Albinusdreef 2, 2333 ZA Leiden, Visiting address: Einthovenweg 20, Leiden
0031 (0)71 5268642
The BioSemantics group applies and develops computational methods that help with the interpretation of life science data. For instance, we can prioritise genes from gene expression experiments using knowledge from all abstracts in PubMed, or link your own data to a wide range of data including drug data, pathways, protein interactions, and literature.
The group also has expertise on best practices for data interoperability and computer-supported good research practice. We and our international collaborators work on standards that (i) make (extremely large) datasets more understandable, (ii) easier to connect with other data, (iii) applicable to various forms of reasoning over linked data sets. We can also help to make your data citable (nanopub.org). For instance, if you produce more data that you can publish in a traditional journal, or if you curate data for others, than we can help ensure that you get credit for these data contributions to science. The standards that we apply are in line with emerging international standards for reproducible science, and drive their development. We have worked on examples with institutes such as the RIKEN Institute in Japan, and projects such as RD-Connect (Rare Diseases, EU FP7) and OpenPHACTS (drug discovery, IMI).
The biosemantics group thus specialises in creating and using substrates for knowledge discovery and can help make your data such a substrate, intelligently linked to already existing substrates.
- Biomedical & health
- omics data integration
- system biology
- Semantic Web / Linked Data
- Human Genetics
- Rare diseases
- Population genetics (GWAS)
Expertise and Track Record
Our enabling technologies include:
– Gene prioritization methods
– Services to investigate many types of biological concepts (e.g. differentially expressed genes or GWAS results), using all relations that we can mine from literature and databases.
– Biological relations extracted from literature, both explicitly mentioned in articles, as well as implicit relations that we infer from the network of explicit relations
– A trusted private partner, Euretos, for applying knowledge exploration with professional software and under professional service level agreements.
• We supported the creation of nanopublications within the LUMC and with partners such as the RIKEN institute of Japan. Internationally we set up biweekly telephone conferences. Examples are posted and shared on Nanopub.org.
• We support a wider community by dissemination via EU FP7 technology projects (OpenPHACTS, wf4ever), such as the organisation of an ISMB workshop (2013 ) and technology tracks (2011, 2013)
• For NBIC, we chair the Interoperability Task Force meeting that stimulates discussion about the use of interoperability standards, and coordinate the NBIC training course on Life Science Information Management (2009, 2011, 2013), including coordination, introduction by Barend Mons (2009), and Anni Training (2011).
• We have organised a BioSemantics User Day (LUMC, 2011); tutorials are available from our web site and are used in various courses.
• NBIC, Scientific Director (Mons), Interoperability Task Force leader (Roos),
• Founder of DISC and CWA (Mons)
• Advisor to myExperiment.org (Roos)
• Life Science Domain integrator Netherlands e-Science centre (Mons)
• Guest of the UvA Informatics Institute for COMMIT (Roos)
• Leader of the Linked Data and Ontology Task Force for RD-Connect (EU FP7, Roos)
• Work package leader OpenPHACTS (Mons)
• Member of W3C community working group for Research Objects (Roos)
• Member and initiator of the Nanopublication developer community (Mons, Schultes, Thompson, Roos)