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Bridging Ontologies and Text Mining (BOTM)

From terminologies to ontologies … from text mining to fact databases:
How to bring resources together?

Two-day Workshop

Title: “Bridging Ontologies and Text Mining (BOTM)”
Date: 12th-13th of September 2007
Venue: EBI, Hinxton, Cambridgeshire, UK
Organisers: EBI and the BOOTStrep consortium
Registration Deadline: 30th August 2007

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Motivation

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.

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Setup

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).

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Appreciation

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.

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Workshop Program

Click here to view a printable version of the schedule.

Time	Bridging Ontologies and Text Mining (BOTM) Program
Wednesday 12-Sep-2007
09.30 - 10.00	Coffee reception
10.00 - 12.15	BioLexicon, Bio-Terminologies and related resources Keynote speaker: Olivier Bodenreider (NLM, U.S.A.)
12.15 - 13.30	Lunch
13.30 - 15.45	Bio-Ontologies Keynote speaker: to be defined
15.45 - 16.00	Coffee break
16.00 - 18.15	Biomedical annotation of corpora, Event annotation Keynote speaker: Jin Dong Kim (Tsujii lab, Tokyo University)
18.15	Drinks and nibbles
19.30	Dinner on site
Thursday 13-Sep-2007
08.30 - 10.45	Bio-NLP Keynote speaker Kevin Cohen (University of Colerado)
10.45- 11.00	Coffee break
11.00 - 13.15	Biomedical fact databases Keynote speaker: Isabel Rojas (EML, Heidelberg)
13.15 - 14.15	Lunch
14.15 - 16.15	Industry Program Discussion Discussion on needs from the industry on TM solutions and ontologies Members of the industry program will be asked to bring forward questions that they concern.
16.15 - 16.30	Coffee break
16.30 - 18.30	Software Demonstration Hands on demonstration of TM solutions available from the EBI and elsewhere

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Location

The workshop will be hosted by the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. The Auditorium and accommodation are on site at the Genome Campus. London Stansted Airport is at near distance.

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Accommodation

Regarding accommodation there are three alternatives: either on site or in Cambridge or in hotels nearby. Unfortunately, the first option is not valid since the biggest chunk of accommodation with the Wellcome Trust Conference Centre is already fully booked due to another event. We recommend that you book your accommodation either with the Arundel House Hotel (central Cambridge) or at the Travelodge (train station). In principle we will take care for a shuttle bus between Cambridge and Hinxton. Since we have to optimize the travel routes, we want to get your feedback, where you are staying (ref. to registration).

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Registration Details

Registration Deadline: 30th August 2007 - When you register you will be sent an automatically generated e-mail message that includes all your details and registration number. Please keep this e-mail for your records.

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