Homepage: BCB

Funding: Bundesministerium für Bildung und Forschung

Period: 2002 - 2006

Project partner: Charite, Max-Planck-Institute for Molecular Genetics, Freie Universität Berlin, Technische Fachhochschule Berlin, Max-Delbrück-Zentrum, Zuse Institut Berlin

The promise of Bioinformatics is to bridge the gap between genome research and medicine. It is the goal of the Berlin Center for Genome Based Bioinformatics (BCB) to realize this vision. The cooperating groups of BCB will attack the major problems in the informational synthesis of genome data

• genomic annotation and knowledge management,
• prediction of structure and function of gene products,
• cellular and disease modelling.

Scientific efforts will be closely integrated with and complemented by educational efforts specifically promoting short-term education of bioinformatics specialists through a 1.5 year curriculum at Technische Fachhochschule Berlin (TFH), and a MSc course in bioinformatics at Freie Universität Berlin (FUB) in close collaboration with Humboldt Universität zu Berlin (HUB).

Homepage: Columba

Funding: Bundesministerium für Bildung und Forschung

Period: 2004 - 2007

Project partner: Kristian Rother, Robert Preissner (Charitè); Prof. Freytag (HUB Informatik), Thomas Steinke (ZIB), Ina Koch (TFH Berlin)

Researchers interested in the analysis of protein structures often require not only the actual structure, but also textual annotation that is spread over different datasources.

In the project Columba we integrate many resources on proteins. Columba is centered around protein structures obtained from the Protein Data Bank (PDB). We add as much annotations as possible to the structures by describing their properties. These annotation include folding classification from SCOP and CATH, secondary structures calculated with DSSP, enzyme annotation from the ENZYME database, participation in metabolic pathways from KEGG, taxonomic classification from the NCBI Taxonomy, and function characterisation from Gene Ontology.

Homepage: Linguistics - Bioinformatics

Funding: Berliner Senat

Period: 2003 - 2007

Project partner: Prof. Lüdeling, Prof. Donhauser (Institut für Deutsche Sprache, HUB)

The project studies the two areas where linguistics and bioinformatics try to solve common problems. First, evolutionary biology tries to uncover the ancestral relationships between species. Similarly, historical linguistics is interested in the relationships of languages and dialects. Both use phylogenetic methods for this analysis. Second, biological databases annotate their objects with controlled vocabularies, ontologies, and thesauri, to denote gene function and structure. In a similar fashion, corpora in linguistic research are annotated with multiple and possible structured layers of knowledge describing morphology, syntax, and semantics of words and sentences. Both rely on efficient methods for dealing with large amounts of complex and structured annotation. In the project, we exploit and further develop synergies between these independent, yet highly related branches of research.

Homepage: DDD

Funding:

Period: 2004 - 2006

Project partner: Prof. Lüdeling, Prof. Donhauser (Institut für Deutsche Sprache, HUB), plus 16 further partners throughout Germany

The project Deutsch.Diachron.Digital is a German-wide and interdisciplinary initiative for the development of a digital reference corpus of German, starting from the very first manuscripts of predecessors of the German language to current time. Within this consortium, our group is responsible for the development of the central corpus database.