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
2024
The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
arXiv preprint arXiv:2405.04734, 2024
Toward a common standard for data and specimen provenance in life sciences
Learning health systems 8 (1), e10365, 2024
2023
ELIXIR biovalidator for semantic validation of life science metadata (vol 38, pg 3141, 2022)
BIOINFORMATICS 39 (1), 2023
Accelerating cancer omics and precision oncology in health care and research: a Lancet Oncology Commission
The lancet oncology 24 (2), 123-125, 2023
Features of a FAIR vocabulary
Journal of Biomedical Semantics 14 (1), 6, 2023
FAIR in action-a flexible framework to guide FAIRification
Scientific data 10 (1), 291, 2023
2022
Features of a FAIR Vocabulary
[no publisher info]
ELIXIR biovalidator for semantic validation of life science metadata
Bioinformatics 38 (11), 3141-3142, 2022
BioSamples database: FAIRer samples metadata to accelerate research data management
Nucleic acids research 50 (D1), D1500-D1507, 2022
The GA4GH Phenopacket schema defines a computable representation of clinical data
Nature biotechnology 40 (6), 817-820, 2022
2021
The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine
Cold Spring Harbor Laboratory
BioSamples database: FAIRer samples metadata to accelerate research data management
Nucleic Acids Research
The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine
medRxiv, 2021.11. 27.21266944, 2021
Empirical validation of an automated approach to data use oversight
Cell Genomics 1 (2), 2021
GA4GH Passport standard for digital identity and access permissions
Cell Genomics 1 (2), 2021
The Data Use Ontology to streamline responsible access to human biomedical datasets
Cell Genomics 1 (2), 2021
The european nucleotide archive in 2020
Nucleic acids research 49 (D1), D82-D85, 2021
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
Database 2021, baab069, 2021
GA4GH: International policies and standards for data sharing across genomic research and healthcare
Cell genomics 1 (2), 2021
2020
SBML Level 3: an extensible format for the exchange and reuse of biological models
Molecular systems biology 16 (8), e9110, 2020
FAIR principles: interpretations and implementation considerations
Data intelligence 2 (1-2), 10-29, 2020
2019
Where does an Ontology start?
ICBO, 1, 2019
BioSamples database: an updated sample metadata hub
Nucleic acids research 47 (D1), D1172-D1178, 2019
The gene ontology resource: 20 years and still GOing strong
Nucleic acids research 47 (D1), D330-D338, 2019
2018
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis
Journal of biomedical semantics 9, 1-10, 2018
The integrated rapid infectious disease analysis (IRIDA) platform
BioRxiv, 381830, 2018
Prospects for fungal bioremediation of acidic radioactive waste sites: characterization and genome sequence of Rhodotorula taiwanensis MD1149
Frontiers in microbiology 8, 305317, 2018
2017
Dead simple OWL design patterns
Journal of biomedical semantics 8, 1-7, 2017
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
PLoS biology 15 (6), e2001414, 2017
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
Nucleic acids research 45 (D1), D347-D352, 2017
2016
Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims.
SWAT4LS 2016, 2016
Ten Simple Rules for Biomedical Ontology Development.
ICBO/BioCreative, 2016
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
Database 2016, baw055, 2016
The ontology for biomedical investigations
PloS one 11 (4), e0154556, 2016
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
Nucleic acids research, gkw1004, 2016
2015
Basic Formal Ontology 2.0
[no publisher info]
UniProt-GOA: A central resource for data integration and GO annotation.
SWAT4LS 2015, 227-228, 2015
flowCL: ontology-based cell population labelling in flow cytometry
Bioinformatics 31 (8), 1337-1339, 2015
Basic Formal Ontology 2.0: Specification and user’s guide
National Center for Ontological Research: Buffalo, NY, USA, 50, 2015
Finding our way through phenotypes
PLoS biology 13 (1), e1002033, 2015
2014
Semantic models in biomedicine: Building interoperating ontologies for biomedical data representation and processing in pharmacovigilance
University of British Columbia, 2014
The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective
PloS one 9 (3), e92632, 2014
2013
2012
Adverse Events Following Immunization
International Conference on Biomedical Ontology (ICBO) 2012, 2012
Knowledge representation in Health Research: the modeling of Adverse Events Following Immunization (EC abstract)
International Conference on Biomedical Ontology (ICBO) 2012 - Early Career …, 2012
Adverse events following immunization: reporting standardization, automatic case classification and signal detection (poster)
International Conference on Biomedical Ontology (ICBO) 2012, 2012
2011
Controlled vocabularies and semantics in systems biology
Molecular Systems Biology, 2011
Building the OBO Foundry ² One Policy at a Time
[no publisher info]
Towards an Adverse Event Reporting Ontology.
ICBO, 2011
Overcoming the ontology enrichment bottleneck with quick term templates
Applied ontology 6 (1), 13-22, 2011
MIREOT: The minimum information to reference an external ontology term
Applied Ontology 6 (1), 23-33, 2011
Controlled vocabularies and semantics in systems biology
Molecular systems biology 7 (1), 543, 2011
2010
Technical Note OntoFox: web-based support for ontology reuse
[no publisher info]
Ontology representation and ANOVA analysis of vaccine protection investigation
Bio-Ontologies 2010: Semantic Applications in Life Sciences, 18th Annual …, 2010
BioModels. net Web Services, a free and integrated toolkit for computational modelling software
Briefings in bioinformatics 11 (3), 270-277, 2010
OntoFox: web-based support for ontology reuse
BMC research notes 3, 1-12, 2010
Modeling biomedical experimental processes with OBI
Journal of biomedical semantics 1, 1-11, 2010
2009
MIREOT: the Minimum Information to Reference an External Ontology Term
Nature Precedings, 1-1, 2009
Overcoming the ontology enrichment bottleneck with quick term templates
Nature Precedings, 1-1, 2009
The systems biology graphical notation
Nature biotechnology 27 (8), 735-741, 2009
2008
The OWL of Biomedical Investigations.
OWLED 432, 2008
2007
Adding semantics in kinetics models of biochemical pathways
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
Journal of structural and functional genomics 7, 77-91, 2006
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
Nucleic acids research 34 (suppl_1), D689-D691, 2006