna-Assunta
    Publication type:
    journal article

  • Data discovery with DATS: exemplar adoptions and lessons learned.

    Published in:
    2018
    By:
    • Gonzalez-Beltran, Alejandra N;
    • Campbell, John;
    • Dunn, Patrick;
    • Guijarro, Diana;
    • Ionescu, Sanda;
    • Kim, Hyeoneui;
    • Lyle, Jared;
    • Wiser, Jeffrey;
    • Sansone, Susanna-Assunta;
    • Rocca-Serra, Philippe
    Publication type:
    journal article

  • The center for expanded data annotation and retrieval.

    Published in:
    2015
    By:
    • Musen, Mark A.;
    • Bean, Carol A.;
    • Kei-Hoi Cheung;
    • Dumontier, Michel;
    • Durante, Kim A.;
    • Gevaert, Olivier;
    • Gonzalez-Beltran, Alejandra;
    • Khatri, Purvesh;
    • Kleinstein, Steven H.;
    • O'Connor, Martin J.;
    • Pouliot, Yannick;
    • Rocca-Serra, Philippe;
    • Sansone, Susanna-Assunta;
    • Wiser, Jeffrey A.;
    • Cheung, Kei-Hoi;
    • CEDAR team
    Publication type:
    journal article

  • Data standards can boost metabolomics research, and if there is a will, there is a way.

    Published in:
    Metabolomics, 2016, v. 12, n. 1, p. N.PAG, doi. 10.1007/s11306-015-0879-3
    By:
    • Rocca-Serra, Philippe;
    • Salek, Reza M.;
    • Arita, Masanori;
    • Correa, Elon;
    • Dayalan, Saravanan;
    • Gonzalez-Beltran, Alejandra;
    • Ebbels, Tim;
    • Goodacre, Royston;
    • Hastings, Janna;
    • Haug, Kenneth;
    • Koulman, Albert;
    • Nikolski, Macha;
    • Oresic, Matej;
    • Sansone, Susanna-Assunta;
    • Schober, Daniel;
    • Smith, James;
    • Steinbeck, Christoph;
    • Viant, Mark R.;
    • Neumann, Steffen
    Publication type:
    Article

  • linkedISA: semantic representation of ISA-Tab experimental metadata.

    Published in:
    BMC Bioinformatics, 2014, v. 15, n. Suppl 14, p. 1, doi. 10.1186/1471-2105-15-S14-S4
    By:
    • González-Beltrán, Alejandra;
    • Maguire, Eamonn;
    • Sansone, Susanna-Assunta;
    • Rocca-Serra, Philippe
    Publication type:
    Article

  • The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.

    Published in:
    BMC Bioinformatics, 2014, v. 15, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-15-S1-S11
    By:
    • González-Beltrán, Alejandra;
    • Neumann, Steffen;
    • Maguire, Eamonn;
    • Sansone, Susanna-Assunta;
    • Rocca-Serra, Philippe
    Publication type:
    Article

  • Federated ontology-based queries over cancer data.

    Published in:
    BMC Bioinformatics, 2012, v. 13, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-13-S1-S9
    By:
    • González-Beltrán, Alejandra;
    • Tagger, Ben;
    • Finkelstein, Anthony
    Publication type:
    Article

  • Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

    Published in:
    PLoS Biology, 2017, v. 15, n. 6, p. 1, doi. 10.1371/journal.pbio.2001414
    By:
    • McMurry, Julie A.;
    • Juty, Nick;
    • Blomberg, Niklas;
    • Burdett, Tony;
    • Conlin, Tom;
    • Conte, Nathalie;
    • Courtot, Mélanie;
    • Deck, John;
    • Dumontier, Michel;
    • Fellows, Donal K.;
    • Gonzalez-Beltran, Alejandra;
    • Gormanns, Philipp;
    • Grethe, Jeffrey;
    • Hastings, Janna;
    • Hériché, Jean-Karim;
    • Hermjakob, Henning;
    • Ison, Jon C.;
    • Jimenez, Rafael C.;
    • Jupp, Simon;
    • Kunze, John
    Publication type:
    Article

  • BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw075
    By:
    • McQuilton, Peter;
    • Gonzalez-Beltran, Alejandra;
    • Rocca-Serra, Philippe;
    • Thurston, Milo;
    • Lister, Allyson;
    • Maguire, Eamonn;
    • Sansone, Susanna-Assunta
    Publication type:
    Article

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

    Published in:
    Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bau132
    By:
    • Rocca-Serra, Philippe;
    • Walls, Ramona;
    • Parnell, Jacob;
    • Gallery, Rachel;
    • Jie Zheng;
    • Sansone, Susanna-Assunta;
    • Gonzalez-Beltran, Alejandra
    Publication type:
    Article

  • The MetaboLights repository: curation challenges in metabolomics.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2013, v. 2013, p. 1, doi. 10.1093/database/bat029
    By:
    • Salek, Reza M.;
    • Haug, Kenneth;
    • Conesa, Pablo;
    • Hastings, Janna;
    • Williams, Mark;
    • Mahendraker, Tejasvi;
    • Maguire, Eamonn;
    • González-Beltrán, Alejandra N.;
    • Rocca-Serra, Philippe;
    • Sansone, Susanna-Assunta;
    • Steinbeck, Christoph
    Publication type:
    Article

  • Semantic concept schema of the linear mixed model of experimental observations.

    Published in:
    Scientific Data, 2020, v. 7, n. 1, p. 1, doi. 10.1038/s41597-020-0409-7
    By:
    • Ćwiek-Kupczyńska, Hanna;
    • Filipiak, Katarzyna;
    • Markiewicz, Augustyn;
    • Rocca-Serra, Philippe;
    • Gonzalez-Beltran, Alejandra N.;
    • Sansone, Susanna-Assunta;
    • Millet, Emilie J.;
    • van Eeuwijk, Fred;
    • Ławrynowicz, Agnieszka;
    • Krajewski, Paweł
    Publication type:
    Article

  • Interoperable and scalable data analysis with microservices: applications in metabolomics.

    Published in:
    Bioinformatics, 2019, v. 35, n. 19, p. 3752, doi. 10.1093/bioinformatics/btz160
    By:
    • Khoonsari, Payam Emami;
    • Moreno, Pablo;
    • Bergmann, Sven;
    • Burman, Joachim;
    • Capuccini, Marco;
    • Carone, Matteo;
    • Cascante, Marta;
    • Atauri, Pedro de;
    • Foguet, Carles;
    • Gonzalez-Beltran, Alejandra N;
    • Hankemeier, Thomas;
    • Haug, Kenneth;
    • He, Sijin;
    • Herman, Stephanie;
    • Johnson, David;
    • Kale, Namrata;
    • Larsson, Anders;
    • Neumann, Steffen;
    • Peters, Kristian;
    • Pireddu, Luca
    Publication type:
    Article

  • ISA API: An open platform for interoperable life science experimental metadata.

    Published in:
    GigaScience, 2021, v. 10, n. 9, p. 1, doi. 10.1093/gigascience/giab060
    By:
    • Johnson, David;
    • Batista, Dominique;
    • Cochrane, Keeva;
    • Davey, Robert P;
    • Etuk, Anthony;
    • Gonzalez-Beltran, Alejandra;
    • Haug, Kenneth;
    • Izzo, Massimiliano;
    • Larralde, Martin;
    • Lawson, Thomas N;
    • Minotto, Alice;
    • Moreno, Pablo;
    • Nainala, Venkata Chandrasekhar;
    • O'Donovan, Claire;
    • Pireddu, Luca;
    • Roger, Pierrick;
    • Shaw, Felix;
    • Steinbeck, Christoph;
    • Weber, Ralf J M;
    • Sansone, Susanna-Assunta
    Publication type:
    Article

  • Community standards for open cell migration data.

    Published in:
    GigaScience, 2020, v. 9, n. 5, p. N.PAG, doi. 10.1093/gigascience/giaa041
    By:
    • Gonzalez-Beltran, Alejandra N;
    • Masuzzo, Paola;
    • Ampe, Christophe;
    • Bakker, Gert-Jan;
    • Besson, Sébastien;
    • Eibl, Robert H;
    • Friedl, Peter;
    • Gunzer, Matthias;
    • Kittisopikul, Mark;
    • Dévédec, Sylvia E Le;
    • Leo, Simone;
    • Moore, Josh;
    • Paran, Yael;
    • Prilusky, Jaime;
    • Rocca-Serra, Philippe;
    • Roudot, Philippe;
    • Schuster, Marc;
    • Sergeant, Gwendolien;
    • Swedlow, Jason R;
    • van Erp, Merijn
    Publication type:
    Article

  • PhenoMeNal: processing and analysis of metabolomics data in the cloud.

    Published in:
    GigaScience, 2019, v. 8, n. 2, p. N.PAG, doi. 10.1093/gigascience/giy149
    By:
    • Peters, Kristian;
    • Bradbury, James;
    • Bergmann, Sven;
    • Capuccini, Marco;
    • Cascante, Marta;
    • de Atauri, Pedro;
    • Ebbels, Timothy M D;
    • Foguet, Carles;
    • Glen, Robert;
    • Gonzalez-Beltran, Alejandra;
    • Günther, Ulrich L;
    • Handakas, Evangelos;
    • Hankemeier, Thomas;
    • Haug, Kenneth;
    • Herman, Stephanie;
    • Holub, Petr;
    • Izzo, Massimiliano;
    • Jacob, Daniel;
    • Johnson, David;
    • Jourdan, Fabien
    Publication type:
    Article

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

    Published in:
    Nucleic Acids Research, 2014, v. 42, n. D1, p. D600, doi. 10.1093/nar/gkt961
    By:
    • Hunter, Sarah;
    • Corbett, Matthew;
    • Denise, Hubert;
    • Fraser, Matthew;
    • Gonzalez-Beltran, Alejandra;
    • Hunter, Christopher;
    • Jones, Philip;
    • Leinonen, Rasko;
    • McAnulla, Craig;
    • Maguire, Eamonn;
    • Maslen, John;
    • Mitchell, Alex;
    • Nuka, Gift;
    • Oisel, Arnaud;
    • Pesseat, Sebastien;
    • Radhakrishnan, Rajesh;
    • Rocca-Serra, Philippe;
    • Scheremetjew, Maxim;
    • Sterk, Peter;
    • Vaughan, Daniel
    Publication type:
    Article

  • MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.

    Published in:
    Nucleic Acids Research, 2013, v. 41, p. D781, doi. 10.1093/nar/gks1004
    By:
    • Kenneth Haug;
    • Salek, Reza M.;
    • Conesa, Pablo;
    • Hastings, Janna;
    • de Matos, Paula;
    • Rijnbeek, Mark;
    • Mahendraker, Tejasvi;
    • Williams, Mark;
    • Neumann, Steffen;
    • Rocca-Serra, Philippe;
    • Maguire, Eamonn;
    • González-Beltrán, Alejandra;
    • Sansone, Susanna-Assunta;
    • Griffin, Julian L.;
    • Steinbeck, Christoph
    Publication type:
    Article

  • OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets.

    Published in:
    Bioinformatics, 2013, v. 29, n. 4, p. 525, doi. 10.1093/bioinformatics/bts718
    By:
    • Maguire, Eamonn;
    • González-Beltrán, Alejandra;
    • Whetzel, Patricia L.;
    • Sansone, Susanna-Assunta;
    • Rocca-Serra, Philippe
    Publication type:
    Article

  • Machine actionable metadata models.

    Published in:
    Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01707-6
    By:
    • Batista, Dominique;
    • Gonzalez-Beltran, Alejandra;
    • Sansone, Susanna-Assunta;
    • Rocca-Serra, Philippe
    Publication type:
    Article

  • FAIRsharing as a community approach to standards, repositories and policies.

    Published in:
    2019
    By:
    • Sansone, Susanna-Assunta;
    • McQuilton, Peter;
    • Rocca-Serra, Philippe;
    • Gonzalez-Beltran, Alejandra;
    • Izzo, Massimiliano;
    • Lister, Allyson L.;
    • Thurston, Milo
    Publication type:
    Letter

  • Addendum: The FAIR Guiding Principles for scientific data management and stewardship.

    Published in:
    2019
    By:
    • Wilkinson, Mark D.;
    • Dumontier, Michel;
    • Jan Aalbersberg, Ijsbrand;
    • Appleton, Gabrielle;
    • Axton, Myles;
    • Baak, Arie;
    • Blomberg, Niklas;
    • Boiten, Jan-Willem;
    • da Silva Santos, Luiz Bonino;
    • Bourne, Philip E.;
    • Bouwman, Jildau;
    • Brookes, Anthony J.;
    • Clark, Tim;
    • Crosas, Mercè;
    • Dillo, Ingrid;
    • Dumon, Olivier;
    • Edmunds, Scott;
    • Evelo, Chris T.;
    • Finkers, Richard;
    • Gonzalez-Beltran, Alejandra
    Publication type:
    Correction Notice

  • The Ontology for Biomedical Investigations.

    Published in:
    PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0154556
    By:
    • Bandrowski, Anita;
    • Brinkman, Ryan;
    • Brochhausen, Mathias;
    • Brush, Matthew H.;
    • Bug, Bill;
    • Chibucos, Marcus C.;
    • Clancy, Kevin;
    • Courtot, Mélanie;
    • Derom, Dirk;
    • Dumontier, Michel;
    • Fan, Liju;
    • Fostel, Jennifer;
    • Fragoso, Gilberto;
    • Gibson, Frank;
    • Gonzalez-Beltran, Alejandra;
    • Haendel, Melissa A.;
    • He, Yongqun;
    • Heiskanen, Mervi;
    • Hernandez-Boussard, Tina;
    • Jensen, Mark
    Publication type:
    Article

  • From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.

    Published in:
    PLoS ONE, 2015, v. 10, n. 7, p. 1, doi. 10.1371/journal.pone.0127612
    By:
    • González-Beltrán, Alejandra;
    • Li, Peter;
    • Zhao, Jun;
    • Avila-Garcia, Maria Susana;
    • Roos, Marco;
    • Thompson, Mark;
    • van der Horst, Eelke;
    • Kaliyaperumal, Rajaram;
    • Luo, Ruibang;
    • Lee, Tin-Lap;
    • Lam, Tak-wah;
    • Edmunds, Scott C.;
    • Sansone, Susanna-Assunta;
    • Rocca-Serra, Philippe
    Publication type:
    Article

  • Ten simple rules for making a vocabulary FAIR.

    Published in:
    PLoS Computational Biology, 2021, v. 17, n. 6, p. 1, doi. 10.1371/journal.pcbi.1009041
    By:
    • Cox, Simon J. D.;
    • Gonzalez-Beltran, Alejandra N.;
    • Magagna, Barbara;
    • Marinescu, Maria-Cristina
    Publication type:
    Article