Works by Courtot, Melanie

Results: 27

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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