An intuitive R-based web application. Genes2GO uses the biomaRt package of Bioconductor in order to retrieve custom sets of gene ontology annotations for any list of genes from organisms covered by the Ensembl database. 

The tool is now decommissioned


WordVis lets you find words in the English dictionary, see synonyms grouped by meaning, and browse them in a fluid, interactive web of words and meanings. With WordVis you can explore the English language and perfect your language skills.



An exhaustive collection of TFs annotated according to experimental and other evidence on their function as true DbTFs. provides a high-quality and comprehensive knowledge source for genome-scale regulatory network studies.



OLSVis is an interactive visualisation of EBI’s Ontology Lookup Service (OLS). It is an application of WordVis’ visualiser.



VSM is a tool that lets people manually create computable information, with both high ease of use, and high expressive power.

We aimed for VSM to be applicable to the widest range of use-cases, i.e.: it works for diverse, heterogeneous information. Simultaneously, VSM keeps any inherent complexity in the captured information manageable for humans, i.e.: we focused on high user-friendliness towards curators.


BioGateway 2.0 endpoint

A semantically integrated resource comprising the entire set of the OBO foundry candidate ontologies, the GO annotation files, the SWISS-PROT protein set, the NCBI taxonomy and several in-house ontologies. BioGateway provides a single entry point to query these resources through SPARQL. It constitutes a key component for a Semantic Systems Biology approach to generate new hypotheses concerning systems properties. 

Link: C

BioGateway Cytoscape App

The BioGateway App is a Cytoscape plugin designed to provide easy query access to the BioGateway RDF triple store, which contains functional and interaction information for proteins from several curated resources. For explorative network building, we have added a comprehensive dataset with regulatory relationships of mammalian DNA binding transcription factors and their target genes, compiled both from curated resources and from a text mining effort. Query results are visualised using the inherent flexibility of the Cytoscape framework, and network links can be checked against curated database records or against the original publication.


BioGateway 3.0 endpoint

Coming soon!



Cell Cycle Ontology

An application ontology integrating knowledge about the eukaryotic cell cycle.


GEXKB graphs

GeXO, ReXO and ReTO are nested, each ontologies connected to top nodes from the upper level ontology (ULO) the common root of the three ontologies. Black and red edges depict ‘is_a’ and ‘part_of’ relations, respectively. The three ontologies cover an increasingly wider domain. Each GO sub-domain term (e.g. GO:0010467; denoting ‘gene expression’) and its descendants are linked to the ULO as a subclass of ‘Biological Process’ represented by the ‘dotted edges’.




Main publications

Systems Biology
E Tsirvouli, V Touré, B Niederdorfer, M Vázquez, Å Flobak, M Kuiper
Frontiers in molecular biosciences 7, 300
Discovery of drug synergies in gastric cancer cells predicted by logical modeling
Å Flobak, A Baudot, E Remy, L Thommesen, D Thieffry, M Kuiper, …
PLoS computational biology 11 (8), e1004426
Standards and Ontologies
M Kuiper, J Bonello, JT Fernández-Breis, P Bucher, ME Futschik, …
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1865 (1), 194768
Gene Ontology representation for transcription factor functions
P Gaudet, C Logie, RC Lovering, M Kuiper, A Lægreid, PD Thomas
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1864 (11-12 …
The Gene Ontology resource: enriching a GOld mine
Gene Ontology Consortium
Nucleic acids research 49 (D1), D325-D334
The gene ontology resource: 20 years and still GOing strong
Gene Ontology Consortium
Nucleic acids research 47 (D1), D330-D338
The minimum information about a molecular interaction causal statement (MI2CAST)
V Touré, S Vercruysse, ML Acencio, RC Lovering, S Orchard, G Bradley, …
Bioinformatics 36 (24), 5712-5718
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination
L Perfetto, ML Acencio, G Bradley, G Cesareni, N Del Toro, D Fazekas, …
Bioinformatics 35 (19), 3779-3785
ExTRI: Extraction of transcription regulation interactions from literature
M Vazquez, M Krallinger, F Leitner, M Kuiper, A Valencia, A Laegreid
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1865 (1), 194778
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator
V Touré, J Zobolas, M Kuiper, S Vercruysse
Database 2021
UniBioDicts: unified access to biological dictionaries
J Zobolas, V Touré, M Kuiper, S Vercruysse
Bioinformatics 37 (1), 143-144
Semantic Systems Biology
Current Protocols in Bioinformatics 72 (1), e106
The Cytoscape BioGateway app: explorative network building from an RDF store
S Holmås, R Riudavets Puig, ML Acencio, V Mironov, M Kuiper
Bioinformatics 36 (6), 1966-1967
BioGateway: a semantic systems biology tool for the life sciences
E Antezana, W Blondé, M Egaña, A Rutherford, R Stevens, B De Baets, …
BMC bioinformatics 10 (10), 1-15
Biological knowledge management: the emerging role of the Semantic Web technologies
E Antezana, M Kuiper, V Mironov
Briefings in bioinformatics 10 (4), 392-407
Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons
A Chatterjee, T Swierstra, M Kuiper
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 194779
Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures
R Nydal, G Bennett, M Kuiper, A Lægreid
Medicine, Health Care and Philosophy 23 (3), 471-484
Scientific knowledge in the age of computation: Explicated, computable and manageable?
S Efstathiou, R Nydal, A Laegreid, M Kuiper
Theoria. Revista de Teoría, Historia y Fundamentos de la Ciencia 34 (2), 213-236