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EBIGroupsRebholz Group

Rebholz Group

The research team (“Rebholz group”) is headed by Dietrich Rebholz-Schuhmann.  The team processes biomedical data resources and the biomedical scientific literature to produce innovative solutions and to gain new insights relevant for biomedical research and computational linguistics.

The group focuses on extraction of facts from scientific literature in molecular biology. Ongoing research is concerned with the identification of bioactivities of chemical entities, functional annotation of proteins/genes, the identification of gene-disease associations and discourse analysis of full text documents. Past research was concerned with the annotation of protein residues, extraction of gene regulatory events based on ontological knowledge, identification of named entities and the extraction of mutations from the literature (see the full publication list for further details). Also, recent projects have set the focus to the development of solutions that standardise the transformation of the literature into a Triple Store representation ( SESL project, LexEBI , IeXML).

The identification of gene-disease associations is based on different approaches mining the scientific literature and use of ontological resources for the cross-comparison of genetic databases. An interface for interactive exploration is in preparation and will be available in the second half of 2011.

Internships, Pre-Doc visiting, Post-Doc fellowship: A few projects (and funding) are available in the area of:

  • Semantic normalisation of the scientific literature for multi-type indexing.
  • Integration of phenotypic ontological resources in a reasoning infrastructure: exploration and evaluation

Projects, resources and tools:   

  • Further information on past projects, past interns and internships, PhD supervision can be found here.
  • For a complete list of latest resources please refer to http://www.ebi.ac.uk/Rebholz-srv/
  • For the main text processing engine Whatizit
    and for the Java client for automated access (SOAP Web Service)
  • For the terminological resource LexEBI
  • For the CALBC project (resources coming soon)
  • For the SESL project (triple store opening soon)


For enquiries, problems with our software and membership to mailing lists, please email to: textmining-support@ebi.ac.uk.




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Xtreme Reasoning Jamboree (XR-Jam) - Validation of assertions in different biomedical data resources

This project is a small-scale jamboree for about one year to explore different solutions for the validation of biomedical knowledge based on different information technology based solutions. For more detail please refer tohttp://www.ebi.ac.uk/Rebholz-srv/XR-Jam. The jamboree adresses bioinformaticians and biologists, logicians and ontologists, computer scientists, and computational linguists.


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2nd CALBC workshop

The workshop addresses the results of the CALBC project to the current state and focuses in particular on the outcome of the second challenges. The workshop gives also an overview on the different resources that have been build as part of the CALBC project. A selection of keynote speakers give an overview on their work. 
http://www.ebi.ac.uk/Rebholz-srv/CALBC/workshop2


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XtremeLinking Open Data in Biology using Ontologies and Literature Mining

In the tutorial we will explain the use of ontologies and semantic Web technology for the integration of biological data from different data resources including the scientific literature. 
http://www.ebi.ac.uk/Rebholz-srv/semantics_WS_May2011.html


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