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Knowledge & Content Technologies

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BOOTStrep - Bootstrapping Of Ontologies and Terminologies STrategic REsearch Project

BOOTStrep pulled together already existing biological fact databases as well as various terminological repositories and has implemented a text analysis system which continuously increases its coverage by analysing biological documents.


Biological knowledge, up until now, is scattered in heterogeneous database formats and locked in unstructured natural language documents. The intended integration of biological knowledge in a homogeneous conceptual framework will ease access to this fragmented knowledge and substantially increase its usability for R & D purposes, e.g., in the European bio-tech and pharmaceutical industry.

Main innovations

Knowledge integration and reuse in the biology domain have been the main goals of the BOOTStrep project. The resources and text mining tools developed within the project were expected to boost the performance in various bio application tasks. In particular, BOOTStrep aimed at

  • exploiting already existing terminological resources (thesauri, classification systems, etc.) and combining them within a common, standardized conceptual representation framework. Based on this domain-specific background knowledge advanced natural language technologies have been employed for the analysis of biological documents in order to fill conceptual gaps in these resources by automatically acquiring new terms, concepts and relations,
  • creating, incrementally maintaining and continuously updating a repository of biological facts based on employing a comprehensive bio-lexicon and a standards-based formal bio-ontology for text analysis. Facts have been extracted from biological documents in a fully automatic way, they are subsequently filtered and validated for novelty, redundancy, contradiction, etc.,
  • developing resources and resource-building NLP tools for text-based knowledge harvesting in order to support information extraction and text mining in the biology domain,
  • allowing multilingual public access to continuously updated and validated biological fact repositories.
More details
Administrative Details
  • BOOTStrep (FP6 - 028099) is a Specific Targeted Research Project (STREP) of the European Union's 6 th Framework Programme, Thematic Priority 2 (Information Society Technologies) within the fourth call of the programme. It addressed the strategic objective "Semantic-based Knowledge and Content Systems".
  • BOOTStrep started on April 1, 2006 and ended on March 31, 2009.
  • The overall budget has been of 3.6 million euro.
  • Six partners from four European countries (Germany, U.K., Italy, France) and one Asian partner from Singapore have been involved in the project.
List of Participants
  • Project Coordinator - Friedrich-Schiller Universität Jena (FSU), Germany
  • European Molecular Biology Institute / European Biology Informatics (EMBL-EBI), UK
  • Consiglio Nazionale delle Ricerche - Istituto di Linguistica Computazionale (CNR-ILC), Italy
  • University of Manchester (UoM), UK
  • Université de Rennes (UR1), France
  • Institute for Infocomm Research (I2R), Singapore
  • Universitätsklinikum Freiburg (UKLFR), Germany
Contact Persons
Prof. Dr. Udo Hahn (Project Leader)
Institut für Germanistische Sprachwissenschaft der Universität Jena
Fürstengraben 30, 07743 Jena, GERMANY
EMail: (email removed)
Mareile Hilleyi Knees (Project Manager)
EMail: (email removed)
Events in connection with BOOTStrep
  • IBM UIMA Innovation Award 2007 for Prof. Dr Udo Hahn and the JULIE Lab.
  • BOTM : BOOTStrep organised the mid-term-workshop 'Bridging Ontologies and Text Mining' in Cambridgeshire, UK on 12-13 September 2007.
  • UIMA Innovation Award 2006 for Dr Sophia Ananiadou, June 12, 2006
    IBM is pleased to announce the recipients of the 2006 UIMA Innovation Award program for faculty, an award competition designed to encourage the use of open source and open standards-based tools for academic curricula and research. Dr Sophia Ananiadou from the National Centre for Text Mining won the title for "Integration of a (typed feature structure) TFS-based Logic Programming System with UIMA".
  • BOOTStrep Kick-Off, April 12-13, 2006, Jena
    Following the 2 nd International Symposium on Semantic Mining in Biomedicine (SMBM 2006), the opening event of the European Union (EU) funded project BOOTStrep takes place April 12-13, 2006 at Friedrich-Schiller-University Jena.
    Scientists from England, Italy, France, Singapore and Germany are meeting for the official opening event under the lead of Prof. Hahn, the chair of computational linguistics at Friedrich-Schiller-University for two years now. Primary goal of the kick-off event is, besides the intensification of the personal contacts, the development of a common view on the project, and the agreement on the first working steps.
  • The 2 nd International Symposium on Semantic Mining in Biomedicine (SMBM) organised by the EU Network of Excellence SemanticMining and the Jena University Language & Information Engineeing (JULIE) Lab., 9-12 April 2006, Friedrich-Schiller-Universität Jena, Germany.
  • Workshop on Text Mining, Ontologies and NLP in Biomedicine , March 20-21, 2006, Manchester
    Several distinct but closely related technological fields such as Natural language Processing and Text Mining, Intelligent Information Retrieval, Ontology Engineering and Knowledge Management, Knowledge Discovery, etc. have shown remarkable progress in recent years, which will bring revolution into the ways of conducting science. In particular, due to its rapid expansion and development as well as its data/knowledge intensive nature, life science and biomedical fields have been and will be at the centre of such methodological revolution. We invited researchers in Information Technology who had been successfully applying their research results to life science and those in biomedical fields who have been developing new Information-based approaches in biomedical fields. We are pleased to say that the aim of the workshop, i.e. bringing together researchers from different areas allowing exchange of ideas was successfully achieved and that we enjoyed alive and constructive discussion at the workshop.