Found: 27

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  • Toward a common standard for data and specimen provenance in life sciences.

    Published in:
    Learning Health Systems, 2024, v. 8, n. 1, p. 1, doi. 10.1002/lrh2.10365
    By:
    • Wittner, Rudolf;
    • Holub, Petr;
    • Mascia, Cecilia;
    • Frexia, Francesca;
    • Müller, Heimo;
    • Plass, Markus;
    • Allocca, Clare;
    • Betsou, Fay;
    • Burdett, Tony;
    • Cancio, Ibon;
    • Chapman, Adriane;
    • Chapman, Martin;
    • Courtot, Mélanie;
    • Curcin, Vasa;
    • Eder, Johann;
    • Elliot, Mark;
    • Exter, Katrina;
    • Goble, Carole;
    • Golebiewski, Martin;
    • Kisler, Bron
    Publication type:
    Article

  • Features of a FAIR vocabulary.

    Published in:
    Journal of Biomedical Semantics, 2023, v. 14, n. 1, p. 1, doi. 10.1186/s13326-023-00286-8
    By:
    • Xu, Fuqi;
    • Juty, Nick;
    • Goble, Carole;
    • Jupp, Simon;
    • Parkinson, Helen;
    • Courtot, Mélanie
    Publication type:
    Article

  • FAIR in action - a flexible framework to guide FAIRification.

    Published in:
    Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-023-02167-2
    By:
    • Welter, Danielle;
    • Juty, Nick;
    • Rocca-Serra, Philippe;
    • Xu, Fuqi;
    • Henderson, David;
    • Gu, Wei;
    • Strubel, Jolanda;
    • Giessmann, Robert T.;
    • Emam, Ibrahim;
    • Gadiya, Yojana;
    • Abbassi-Daloii, Tooba;
    • Alharbi, Ebtisam;
    • Gray, Alasdair J. G.;
    • Courtot, Melanie;
    • Gribbon, Philip;
    • Ioannidis, Vassilios;
    • Reilly, Dorothy S.;
    • Lynch, Nick;
    • Boiten, Jan-Willem;
    • Satagopam, Venkata
    Publication type:
    Article

  • ELIXIR biovalidator for semantic validation of life science metadata.

    Published in:
    Bioinformatics, 2022, v. 38, n. 11, p. 3141, doi. 10.1093/bioinformatics/btac195
    By:
    • Liyanage, Isuru;
    • Burdett, Tony;
    • Droesbeke, Bert;
    • Erdos, Karoly;
    • Fernandez, Rolando;
    • Gray, Alasdair;
    • Haseeb, Muhammad;
    • Jupp, Simon;
    • Penim, Flavia;
    • Pommier, Cyril;
    • Rocca-Serra, Philippe;
    • Courtot, Mélanie;
    • Coppens, Frederik
    Publication type:
    Article

  • The GA4GH Phenopacket schema defines a computable representation of clinical data.

    Published in:
    2022
    By:
    • Jacobsen, Julius O. B.;
    • Baudis, Michael;
    • Baynam, Gareth S.;
    • Beckmann, Jacques S.;
    • Beltran, Sergi;
    • Buske, Orion J.;
    • Callahan, Tiffany J.;
    • Chute, Christopher G.;
    • Courtot, Mélanie;
    • Danis, Daniel;
    • Elemento, Olivier;
    • Essenwanger, Andrea;
    • Freimuth, Robert R.;
    • Gargano, Michael A.;
    • Groza, Tudor;
    • Hamosh, Ada;
    • Harris, Nomi L.;
    • Kaliyaperumal, Rajaram;
    • Lloyd, Kevin C. Kent;
    • Khalifa, Aly
    Publication type:
    Letter

  • BioSamples database: FAIRer samples metadata to accelerate research data management.

    Published in:
    Nucleic Acids Research, 2022, v. 50, n. D1, p. D1500, doi. 10.1093/nar/gkab1046
    By:
    • Courtot, Mélanie;
    • Gupta, Dipayan;
    • Liyanage, Isuru;
    • Xu, Fuqi;
    • Burdett, Tony
    Publication type:
    Article

  • The European Nucleotide Archive in 2020.

    Published in:
    Nucleic Acids Research, 2021, v. 49, n. D1, p. D82, doi. 10.1093/nar/gkaa1028
    By:
    • Harrison, Peter W;
    • Ahamed, Alisha;
    • Aslam, Raheela;
    • Alako, Blaise T F;
    • Burgin, Josephine;
    • Buso, Nicola;
    • Courtot, Mélanie;
    • Fan, Jun;
    • Gupta, Dipayan;
    • Haseeb, Muhammad;
    • Holt, Sam;
    • Ibrahim, Talal;
    • Ivanov, Eugene;
    • Jayathilaka, Suran;
    • Balavenkataraman Kadhirvelu, Vishnukumar;
    • Kumar, Manish;
    • Lopez, Rodrigo;
    • Kay, Simon;
    • Leinonen, Rasko;
    • Liu, Xin
    Publication type:
    Article

  • OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab069
    By:
    • Jackson, Rebecca;
    • Matentzoglu, Nicolas;
    • Overton, James A;
    • Vita, Randi;
    • Balhoff, James P;
    • Buttigieg, Pier Luigi;
    • Carbon, Seth;
    • Courtot, Melanie;
    • Diehl, Alexander D;
    • Dooley, Damion M;
    • Duncan, William D;
    • Harris, Nomi L;
    • Haendel, Melissa A;
    • Lewis, Suzanna E;
    • Natale, Darren A;
    • Osumi-Sutherland, David;
    • Ruttenberg, Alan;
    • Schriml, Lynn M;
    • Smith, Barry;
    • Stoeckert Jr., Christian J
    Publication type:
    Article

  • BioSamples database: an updated sample metadata hub.

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. D1, p. D1172, doi. 10.1093/nar/gky1061
    By:
    • Courtot, Mélanie;
    • Cherubin, Luca;
    • Faulconbridge, Adam;
    • Vaughan, Daniel;
    • Green, Matthew;
    • Richardson, David;
    • Harrison, Peter;
    • Whetzel, Patricia L;
    • Parkinson, Helen;
    • Burdett, Tony
    Publication type:
    Article

  • Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.

    Published in:
    Journal of Biomedical Semantics, 2018, v. 9, p. 1, doi. 10.1186/s13326-018-0175-z
    By:
    • Osumi-Sutherland, David J.;
    • Ponta, Enrico;
    • Courtot, Melanie;
    • Parkinson, Helen;
    • Badi, Laura
    Publication type:
    Article

  • Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.

    Published in:
    Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2017.02528
    By:
    • Tkavc, Rok;
    • Matrosova, Vera Y.;
    • Grichenko, Olga E.;
    • Gostinčar, Cene;
    • Volpe, Robert P.;
    • Klimenkova, Polina;
    • Gaidamakova, Elena K.;
    • Zhou, Carol E.;
    • Stewart, Benjamin J.;
    • Lyman, Mathew G.;
    • Malfatti, Stephanie A.;
    • Rubinfeld, Bonnee;
    • Courtot, Melanie;
    • Singh, Jatinder;
    • Dalgard, Clifton L.;
    • Hamilton, Theron;
    • Frey, Kenneth G.;
    • Gunde-Cimerman, Nina;
    • Dugan, Lawrence;
    • Daly, Michael J.
    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

  • Dead simple OWL design patterns.

    Published in:
    Journal of Biomedical Semantics, 2017, v. 8, p. 1, doi. 10.1186/s13326-017-0126-0
    By:
    • Osumi-Sutherland, David;
    • Courtot, Melanie;
    • Balhoff, James P.;
    • Mungall, Christopher
    Publication type:
    Article

  • Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

    Published in:
    Nucleic Acids Research, 2017, v. 45, n. D1, p. D347, doi. 10.1093/nar/gkw918
    By:
    • Ong, Edison;
    • Zuoshuang Xiang;
    • Bin Zhao;
    • Yue Liu;
    • Yu Lin;
    • Jie Zheng;
    • Mungall, Chris;
    • Courtot, Mélanie;
    • Ruttenberg, Alan;
    • Yongqun He
    Publication type:
    Article

  • CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.

    Published in:
    Nucleic Acids Research, 2017, v. 45, n. D1, p. D566, doi. 10.1093/nar/gkw1004
    By:
    • Baofeng Jia;
    • Raphenya, Amogelang R.;
    • Alcock, Brian;
    • Waglechner, Nicholas;
    • Peiyao Guo;
    • Tsang, Kara K.;
    • Lago, Briony A.;
    • Dave, Biren M.;
    • Pereira, Sheldon;
    • Sharma, Arjun N.;
    • Doshi, Sachin;
    • Courtot, Mélanie;
    • Lo, Raymond;
    • Williams, Laura E.;
    • Frye, Jonathan G.;
    • Elsayegh, Tariq;
    • Sardar, Daim;
    • Westman, Erin L.;
    • Pawlowski, Andrew C.;
    • Johnson, Timothy A.
    Publication type:
    Article

  • 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

  • flowCL: ontology-based cell population labelling in flow cytometry.

    Published in:
    Bioinformatics, 2015, v. 31, n. 8, p. 1337, doi. 10.1093/bioinformatics/btu807
    By:
    • Courtot, Mélanie;
    • Meskas, Justin;
    • Diehl, Alexander D.;
    • Droumeva, Radina;
    • Gottardo, Raphael;
    • Jalali, Adrin;
    • Taghiyar, Mohammad Jafar;
    • Maecker, Holden T.;
    • McCoy, J. Philip;
    • Ruttenberg, Alan;
    • Scheuermann, Richard H.;
    • Brinkman, Ryan R.
    Publication type:
    Article

  • flowCL: ontology-based cell population labelling in flow cytometry.

    Published in:
    2015
    By:
    • Courtot, Mélanie;
    • Meskas, Justin;
    • Diehl, Alexander D.;
    • Droumeva, Radina;
    • Gottardo, Raphael;
    • Jalali, Adrin;
    • Taghiyar, Mohammad Jafar;
    • Maecker, Holden T.;
    • McCoy, J. Philip;
    • Ruttenberg, Alan;
    • Scheuermann, Richard H.;
    • Brinkman, Ryan R.
    Publication type:
    Product Review

  • Finding Our Way through Phenotypes.

    Published in:
    2015
    By:
    • Deans, Andrew R.;
    • Lewis, Suzanna E.;
    • Huala, Eva;
    • Anzaldo, Salvatore S.;
    • Ashburner, Michael;
    • Balhoff, James P.;
    • Blackburn, David C.;
    • Blake, Judith A.;
    • Burleigh, J. Gordon;
    • Chanet, Bruno;
    • Cooper, Laurel D.;
    • Courtot, Mélanie;
    • Csösz, Sándor;
    • Cui, Hong;
    • Dahdul, Wasila;
    • Das, Sandip;
    • Dececchi, T. Alexander;
    • Dettai, Agnes;
    • Diogo, Rui;
    • Druzinsky, Robert E.
    Publication type:
    Opinion

  • The Logic of Surveillance Guidelines: An Analysis of Vaccine Adverse Event Reports from an Ontological Perspective.

    Published in:
    PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0092632
    By:
    • Courtot, Mélanie;
    • Brinkman, Ryan R.;
    • Ruttenberg, Alan
    Publication type:
    Article

  • Controlled vocabularies and semantics in systems biology.

    Published in:
    Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.77
    By:
    • Courtot, Mélanie;
    • Juty, Nick;
    • Knüpfer, Christian;
    • Waltemath, Dagmar;
    • Zhukova, Anna;
    • Dräger, Andreas;
    • Dumontier, Michel;
    • Finney, Andrew;
    • Golebiewski, Martin;
    • Hastings, Janna;
    • Hoops, Stefan;
    • Keating, Sarah;
    • Kell, Douglas B;
    • Kerrien, Samuel;
    • Lawson, James;
    • Lister, Allyson;
    • Lu, James;
    • Machne, Rainer;
    • Mendes, Pedro;
    • Pocock, Matthew
    Publication type:
    Article

  • BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

    Published in:
    Briefings in Bioinformatics, 2010, v. 11, n. 3, p. 270, doi. 10.1093/bib/bbp056
    By:
    • Chen Li;
    • Courtot, Mélanie;
    • Le Novère, Nicolas;
    • Laibe, Camille
    Publication type:
    Article

  • Modeling biomedical experimental processes with OBI.

    Published in:
    Journal of Biomedical Semantics, 2010, v. 1, n. Suppl 1, p. 1, doi. 10.1186/2041-1480-1-S1-S7
    By:
    • Brinkman, Ryan R.;
    • Courtot, Mélanie;
    • Derom, Dirk;
    • Fostel, Jennifer M.;
    • Yongqun He;
    • Lord, Phillip;
    • Malone, James;
    • Parkinson, Helen;
    • Peters, Bjoern;
    • Rocca-Serra, Philippe;
    • Ruttenberg, Alan;
    • Sansone, Susanna-Assunta;
    • Soldatova, Larisa N.;
    • Stoeckert, Jr., Christian J.;
    • Turner, Jessica A.;
    • Jie Zheng
    Publication type:
    Article

  • OntoFox: web-based support for ontology reuse.

    Published in:
    BMC Research Notes, 2010, v. 3, p. 175, doi. 10.1186/1756-0500-3-175
    By:
    • Zuoshuang Xiang;
    • Courtot, Mélanie;
    • Brinkman, Ryan R.;
    • Ruttenberg, Alan;
    • Yongqun He
    Publication type:
    Article

  • Erratum: The Systems Biology Graphical Notation.

    Published in:
    2009
    By:
    • Le Novère, Nicolas;
    • Hucka, Michael;
    • Mi, Huaiyu;
    • Moodie, Stuart;
    • Schreiber, Falk;
    • Sorokin, Anatoly;
    • Demir, Emek;
    • Wegner, Katja;
    • Aladjem, Mirit I;
    • Wimalaratne, Sarala M;
    • Bergman, Frank T;
    • Gauges, Ralph;
    • Ghazal, Peter;
    • Kawaji, Hideya;
    • Li, Lu;
    • Matsuoka, Yukiko;
    • Villéger, Alice;
    • Boyd, Sarah E;
    • Calzone, Laurence;
    • Courtot, Melanie
    Publication type:
    Correction notice

  • The Systems Biology Graphical Notation.

    Published in:
    Nature Biotechnology, 2009, v. 27, n. 8, p. 735, doi. 10.1038/nbt.1558
    By:
    • Le Novére, Nicolas;
    • Hucka, Michael;
    • Mi, Huaiyu;
    • Moodie, Stuart;
    • Schreiber, Falk;
    • Sorokin, Anatoly;
    • Demir, Emek;
    • Wegner, Katja;
    • Aladjem, Mirit I.;
    • Wimalaratne, Sarala M.;
    • Bergman, Frank T.;
    • Gauges, Ralph;
    • Ghazal, Peter;
    • Kawaji, Hideya;
    • Li, Lu;
    • Matsuoka, Yukiko;
    • Villéger, Alice;
    • Boyd, Sarah E.;
    • Calzone, Laurence;
    • Courtot, Melanie
    Publication type:
    Article

  • BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

    Published in:
    Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d689, doi. 10.1093/nar/gkj092
    By:
    • Le Novère, Nicolas;
    • Bornstein, Benjamin;
    • Broicher, Alexander;
    • Courtot, Mélanie;
    • Donizelli, Marco;
    • Dharuri, Harish;
    • Li, Lu;
    • Sauro, Herbert;
    • Schilstra, Maria;
    • Shapiro, Bruce;
    • Snoep, Jacky L.;
    • Hucka, Michael
    Publication type:
    Article