The German Ministry of Education and Research (BMBF) is funding the new Jena Centre of Systems Biology of Ageing (JenAge). JenAge is a research endeavour of researchers from several academic institutions in the city of Jena.
Udo Hahn, FSU, Institut für Germanistische Sprachwissenschaft, Lehrstuhl für Computerlinguistik /JULIE Lab
Michael Ristow, FSU, Institut für Ernährungswissenschaften, Lehrstuhl für Humanernährung
Stefan Schuster, FSU, Lehrstuhl für Bioinformatik
Otto Witte, UKJ, Klinik für Neurologie
Reinhard Guthke, HKI, AG Systembiologie/Bioinformatik
Alessandro Cellerino, FLI, AG Biologie des Alterns
Stephan Diekmann & Peter Hemmerich, FLI, AG Molekularbiologie
Christoph Englert, FLI, AG Molekulare Genetik
Matthias Platzer, FLI, AG Genomanalyse
Jürgen Sühnel, FLI, AG Biocomputing
The JenAge Centre aims to identify conserved transcriptional and metabolic networks activated by mild stress and to investigate their role in preserving functional integrity in old age. JenAge will use a multi-species approach to characterise network modulations by environmental, pharmacological and life-style perturbations. In an iterative process, experimental data will be communicated to the analysis and modelling groups to generate testable hypotheses which will in turn be validated by genetic and other manipulations in model organisms.
Automatic text mining will be used to cope with the ever-increasing flood of age-related scientific documents in a systematic way and to generate plausible hypotheses on ageing and age-related diseases through text analytics. This textual information will be used, together with data from other databases and from the JenAge Centre, to set up a new public database on molecular, cellular and organismic aspects of ageing.
The general JenAge objective is to gain new insights into the complex interplay of maintenance and repair networks that govern the lifelong accumulation of damage and finally lead to age-related diseases and death. Overall, the knowledge acquired within this initiative will contribute to sustained health in an ageing society.
Link to the press release (in German)
The JULIE Lab is one of the academic collaborators in the CALBC project. CALBC (Collaborative Annotation of a Large Biomedical Corpus) is a European support action funded in the EC's 7th Framework Programme. Its focus is the automatic generation of a very large, community-wide shared text corpus annotated fully automatically with biomedical entities. We propose to create a broadly scoped and diversely annotated corpus (150,000 immunology-related abstracts from Medilne annotated with approximately a dozen semantic types) by automatically integrating the annotations from different named entity recognition systems.
A specific CALBC challenge will be run which consists of building a large, diversely annotated corpus. Participation is open to any team that is willing to submit annotations obtained with their own named entity recognition system(s). The annotations of all participating systems will be automatically harmonized with additional metadata to develop a silver standard corpus (no golden data will be supplied. The integrated corpus will therefore have a broader scope than any single system available up until now.
Overview to the CALBC Challenge and the challenge timeline
Project flyer (418 kB, 2009-07-29)
(UIMA)Since 2006, the JULIE Lab employs UIMA. For more information about our work in context of UIMA check these links:
Link to 2nd German UIMA Workshop at GSCL 2009
Link to the LREC 2008 UIMA Workshop
Link to the UIMA Tutorial hold at SMBM 2008
Link to the IBM UIMA Inovation Award 2007
Link to the IBM Innovation Award 2008
The JULIE Lab is one of the founding groups of the BioTem-Initiative. This is a consortium of leading German research groups in the fast-growing field of biomedical text mining. Our goal is to make the importance of biomedical text mining visible to the German research funding authorities and to ultimately establish a German virtual center for text mining on an institutional level.
Login