BOOTStrep BioNLP 2009 Shared Task - Results (March 2009):

The FSU Jena Team participated in the BioNLP 2009 Shared Task on Event Extraction and was ranked 2nd place among 24 participants with an overall average F-score of 46.7 (

BOOTStrep Final Workshop "Semantic Enrichment of the Scientific Literature 2009 (SESL 2009)"

Date: 30th-31th of March 2009
Place: Wellcome Trust Conference Center, Hinxton, Cambridge, UK

Over the last 10 years, innovation has changed the ways in which scientific publications are gathered and delivered to the public. Since the start of the electronic era:

These changes require novel ways to capture and deliver the content to the public and to exchange the content and the annotations between different sites. This has led to increased activities to capture more information from the authors, to align it with the bioinformatics data resources, to deliver the content as part of the scientific literature and to improve the interoperability between existing automatic systems for text processing and exploitation. This workshop will focus on semantic enrichment of the scientific literature. To this end, workshop participants will have the opportunity to hear about and discuss solutions that capture information from the authors directly and that deliver documents with their annotations. Furthermore, we will discuss the needs of different user groups for the benefits from the scientific literature of the future, e.g. librarians, researchers, automatic text processing and data mining research community, ontologists, others.

For further information see:

For the actual programme see: SESL 2009 Programme

BioNLP 2009 Shared Task

BioNLP’09 will host a shared task, concerning the recognition of bio-molecular events that appear in biomedical literature. The event will be chaired by Jun’ichi Tsujii, of the National Centre for Text Mining and the University of Tokyo.

BioNLP 2009

BioNLP 2009 is being held in conjunction with the NAACL-HLT 2009 meeting in Boulder, Colorado, under the auspices of SIGBioMed, the ACL's special interest group for biomedical natural language processing. The meeting will be held June 4-5, 2009.

Sophia Ananaidou is a member of the organising commitee, whilst Su Jian is a member of the PC.

Launch of U-Compare: an integrated text mining/natural language processing system

U-Compare is an integrated text mining/natural language processing system based on the UIMA Framework, which provides access to a large collection of ready-to-use interoperable natural language processing components.

U-Compare is currently the world's largest UIMA component repository. It allows users to build complex NLP workflows via an easy drag-and-drop interface, and makes visualization and comparison of the outputs of these workflows simple.

U-Compare is the result of a collaboration between the National Centre for Text Mining at the University of Manchester, the Tsujii Laboratory at the University of Tokyo and the Center for Computational Pharmacology at the University of Colorado.

Launch of ACL BioMed Special Interest Group

A new Special Interest Group of ACL (SIGBioMed) has been launched. It is dedicated to language processing in the biological, biomedical, and clinical domain. Dr. Sophia Ananiadou is a member of the organising commitee.

The purpose of the BioMed SIG is to bring together researchers in NLP, bioinformatics, medical informatics, and computational biology, providing a venue (both wiki and workshop) for the promotion and dissemination of original research in this area.

IBM UIMA Award 2008

Dr Sophia Ananiadou and NaCTeM have received the 2008 UIMA Innovation Award in cooperation with the University of Tokyo. The topic of the award is: Enhanced Comparator of Natural Language Processing Tools using UIMA

IBM UIMA Award 2008

Prof. Dr. Udo Hahn and the JULIE Lab team received the IBM Information Analytics Innovation Award 2008.

I2R bionlp tool demo

The 2rd International Symposium on Languages in Biology and Medicine (LBM 2007)

Being PC chair, Su Jian has organized LBM 2007 on December 6-7 2007 in Singapore. Bio-text mining and ontology being the two major topics in the symposium, and many BOOStrep members, Sophia Ananiadou, Annita Burgun, Udo Hahn, Dietrich Rebholz, Stefen Schulz served as PC members. Sophia has delivered a keynote speech and being a panelist in the final panel discussion in the symposium, Dietrich also chairing a Text Mining session.

BOOTStrep browser

ACL 2008 Workshop

BioNLP 2008 is being held in conjunction with the ACL 2008 meeting in Columbus, OH. This is the 7th BioNLP workshop. Sophia Ananiadou is one of the co-organisers. Among the PC members are Su Jian, Olivier Bodenreider, Kevin Cohen and Pierre Zweigenbaum, all members or associated with the BOOTStrep consortium.

Smart dictionary look up

This has been developed as part of the BOOTStrep project. The system retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm.

LREC 2008 Workshop on "Building and evaluating resources for biomedical text mining"

The LREC 2008 Workshop on "Building and evaluating resources for biomedical text mining" will be held in conjunction with LREC 2008 in Marrakech, Morocco, May 31, 2008.

For more details see This workshop is organised by Sophia Ananiadou, Monica Monachini, Goran Nenadic and Jian Su. Among the PC members are Nicoletta Calzolari, Udo Hahn, John Mc Naught, Simonetta Montemagni, Dietrich Rebholz-Schuhmann, Stefan Schulz - all members of the BOOTStrep consortium.

The first international workshop dedicated to UIMA topics

"Towards Enhanced Interoperability for Large HLT Systems: UIMA for NLP" will be held in conjunction with LREC 2008 in Marrakech, Morocco, May 31, 2008

One of the chairmen of this workshop and member of the organising committee is Udo Hahn (FSU Jena).

Website for the Gene Regulation Ontology (GRO) is available now!

The Gene Regulation Ontology as developed within the BOOTStrep project has got its own website, hosted at EBI: The website provides the ontology for download and gives additional information about the resource.

MEDEVI is a novel search engine that retrieves and aligns sentences from Medline abstracts.

MEDEVI has been developed as part of the BOOTStrep project. The search engine identifies sentences in Medline abstracts that contain the query terms. All sentences are sorted, prioritized and aligned according to the query terms. Kim,J.J., Pezik,P., and Rebholz-Schuhmann,D. (2008) MEDEVI: Retrieving textual evidence of relations between biomedical concepts from Medline. Bioinformatics 2008 (online open access).

Evaluation of the Term Repository against standard corpora

The BOOTStrep consortium is developing a lexical resource, called the Bio Lexicon. In the current state, the core content called the Term Repository has generated and exchanged with the partners to augment the content with terms from the literature (NACTEM/UOM) and to feed the results into a database schema that fulfils standard requirements of a lexical resource (CNR, Pisa). The content of the Term Repository has been assessed against the corpus of the BIOCREATIVE II / Task 1b challenge (gene name normalisation). Pezik, P. Jimeno, A. Lee, V., Rebholz-Schuhmann, D. (2008) Static Dictionary Features for Term Polysemy Identification. Proceedings of the Language Resources and Evaluation Conference (LREC-2008), workshop on "Building and evaluating resources for biomedical text mining", Marrakech (Morocco), 28-30 May 2008 (accepted)

The Gene Regulation Ontology (GRO) is available at the Open Biomedical Ontologies (OBO) library!

The BOOTStrep Gene Regulation Ontology has been submitted to the Open Biomedical Ontologies (OBO) library and is currently under review. By now it can be found at

Updates of the JULIE Lab Component Repository (JCORE) are recently released.

For more details see

Adapted version of the BOOTStrep term retrieval Web interface

An adapted version of the BOOTStrep term retrieval Web interface is available at It works for German and English.

Dr Sophia Ananiadou and the National Centre for Text Mining won for the second time the UIMA award

Prof. Dr. Udo Hahn and the JULIE Lab have won the 2007 IBM UIMA Innovation Award

For more details see and

Announcing the BOOTStrep Mid-Term-Workshop "Bridging Ontologies and Text Mining (BOTM)"

Date: 12th-13th of September 2007
Place: EBI, Hinxton, Cambridgeshire, UK

Medicine and molecular biology are nowadays data driven sciences, where electronic access to information resources and to analytical tools for electronic data is crucial for the success of ongoing research. Increasingly different parts of the research community are collaborating to generate common benefits. This is the case for the domains of ontological research, bioinformatics databases and text mining. This workshop offers an opportunity to discuss research questions arising from all three domains. Relevant input will be provided from members of the EU research project “BOOTStrep”.

BOOTStrep (Bootstrapping Of Ontologies and Terminologies STrategic REsearch Project) is funded in the EC´s 6th Framework Programme. The project started in April 2006 and has generated several resources that will be presented and discussed as part of the workshop: a lexical resource (“BioLexicon”), an ontology on gene regulation (“GRO”), and a UIMA based software package combining a number of text mining solutions. A fact database will be developed in the course of the 2007.

The workshop targets members of the research community in bioinformatics, medical informatics, ontological research, computational linguistics and computer science to discuss interoperability across domains. We will investigate on the expectations towards the different resources and their limitations from the perspective of all mentioned domains.

Every session will start with a presentation given by a member of the BOOTStrep project covering the topic of the session (30 min). Thereafter the keynote speaker presents ongoing research work in the field (45 min). The final discussion will give enough opportunity to exchange views on selected questions (60 min).
This workshop is unusual in the sense that it will be inspired by ongoing research work in a collaborative European project. The goal is to explore relevant research topics on the basis of experienced researchers confronted with the results from an ambitious project.

It is organised in co-operation between the EBI and the BOOTStrep consortium consisting of 7 partners from 5 countries, supported by the European Commission's 6th Framework. The workshop will be hosted by the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. The Auditorium and accomodation are on site at the Genome Campus. London Stansted Airport is at near distance.

For further information see:

Free download of NLP components (18/06/2007)

FSU Jena has started putting their NLP components for UIMA for free download on their website ( This page got recently linked from the Penn Bio IE website ( and from the Apache UIMA website (

BOOTStrep Annual Public Report 2006 (24/11/2006)

The BOOTStrep Annual Public Report 2006 is available for download.

2006 UIMA Innovation Award for Dr Sophia Ananiadou (12/06/2006)

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".

For further information see:

BOOTStrep Kick-Off-Meeting Jena (12-13/04/2006)

Following the 2nd International Symposium on Semantic Mining in Biomedicine (SMBM 2006), the opening event of the European Union (EU) funded project BOOTStrep (Bootstrapping Of Ontologies and Terminologies STrategic REsearch Project) 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.

2nd International Symposium on Semantic Mining in Biomedicine in Jena (09-12/04/2006)

The 2nd International Symposium on Semantic Mining in Biomedicine (SMBM) is organised by the EU Network of Excellence Semantic Mining and the Jena University Language & Information Engineeing (JULIE) Lab.

For additional information visit

Workshop on Text Mining, Ontologies and NLP in Biomedicine in Manchester (20-21/03/2006)

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.
For additional information visit