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My research interests comprise:
- Natural Language Processing (NLP) in the field of life sciences, mostly related to molecular
biology and biomedicine. Especially:
- Biomedical Information Extraction and Text Mining, including:
- Named entity recognition as well as
- fact extraction:
At the moment I'm working (in a co-operation with EMBL, the Bork group) on
the extraction of :
- gene transcription networks,
- protein-protein interactions and
- protein modifications
to be included in the STRING
project.
Some details and downloads are available through STRING-IE
Resources are MedLine abstracts and PubMed full text (see bibliography for further information).
- Ontologies, Taxonomies and knowledge management/engineering in
general and
especially for modelling protein interactions and gene transcriptions.
For research in this field we're collaborating with the
Laboratory of Applied ontologies (LOA) in Rome.
We are mainly interested in learning relations between concepts
from textual data for semi-automatic construction of ontologies.
See bibliography for further
information.
- Intergration of heterogeneous data:
- Integrating Swissprot entries (especially
feature table
entries) for transparent and consistent querying with TIGERSearch.
See bibliography for further
information.
- SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a database on reaction kinetics. From an NLP point of
view this involves terminological issues, ontological issues, text
mining etc.
- NLP in general and with a focus on
- Information extraction,
- Text Mining and
- Semantic Interpretation.
- Teaching: Please have a look at our
BioNLP seminar 2005.
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