Courtot Lab Genome Informatics

Publications

Our research focuses on new methods for improving data quality, based on knowledge representation, automated curation and added-value data. We have published over 50 papers with over 11,000 citations.

All

2025

P136: Data model and portal development supporting centralization of genetic information in a provincial research network
E Tuzlali, L Xiang, L Hughes, B Chan, P Dos Santos, R Mistry, A Catton, ...
Genetics in Medicine Open 3, 102980, 2025
VO: The Vaccine Ontology
J Zheng, AY Lin, A Huffman, AM Masci, R Racz, G Wu, K Roan, E Ong, ...
bioRxiv, 2025.08. 12.669998, 2025
Fixing the plumbing: Building interoperability between wastewater genomic surveillance datasets and systems using the PHA4GE contextual data specification
J Paull, C Barclay, R Cameron, D Dooley, I Gill, D Abraham, R Arteaga, ...
OSF, 2025
Abstract A006: Data Curation and Knowledge Integration Pipeline for Biomarker Discovery
S Majoros, M Shiell, J Wang, J Richardsson, QM Trinh, R Marcellus, ...
Clinical Cancer Research 31 (13_Supplement), A006-A006, 2025
Overture: an open-source genomics data platform
M Shiell, R Bajari, D Andric, J Eubank, BF Chan, AJ Richardsson, A Ali, ...
GigaScience 14, giaf038, 2025

2024

Development of the Ontario Hereditary Cancer Research Network, a unified registry as a resource for individuals with inherited cancer syndromes: an observational registry creation protocol
Kirsten M Farncombe, Lauren K Hughes, Elif Tuzlali, Mohammad Reza Akbari, Irene L Andrulis, ..., Karen Panabaker, Laszlo Radvanyi, Alison Rusnak, Lincoln Stein, Raymond H Kim
BMJ Open
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
Erin E. Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, ..., Lincoln Stein, Sarah P. Otto, Guillaume Bourque, B. Jesse Shapiro, Fiona S. L. Brinkman
Microbial Genomics
Development of the Ontario Hereditary Cancer Research Network, a unified registry as a resource for individuals with inherited cancer syndromes: an observational registry …
KM Farncombe, LK Hughes, E Tuzlali, MR Akbari, IL Andrulis, M Aronson, ...
BMJ open 14 (11), e087023, 2024
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
EE Gill, B Jia, CL Murall, R Poujol, MZ Anwar, NS John, J Richardsson, ...
Microbial Genomics 10 (10), 001293, 2024
Toward a common standard for data and specimen provenance in life sciences
R Wittner, P Holub, C Mascia, F Frexia, H Müller, M Plass, C Allocca, ...
Learning health systems 8 (1), e10365, 2024

2023

Features of a FAIR vocabulary
Fuqi Xu, Nick Juty, Carole Goble, Simon Jupp, Helen Parkinson, Mélanie Courtot
Journal of Biomedical Semantics
The FAIR Cookbook - the essential resource for and by FAIR doers
Philippe Rocca-Serra, Wei Gu, Vassilios Ioannidis, Tooba Abbassi-Daloii, Salvador Capella-Gutierrez, ..., Zachary Warnes, Peter Woollard, Fuqi Xu, Andrea Zaliani, Susanna-Assunta Sansone
Scientific Data
FAIR in action - a flexible framework to guide FAIRification
Danielle Welter, Nick Juty, Philippe Rocca-Serra, Fuqi Xu, David Henderson, ..., Jan-Willem Boiten, Venkata Satagopam, Carole Goble, Susanna-Assunta Sansone, Tony Burdett
Scientific Data
Accelerating cancer omics and precision oncology in health care and research: a Lancet Oncology Commission
Raffaella Casolino, Amber L Johns, Melanie Courtot, Rita T Lawlor, Francesco De Lorenzo, ..., Keunchil Park, Sandra Perdomo, Takayuki Yoshino, Jianmin Wu, Andrew V Biankin
The Lancet Oncology
ELIXIR biovalidator for semantic validation of life science metadata (vol 38, pg 3141, 2022)
I Liyanage, T Burdett, B Droesbeke, K Erdos, R Fernandez, A Gray, ...
BIOINFORMATICS 39 (1), 2023
Accelerating cancer omics and precision oncology in health care and research: a Lancet Oncology Commission
R Casolino, AL Johns, M Courtot, RT Lawlor, F De Lorenzo, D Horgan, ...
The Lancet Oncology 24 (2), 123-125, 2023
Features of a FAIR vocabulary
F Xu, N Juty, C Goble, S Jupp, H Parkinson, M Courtot
Journal of Biomedical Semantics 14 (1), 6, 2023
FAIR in action-a flexible framework to guide FAIRification
D Welter, N Juty, P Rocca-Serra, F Xu, D Henderson, W Gu, J Strubel, ...
Scientific data 10 (1), 291, 2023

2022

The GA4GH Phenopacket schema defines a computable representation of clinical data
Julius O. B. Jacobsen, Michael Baudis, Gareth S. Baynam, Jacques S. Beckmann, Sergi Beltran, ..., Panagiotis I. Sergouniotis, Rachel Thompson, Andreas Zankl, Melissa A. Haendel, Peter N. Robinson
Nature Biotechnology
Building the OBO Foundry-One Policy at a Time
[no author info]
CEURS proceedings: International Conference on Biomedical Ontologies
Adding semantics in kinetics models of biochemical pathways
[no author info]
Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations
Reporting Adverse Events: Basis for a Common Representation.
[no author info]
CEURS proceedings: International Conference on Biomedical Ontologies
Diagnostic criteria and clinical guidelines standardization to automate case classification.
[no author info]
CEURS proceedings: International Conference on Biomedical Ontologies
Reporting adverse events: Basis for a common representation
[no author info]
CEUR Workshop Proceedings
Diagnostic criteria and clinical guidelines standardization to automate case classification
[no author info]
CEUR Workshop Proceedings
UniProt-GOA: A central resource for data integration and GO annotation
[no author info]
CEUR Workshop Proceedings
Cell, chemical and anatomical views of the gene ontology
[no author info]
CEUR Workshop Proceedings
Ten simple rules for biomedical ontology development
[no author info]
CEUR Workshop Proceedings
Slim-o-matic: A semi-automated way to generate Gene Ontology slims
[no author info]
CEUR Workshop Proceedings
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
Nucleic acids research
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Baofeng Jia, Amogelang R Raphenya, Brian Alcock, Nicholas Waglechner, Peiyao Guo, ..., Andrew C Pawlowski, Timothy A Johnson, Fiona S L Brinkman, Gerard D Wright, Andrew G McArthur
Nucleic acids research
Expansion of the Gene Ontology knowledgebase and resources.
[no author info]
Nucleic acids research
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, ..., Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
F1000Research
Features of a FAIR vocabulary
Fuqi Xu, Nick Juty, Carole Goble, Simon Jupp, Helen Parkinson, Mélanie Courtot
Research Square Platform LLC
ELIXIR biovalidator for semantic validation of life science metadata
Isuru Liyanage, Tony Burdett, Bert Droesbeke, Karoly Erdos, Rolando Fernandez, ..., Flavia Penim, Cyril Pommier, Philippe Rocca-Serra, Mélanie Courtot, Frederik Coppens
Bioinformatics
SNP matrix of barley collection from german ex-situ genbank IPK.
S Beier, A Fiebig, C Pommier, I Liyanage, M Lange, PJ Kersey, S Weise, ...
Leibniz Institute of Plant Genetics and Crop Plant Research, 2022
ELIXIR biovalidator for semantic validation of life science metadata
I Liyanage, T Burdett, B Droesbeke, K Erdos, R Fernandez, A Gray, ...
Bioinformatics 38 (11), 3141-3142, 2022
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
S Beier, A Fiebig, C Pommier, I Liyanage, M Lange, PJ Kersey, S Weise, ...
F1000Research 11, ELIXIR-231, 2022
BioSamples database: FAIRer samples metadata to accelerate research data management
M Courtot, D Gupta, I Liyanage, F Xu, T Burdett
Nucleic acids research 50 (D1), D1500-D1507, 2022
The GA4GH Phenopacket schema defines a computable representation of clinical data
JOB Jacobsen, M Baudis, GS Baynam, JS Beckmann, S Beltran, ...
Nature biotechnology 40 (6), 817-820, 2022

2021

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine
Julius O. B. Jacobsen, Michael Baudis, Gareth S. Baynam, Jacques S. Beckmann, Sergi Beltran, ..., Alex H. Wagner, Jeremy L. Warner, Claus Weiland, Melissa A. Haendel, Peter N. Robinson
Cold Spring Harbor Laboratory
BioSamples database: FAIRer samples metadata to accelerate research data management
Mélanie Courtot, Dipayan Gupta, Isuru Liyanage, Fuqi Xu, Tony Burdett
Nucleic Acids Research
The Data Use Ontology to streamline responsible access to human biomedical datasets
Jonathan Lawson, Moran N. Cabili, Giselle Kerry, Tiffany Boughtwood, Adrian Thorogood, ..., Chisato Yamasaki, Lyndon Zass, Jaime M. Guidry Auvil, Tommi H. Nyrönen, Mélanie Courtot
Cell Genomics
GA4GH: International policies and standards for data sharing across genomic research and healthcare
Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, ..., Ksenia Zaytseva, Junjun Zhang, Peter Goodhand, Kathryn North, Ewan Birney
Cell Genomics
GA4GH Passport standard for digital identity and access permissions
Craig Voisin, Mikael Linden, Stephanie O.M. Dyke, Sarion R. Bowers, Pinar Alper, ..., J. Dylan Spalding, Juha Törnroos, Ilya Tulchinsky, Jaime M. Guidry Auvil, Tommi H. Nyrönen
Cell Genomics
Empirical validation of an automated approach to data use oversight
Moran N. Cabili, Jonathan Lawson, Andrea Saltzman, Greg Rushton, Pearl O’Rourke, ..., Laura Lyman Rodriguez, Tommi Nyronen, Mélanie Courtot, Stacey Donnelly, Anthony A. Philippakis
Cell Genomics
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, ..., Nicole A Vasilevsky, Ramona L Walls, Jie Zheng, Christopher J Mungall, Bjoern Peters
Database
OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies
Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, ..., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters
Cold Spring Harbor Laboratory
Towards a Common Standard for Data and Specimen Provenance in Life Sciences
P Holub, R Wittner, C Mascia, F Frexia, H Müller, M Plass, C Allocca, ...
[no publisher info]
The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine
JOB Jacobsen, M Baudis, GS Baynam, JS Beckmann, S Beltran, ...
medRxiv, 2021.11. 27.21266944, 2021
Empirical validation of an automated approach to data use oversight
MN Cabili, J Lawson, A Saltzman, G Rushton, P O’Rourke, J Wilbanks, ...
Cell Genomics 1 (2), 2021
GA4GH Passport standard for digital identity and access permissions
C Voisin, M Linden, SOM Dyke, SR Bowers, P Alper, MP Barkley, ...
Cell Genomics 1 (2), 2021
The Data Use Ontology to streamline responsible access to human biomedical datasets
J Lawson, MN Cabili, G Kerry, T Boughtwood, A Thorogood, P Alper, ...
Cell Genomics 1 (2), 2021
The european nucleotide archive in 2020
PW Harrison, A Ahamed, R Aslam, BTF Alako, J Burgin, N Buso, ...
Nucleic acids research 49 (D1), D82-D85, 2021
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
R Jackson, N Matentzoglu, JA Overton, R Vita, JP Balhoff, PL Buttigieg, ...
Database 2021, baab069, 2021
GA4GH: International policies and standards for data sharing across genomic research and healthcare
HL Rehm, AJH Page, L Smith, JB Adams, G Alterovitz, LJ Babb, ...
Cell genomics 1 (2), 2021

2020

The European Nucleotide Archive in 2020
Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, ..., Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Tony Burdett, Guy Cochrane
Nucleic Acids Research
SBMLLevel 3: an extensible format for the exchange and reuse of biological models
Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, ..., Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker
Molecular Systems Biology
FAIR Principles: Interpretations and Implementation Considerations
Annika Jacobsen, Ricardo de Miranda Azevedo, Nick Juty, Dominique Batista, Simon Coles, ..., Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes
Data Intelligence
FAIR Principles: Interpretations and Implementation Considerations
Annika Jacobsen, Ricardo de Miranda Azevedo, Nick Juty, Dominique Batista, Simon Coles, ..., Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes
Data Intelligence
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
FAIR principles: interpretations and implementation considerations
A Jacobsen, R de Miranda Azevedo, N Juty, D Batista, S Coles, R Cornet, ...
Data intelligence 2 (1-2), 10-29, 2020

2019

CORBEL Prototype implementation of distributed automated data access request, review and authorization and delivery systems
Mikael Linden, Jan-Willem Boiten, Melanie Courtot, Petr Holub, Gert-Jan van de Geijn, ..., Jason Swedlow, Morris Swertz, Juha Törnroos, Pasi Kankaanpää, Erik van Iperen
Zenodo
Where does an Ontology start?
H Harmse, M Courtot, W Read, N Matentzoglu, D Osumi-Sutherland, ...
ICBO, 1, 2019
BioSamples database: an updated sample metadata hub
M Courtot, L Cherubin, A Faulconbridge, D Vaughan, M Green, ...
Nucleic acids research 47 (D1), D1172-D1178, 2019
The gene ontology resource: 20 years and still GOing strong
Gene Ontology Consortium
Nucleic acids research 47 (D1), D330-D338, 2019

2018

BioSamples database: an updated sample metadata hub
Mélanie Courtot, Luca Cherubin, Adam Faulconbridge, Daniel Vaughan, Matthew Green, David Richardson, Peter Harrison, Patricia L Whetzel, Helen Parkinson, Tony Burdett
Nucleic Acids Research
The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform
Thomas C Matthews, Franklin R Bristow, Emma J Griffiths, Aaron Petkau, Josh Adam, ..., Eduardo N Taboada, Robert G Beiko, Fiona SL Brinkman, William WL Hsiao, Gary Van Domselaar
Cold Spring Harbor Laboratory
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis
David J. Osumi-Sutherland, Enrico Ponta, Melanie Courtot, Helen Parkinson, Laura Badi
Journal of Biomedical Semantics
Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149
Rok Tkavc, Vera Y. Matrosova, Olga E. Grichenko, Cene Gostinčar, Robert P. Volpe, ..., Theron Hamilton, Kenneth G. Frey, Nina Gunde-Cimerman, Lawrence Dugan, Michael J. Daly
Frontiers in Microbiology
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis
DJ Osumi-Sutherland, E Ponta, M Courtot, H Parkinson, L Badi
Journal of biomedical semantics 9 (1), 10, 2018
The integrated rapid infectious disease analysis (IRIDA) platform
TC Matthews, FR Bristow, EJ Griffiths, A Petkau, J Adam, D Dooley, ...
BioRxiv, 381830, 2018
Prospects for fungal bioremediation of acidic radioactive waste sites: characterization and genome sequence of Rhodotorula taiwanensis MD1149
R Tkavc, VY Matrosova, OE Grichenko, C Gostinčar, RP Volpe, ...
Frontiers in microbiology 8, 305317, 2018

2017

Dead simple OWL design patterns
David Osumi-Sutherland, Melanie Courtot, James P. Balhoff, Christopher Mungall
Journal of Biomedical Semantics
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
Julie A McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, ..., Katherine Wolstencroft, Carole Goble, Christopher J Mungall, Melissa A Haendel, Helen Parkinson
Cold Spring Harbor Laboratory
Dead simple OWL design patterns
D Osumi-Sutherland, M Courtot, JP Balhoff, C Mungall
Journal of biomedical semantics 8 (1), 18, 2017
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
JA McMurry, N Juty, N Blomberg, T Burdett, T Conlin, N Conte, M Courtot, ...
PLoS biology 15 (6), e2001414, 2017
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
E Ong, Z Xiang, B Zhao, Y Liu, Y Lin, J Zheng, C Mungall, M Courtot, ...
Nucleic acids research 45 (D1), D347-D352, 2017

2016

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
Baofeng Jia, Amogelang R. Raphenya, Brian Alcock, Nicholas Waglechner, Peiyao Guo, ..., Andrew C. Pawlowski, Timothy A. Johnson, Fiona S.L. Brinkman, Gerard D. Wright, Andrew G. McArthur
Nucleic Acids Research
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
Nucleic Acids Research
The Ontology for Biomedical Investigations
Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, ..., Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng
PLOS ONE
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
Sefa Kılıç, Dinara M. Sagitova, Shoshannah Wolfish, Benoit Bely, Mélanie Courtot, ..., Tatiana Tatusova, Claire O’Donovan, Marcus C. Chibucos, Maria J. Martin, Ivan Erill
Database
Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims.
M Courtot, AL Mitchell, M Scheremetjew, JP González, LI Furlong, ...
SWAT4LS 2016, 2016
Ten Simple Rules for Biomedical Ontology Development.
M Courtot, J Malone, C Mungall
ICBO/BioCreative, 2016
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
S Kılıç, DM Sagitova, S Wolfish, B Bely, M Courtot, S Ciufo, T Tatusova, ...
Database 2016, baw055, 2016
The ontology for biomedical investigations
A Bandrowski, R Brinkman, M Brochhausen, MH Brush, B Bug, ...
PloS one 11 (4), e0154556, 2016
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
B Jia, AR Raphenya, B Alcock, N Waglechner, P Guo, KK Tsang, BA Lago, ...
Nucleic acids research, gkw1004, 2016

2015

Finding Our Way through Phenotypes
Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, ..., Christian S. Wirkner, James B. Woolley, Matthew J. Yoder, Aaron M. Zorn, Paula Mabee
PLoS Biology
Basic Formal Ontology 2.0
M Almeida, J Bona, M Brochhausen, W Ceusters, M Courtot, R Dipert, ...
[no publisher info]
Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary.
D Osumi-Sutherland, E Ponta, M Courtot, HE Parkinson, L Badi
SWAT4LS, 84-93, 2015
UniProt-GOA: A central resource for data integration and GO annotation.
M Courtot, A Shypitsyna, E Speretta, A Holmes, T Sawford, T Wardell, ...
SWAT4LS 2015, 227-228, 2015
flowCL: ontology-based cell population labelling in flow cytometry
M Courtot, J Meskas, AD Diehl, R Droumeva, R Gottardo, A Jalali, ...
Bioinformatics 31 (8), 1337-1339, 2015
Basic Formal Ontology 2.0: Specification and user’s guide
B Smith, M Almeida, J Bona, M Brochhausen, W Ceusters, M Courtot, ...
National Center for Ontological Research: Buffalo, NY, USA, 50, 2015
Finding our way through phenotypes
AR Deans, SE Lewis, E Huala, SS Anzaldo, M Ashburner, JP Balhoff, ...
PLoS biology 13 (1), e1002033, 2015

2014

flowCL: ontology-based cell population labelling in flow cytometry
Mélanie Courtot, Justin Meskas, Alexander D. Diehl, Radina Droumeva, Raphael Gottardo, ..., Holden T. Maecker, J. Philip McCoy, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman
Bioinformatics
Semantic models in biomedicine: Building interoperating ontologies for biomedical data representation and processing in pharmacovigilance
Melanie Courtot
University of British Columbia
The Logic of Surveillance Guidelines: An Analysis of Vaccine Adverse Event Reports from an Ontological Perspective
Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg
PLoS ONE
Semantic models in biomedicine: Building interoperating ontologies for biomedical data representation and processing in pharmacovigilance
M Courtot
University of British Columbia, 2014
The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective
M Courtot, RR Brinkman, A Ruttenberg
PloS one 9 (3), e92632, 2014

2013

Diagnostic criteria and clinical guidelines standardization to automate case classification.
M Courtot, J Zheng, CJ Stoeckert Jr, RR Brinkman, A Ruttenberg
ICBO, 101-104, 2013

2012

Adverse Events Following Immunization
M Courtot, RR Brinkman, A Ruttenberg
International Conference on Biomedical Ontology (ICBO) 2012, 2012
Knowledge representation in Health Research: the modeling of Adverse Events Following Immunization (EC abstract)
M Courtot
International Conference on Biomedical Ontology (ICBO) 2012 - Early Career …, 2012
Adverse events following immunization: reporting standardization, automatic case classification and signal detection (poster)
M Courtot, RR Brinkman, A Ruttenberg
International Conference on Biomedical Ontology (ICBO) 2012, 2012

2011

MIREOT: The minimum information to reference an external ontology term
Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, Alan Ruttenberg
Applied Ontology
Controlled vocabularies and semantics in systems biology
Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, ..., Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère
Molecular Systems Biology
Reporting Adverse Events: Basis for a Common Representation.
M Courtot, RR Brinkman, A Ruttenberg
ICBO, 2011
Building the OBO Foundry ² One Policy at a Time
M Courtot, C Mungall, RR Brinkman, A Ruttenberg
[no publisher info]
Towards an Adverse Event Reporting Ontology.
M Courtot, RR Brinkman
ICBO, 2011
Overcoming the ontology enrichment bottleneck with quick term templates
P Rocca-Serra, A Ruttenberg, MJ O'Connor, PL Whetzel, D Schober, ...
Applied ontology 6 (1), 13-22, 2011
MIREOT: The minimum information to reference an external ontology term
M Courtot, F Gibson, AL Lister, J Malone, D Schober, RR Brinkman, ...
Applied Ontology 6 (1), 23-33, 2011
Controlled vocabularies and semantics in systems biology
M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova, A Dräger, ...
Molecular systems biology 7 (1), 543, 2011

2010

Ontology representation and ANOVA analysis of vaccine protection investigation
Yongqun He, Zuoshuang Xiang, Thomas Todd, Mélanie Courtot, Ryan Brinkman, ..., Susanna Assunta Sansone, Jennifer Fostel, Larisa N. Soldatova, Bjoern Peters, Alan Ruttenberg
Bio-Ontologies 2010: Semantic Applications in Life Sciences
OntoFox: web-based support for ontology reuse
Zuoshuang Xiang, Mélanie Courtot, Ryan R Brinkman, Alan Ruttenberg, Yongqun He
BMC Research Notes
Modeling biomedical experimental processes with OBI
Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, ..., Susanna-Assunta Sansone, Larisa N Soldatova, Christian J Stoeckert, Jessica A Turner, Jie Zheng
Journal of Biomedical Semantics
Technical Note OntoFox: web-based support for ontology reuse
Z Xiang, M Courtot, RR Brinkman, A Ruttenberg, Y He
[no publisher info]
Ontology representation and ANOVA analysis of vaccine protection investigation
Y He, Z Xiang, T Todd, M Courtot, RR Brinkman, J Zheng, CJ Stoeckert Jr, ...
Bio-Ontologies 2010: Semantic Applications in Life Sciences, 18th Annual …, 2010
BioModels. net Web Services, a free and integrated toolkit for computational modelling software
C Li, M Courtot, N Le Novère, C Laibe
Briefings in bioinformatics 11 (3), 270-277, 2010
OntoFox: web-based support for ontology reuse
Z Xiang, M Courtot, RR Brinkman, A Ruttenberg, Y He
BMC research notes 3 (1), 175, 2010
Modeling biomedical experimental processes with OBI
RR Brinkman, M Courtot, D Derom, JM Fostel, Y He, P Lord, J Malone, ...
Journal of biomedical semantics 1 (Suppl 1), S7, 2010

2009

BioModels.net Web Services, a free and integrated toolkit for computational modelling software
C. Li, M. Courtot, N. Le Novere, C. Laibe
Briefings in Bioinformatics
Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates
Bjoern Peters, Alan Ruttenberg, Jason Greenbaum, Melanie Courtot, Ryan Brinkman, Patricia Whetzel, Daniel Schober, Susanna Assunta Sansone, Richard Scheuerman, Philippe Rocca-Serra
Nature Precedings
VO: Vaccine Ontology
Yongqun He, Yongqun He, Lindsay Cowell, Alexander Diehl, Harry Mobley, ..., Trish Whetzel, Mark Musen, Brian Athey, Gilbert Omenn, Barry Smith
Nature Precedings
The Systems Biology Graphical Notation
Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, ..., Chris Sander, Herbert Sauro, Jacky L Snoep, Kurt Kohn, Hiroaki Kitano
Nature Biotechnology
MIREOT: the Minimum Information to Reference an External Ontology Term
A Ruttenberg, M Courtot, F Gibson, A Lister, J Malone, D Schober, ...
Nature Precedings, 1-1, 2009
Erratum: The Systems Biology Graphical Notation
A Luna, U Dogrusoz, Y Matsuoka, K Wegner, H Kawaji, S Sahle, SE Boyd, ...
Nature Biotechnology 27, 864-864, 2009
Overcoming the ontology enrichment bottleneck with quick term templates
B Peters, A Ruttenberg, J Greenbaum, M Courtot, R Brinkman, P Whetzel, ...
Nature Precedings, 1-1, 2009
MIREOT: the minimum information to reference an external ontology term
M Courtot, F Gibson, A Lister, J Malone, D Schober, RR Brinkman, ...
Aug-2009, 2009
The systems biology graphical notation
NL Novère, M Hucka, H Mi, S Moodie, F Schreiber, A Sorokin, E Demir, ...
Nature biotechnology 27 (8), 735-741, 2009

2008

The OWL of Biomedical Investigations
Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R Brinkman, Alan Ruttenberg
Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions
The OWL of Biomedical Investigations.
M Courtot, WJ Bug, F Gibson, AL Lister, J Malone, D Schober, ...
OWLED 432, 2008

2007

Adding semantics in kinetics models of biochemical pathways
N Le Novere, M Courtot, C Laibe
Proceedings of the 2nd International Symposium on experimental standard …, 2007

2006

Structural genomics on membrane proteins: comparison of more than 100 GPCRs in 3 expression systems
Kenneth Lundstrom, Renaud Wagner, Christoph Reinhart, Aline Desmyter, Nadia Cherouati, ..., Nicolas André, Gherici Hassaine, Hartmut Michel, Christian Cambillau, Franc Pattus
Journal of Structural and Functional Genomics
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
N. Le Novere
Nucleic Acids Research
Structural genomics on membrane proteins: comparison of more than 100 GPCRs in 3 expression systems
K Lundstrom, R Wagner, C Reinhart, A Desmyter, N Cherouati, T Magnin, ...
Journal of structural and functional genomics 7 (2), 77-91, 2006
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
N Le Novere, B Bornstein, A Broicher, M Courtot, M Donizelli, H Dharuri, ...
Nucleic acids research 34 (suppl_1), D689-D691, 2006

Common Infrastructure for National Cohorts in Europe, Canada, and Africa-CINECA
UO UTartu, SR Mbiyavanga, HJ Westra, M Courtot, J Dursi, M Linden
[no publisher info]