It’s all semantics for the user
The Semantic Systems Biology group at the Norwegian University of Science and Technology is
active in the field of biological knowledge management. The group has developed the BioGateway
platform: a tool and resource set designed to provide the intended end-user, ideally a biologist or
biomedical researcher, with assistance in the interpretation of her experimental data. The BioGateway
platform is fueled by a data semantification pipeline that covers a chain of ontology manipulation,
knowledge integration, pre-computing and reasoning, and data visualization. At various points along
this pipeline we are active in making improvements with regard to performance, to keep the process
tractable. Recently we published the orthAgogue software, boosting the speed of orthology prediction
200 fold. Even more recently, we ventured into a new approach to increase the speed of reasoning in
order to eliminate a significant bottleneck in the generation of relational closures.
End users should, however, not be concerned with the details of this process, for all they care the
technology can remain ‘under the hood’. What they do care about is an intuitive use of semantic
resources and it is there that current interfaces for the design of SPARQL queries or inspection of the
results leave a lot to be desired. Although for a query interface we have no improvements in
preparation, for the visualization of ontologies we have produced the OLS Vis software, an intuitive
and flexible viewer that is able to display complex ontologies.
The group is actively collaborating with end users, which resulted in the construction of a resource for
gene expression regulation analysis: the GeXKB resource. Some examples of the use of GeXKB for
regulatory pathway extension will be provided. The construction of GeXKB prompted us in the
direction of ‘semantifying’ data from the source: the curation of Transcription Factor information
from scientific literature, resulting in the TFcheckpoint database (www.tfcheckpoint.org) and a set of
curation guidelines for other volunteer curators to join in this effort.
We are now engaged in efforts to organize the global community interested in the domain of
transcription regulation research to develop similar rigorous guidelines and apply them to develop an
integrated homogeneous knowledge resource that could be used for instance in the field of gene
regulatory network building and analysis. In order to further enable this work we are now configuring
and using our literature curation environment SciCura (scicura.org, beta version) to facilitate the
linking of proteins and genes, and their experimentally validated function with Uniprot / Entrez
identifiers, and GO / PSI-MI / Brenda Tissue Ontology terms, respectively. We collect detailed
information on gene regulatory events in the form of human-readable statements which are fully
supported by proper database identifiers and ontology terms (an approach that is in fact extensible to
create digital abstracts). These data will become publicly available and also form a crucial component
of the GeXKB knowledge base.
Sources:
Ekseth OK, Kuiper M and Mironov V. Orthagogue: an agile tool for the rapid prediction of orthology relations.
Bioinformatics (Oxford) 2013 Oct 9. [Epub ahead of print]
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M and Lægreid A. Gene
Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation
effort. Database (Oxford), doi: 10.1093/database/bat062.
Chawla K, Tripathi S, Thommesen L, Lægreid A, and Kuiper M. TFcheckpoint: a curated compendium of specific DNAbinding RNA polymerase II transcription factors. Bioinformatics (Oxford). 2013 Oct 1;29(19):2519-20
Antezana E, Mironov V and Kuiper M. The emergence of Semantic Systems Biology. N biotechnology 2013 Mar
25;30(3):286-90.
A Venkatesan, V Mironov, M Kuiper. Towards an integrated knowledge system for capturing gene expression events. ICBO
2012, Graz, Austria, July 21-25.
Vercruysse S, Venkatesan A and Kuiper M. OLSVis: an Animated, Interactive Visual Browser for Bio-ontologies. BMC
Bioinformatics 2012, 13:116.
Vercruysse S and Kuiper M. Jointly creating digital abstracts: dealing with synonymy and polysemy. BMC research notes
2012, 5 (1), 601.