News
New TF-TG resources in BioGateway
We have replaced the TF-TG resources previously available in BioGateway (TRRUST, ExTRI, CytReg, Signor, GEREDB, HTRIdb, and TFactS) with the CollecTRI resource (DOI: 10.1093/nar/gkad841) and TFLink (DOI: 10.1093/database/baac083).
New organisms in the database
We are currently working on the addition of new organisms in the database. Some of the organisms that we plan to add are Gadus morhua, Drosophila melanogaster, Mus musculus, Ursus maritimus, Rattus norvegicus, Zonotrichia albicollis, Taeniopygia guttata and Danio rerio.
The BioGateway App paper has been submitted!
We are happy to inform that we have submitted the BioGateway App paper for publication. More information will be displayed once the paper gets published.
BioGateway Cytoscape App 3.0.0 released
The first version of the Cytoscape App for BioGateway is now released, beginning at version 3.0.0, matching the updated version 3.0 version of the BioGateway Triple Store. It can be downloaded here.
PhDs
Aravind Venkatesan
Application of Semantic Web Technology to Establish Knowledge Management and Discovery in the Life Sciences
Public defense: 13-02-2014
Link: https://brage.bibsys.no/xmlui/handle/11250/245401
Ward Blondé
Metarel, an ontology facilitating advanced querying of biomedical knowledge
Public defense: 22-06-2012
Link: https://biblio.ugent.be/publication/2913369
Erick Antezana
Towards semantic systems biology: biological knowledge management using semantic web technologies
Public defense: 28-09-2009
Publications
Genes2GO: A web application for querying gene sets for specific GO terms
Chawla K and Kuiper M (2016) – W Server, Bioinformation 12(3), 231-232
Finding gene regulatory network candidates using the gene expression knowledge base
Venkatesan, A., Tripathi, S., de Galdeano, A. S., Blondé, W., Lægreid, A., Mironov, V., & Kuiper, M. (2014). BMC bioinformatics, 15(1), 386.
Using the relation ontology Metarel for modelling Linked Data as multi-digraphs
Blondé W, Antezana E, Mironov V, Schulz S, Kuiper M and De Baets B – Semantic Web Journal, 2013.
Putting Semantics in Systems Biology
Kuiper M, Venkatesan A, Antezana E, Vercruysse S, Mironov V, Blondé W – meta, 3 ISSB: 1890-1856, 2012.
Towards an integrated knowledge system for capturing gene expression events
Venkatesan A, Mironov V, Kuiper M: In Proceedings of International Conference on Biomedical Ontology, Graz, Austria, 2012.
Flexibility and Utility of the Cell Cycle Ontology
Mironov V, Antezana E, Egaña M, Blondé W, De Baets B, Stevens R, and Kuiper M – Applied Ontology, 2012.
Gauging triple stores with actual biological data
Mironov V, Seethappan N, Blondé W, Antezana E, Splendiani A and Kuiper M – BMC Bioinformatics, 13(Suppl 1):S3, 2012.
Reasoning with bio-ontologies: using relational closure rules to enable practical querying
Ward Blondé; Vladimir Mironov; Aravind Venkatesan; Erick Antezana; Bernard De Baets; Martin Kuiper: Bioinformatics; doi: 10.1093/bioinformatics/btr164, 2011.
The RDF Foundry: Call for an initiative to build enhanced RDF resources for biological data integration
Aravind Venkatesan, Ward Blondé, Erick Antezana, Mats Skillingstad, M Scott Marshall, Bernard De Baets, Vladimir Mironov, Martin Kuiper – WIMS’11, Proceedings of the International Conference on Web Intelligence, Mining and Semantics, New York, NY, USA, 2011.
Semantic systems biology: enabling integrative biology via semantic web technologies
Erick Antezana, Ward Blondé, Aravind Venkatesan, Bernard De Baets, Vladimir Mironov, Martin Kuiper – WIMS’11, Proceedings of the International Conference on Web Intelligence, Mining and Semantics, New York, NY, USA, 2011.
ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies
Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M: BMC Bioinformatics, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8, 2010.
The Cell Cycle Ontology: An application ontology for the representation and integrated analysis of the cell cycle process
Erick Antezana, Mikel Egaña , Ward Blondé , Aitzol Illarramendi , Iñaki Bilbao , Bernard De Baets , Robert Stevens , Vladimir Mironov and Martin Kuiper: Genome Biology, 10:R58, 2009.
Biological knowledge management: the emerging role of the Semantic Web technologies
Erick Antezana; Martin Kuiper; Vladimir Mironov. Briefings in Bioinformatics; doi: 10.1093/bib/bbp024, 2009.
Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies
2009. Blondé, E. Antezana, B. De Baets, V. Mironov, M. Kuiper. ICBO – International Conference on Biomedical Ontologies, Buffalo, US, July 2009.
Biogateway: A Semantic Systems Biology Tool for the Life Sciences
Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper. BMC bioinformatics, 10(Suppl 10):S11, 2009.
BioGateway: Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project.
Antezana, E., Blondé, W., Egana M., Rutherford, A., Stevens, R., De Baets, B., Mironov, V., Kuiper, M. SWAT4LS – Semantic Web Applications and Tools for Life Sciences, e-Science Institute, Edinburgh, Scotland, UK. November 28, 2008.
ONTO-PERL: An API supporting the development and analysis of bio-ontologies.
E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov. Bioinformatics, 24: 885-887 ; doi:10.1093/bioinformatics/btn042, 2008.
Applying Ontology Design Patterns in bio-ontologies
Mikel Egaña, Alan Rector, Robert Stevens, Erick Antezana. EKAW 2008 – 16th International Conference on Knowledge Engineering and Knowledge Management Knowledge Patterns. 29th September-3rd October – Acitrezza, Catania, Italy, 2008.
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology
Mikel Egaña, Erick Antezana, Martin Kuiper, Robert Stevens. BMC bioinformatics, 9(Suppl 5):S1, 2008.
Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language
2008. Egaña; R. Stevens; E. Antezana. OWLED, Fourth International Workshop – Washington, DC, USA, 2008.
A cell-cycle knowledge integration framework
2006. Antezana; E. Tsiporkova; V. Mironov; and Kuiper, M. DILS 2006, LNBI 4075, pp. 19-34, 2006.
Presentations
Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies
(ICBO – International Conference on Biomedical Ontologies, Buffalo, US, July 2009).
The Cell Cycle Ontology: an overture to Semantic Systems Biology
(Systems Biology Approaches to Study the Cell Cycle, ENFIN Workshop, October 20-21, 2008 Malaga, Spain).
Data integration in life sciences: Cell Cycle Ontology
(Norwegian Bioinformatics Forum 2008, Bergen 9-10 October ).
Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language
(OWLed. Washington DC, 1.4.2008).
The Cell-Cycle Ontology
(Workshop on Ontologies of Cellular Networks. Newark-USA, 28.03.2008)
A formal ontology for the cell-cycle domain
(Intégration des Systèmes d’Information en Biologie-ISIBio. Nancy-France, 21.11.2006).
A cell-cycle knowledge integration framework
(3rd International Workshop on Data Integration in the Life Sciences 2006. 20.7. – 22.7.2006).
Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project.
(SWAT4LS – Semantic Web Applications and Tools for Life Sciences, e-Science Institute, Edinburgh, Scotland, UK. 28.11.2008.)
BioGateway: an RDF store for supporting Systems Biology
(W3C Healthcare and Life Sciences Interest Group (HCLSIG), BioRDF meeting, 06.10.2008)
Data-driven and hypothesis-driven research in Semantic Systems Biology
(Norwegian University of Science and Technology, NTNU. Trondheim-Norway, 29.04.2008)
Posters
Metarel: a Meta-Ontology for Reasoning with Biomedical Relations
Reasoning Web Summer School, Brixen-Bressanone, August 2009.
BioGateway: enabling Semantic Systems Biology
MLSB 2008, The 2nd International Workshop on Machine Learning in Systems Biology.
September 13-14, 2008. Brussels, Belgium.
Semantic Systems Biology: enabling integrative biology by semantic web technologies
ICSB 2008, The 9th International Conference on Systems Biology.
22-28th August, 2008. Gothenburg, Sweden.
BioGateway: integrated RDF for life science queries.
SWAT4LS – Semantic Web Applications and Tools for Life Sciences, e-Science Institute, Edinburgh, Scotland, UK. November 28, 2008.
The Cell Cycle Ontology: an application ontology supporting the Life Sciences.
SWAT4LS – Semantic Web Applications and Tools for Life Sciences, e-Science Institute, Edinburgh, Scotland, UK. November 28, 2008.
The Cell Cycle Ontology: a step towards a Semantic Systems Biology.
EKAW 2008 – 16th International Conference on Knowledge Engineering and Knowledge Management Knowledge Patterns. 29th September-3rd October 2008 – Acitrezza, Catania, Italy.
Semantic Systems Biology: enabling integrative biology by semantic web technologies.
The 9th International Conference on Systems Biology. 22-28th August 2008 – Gothenburg, Sweden.
The Cell Cycle Ontology: an application ontology for data integration.
The 9th International Conference on Systems Biology. 22-28th August 2008 – Gothenburg, Sweden.
Ontology driven data integration for enabling systems biology
(The eighth international conference on systems biology – 2007, Long Beach, California – USA).
Ontology-driven Data Integration for Enabling Systems Biology: Cell-Cycle Ontology.
(Integrative Bioinformatics. 4th annual meeting 2007, Ghent – Belgium).
CCO, a paradigm for knowledge integration.
(Bio-Ontologies SIG Workshop – ISCB/ECCB 2007, Vienna – Austria).
Towards a richer Cell-Cycle Ontology
(BENELEARN conference 2006, Ghent – Belgium).