|
| CNB - Protein Design Group · The MITRE Corporation · |
 | |
| |
| |
| |
|
|
| · CONTACT · |
With the increasing availability of textual information related to biology, including MedLine abstracts and full-text journal articles, research on information extraction is rapidly becoming an essential component of various bioinformatics applications. It is expected that text mining in general, and information extraction in particular, will provide tools to facilitate the annotation of vast amounts of molecular information, including gene sequences, transcription profiles and biological pathways.
The Special Interest Group on Text Mining (or BioLINK) was created to address the need of communication and interchange of ideas in the field of text mining and information extraction applied to biology and biomedicine. Information extraction (IE) is an outgrowth of work in automated natural language processing, which began in the 1950s with work on transformational grammar by Zellig Harris and later Noam Chomsky. Information extraction technology made rapid progress starting in the late 1980s, thanks to a series of conferences focused on evaluation of IE: the Message Understanding Conferences (MUCs). There is also a long history of research on applications in medicine. Applications to the medical field focus on two distinct sub-problems: improved access to the medical literature and extraction of information from patient records.
Despite these successes in other fields Natural Language Processing (NLP) techniques were not introduced in biology until the late 90's (first publication around 1997 at ISMB97). The field is dominated by two, not necessarily convergent, views.
- application oriented, where simple methods are used (maybe too simple) to address "real" biological problems,
- tool oriented, where complex, state of the art NLP methods are used to address problems that are not always relevant to biologists.
Even if this view is exaggerated there exists a problem of misunderstanding and misinterpretation in this field that hinders the development toward powerful text mining systems accepted by biologists (the actual users).
To improve this situation we hold regular open meetings to bring together researchers from the field to interchange ideas and share them with a wider community interested in the latest developments (see events). To get a step further and formulate common goals, standard datasets and uniform evaluation criteria we organized a critical assessment of text mining methods during November/Dicember 2003 (see news) inspired by the CASP evaluations. End of March 2004 we held a workshop in Granada, Spain, where we came together with the participants and potential users of the technology. The handouts with the presentations from the workshop and papers from the participants describing their systems have been made available on our web pages.
| |
| |
| |
| |
 |
|
We already held two very interesting meetings at ISMB2001 and ISMB2002. Talk materials and presentaions from the ISMB 2002 meeting are available here. Note that presentations and additional material from our last meeting at ISMB 2003 in Brisbane are now on-line.
Like in previous years we are going to be present at the next years ISMB. Check us out for information related to the Special Interest Group on Text mining at the ISMB conference.
BioLink 2004: Linking Biological Literature, Ontologies and Databases: Tools for Users.This workshop will bring together researchers from the fields of bioinformatics, natural language processing, ontologies, data mining, and information retrieval. The focus will be on tools that can provide improved access and cross-indexing for the biomedical literature, databases and ontologies. The organizers strongly encourage submission of approaches that support end users and user-defined tasks.URL: www.biolink2004.org
SUBMISSION DEADLINE: January 16, 2004
LOCATION: Boston, USA
DATE: May 7th, 2004
| |
| |
| |
| |
|
|
During November/Dicember 2003 we organized a critical assessment of text mining methods applied to biology. It was inspired by CASP (Critical Assessment of techniques for protein Structure Prediction) and we held a workshop in Granada, Spain, end of March 2004 to discuss the results together with the participants and potential users of the technology. The handouts with the presentations from the workshop and papers from the participants describing their systems have been made available on our web pages. For more information see.
| |
| |
| |
| |
|
|
The mailing list BioLink@listas.cnb.uam.es has been created to address the need of communication and interchange of ideas in the field of text mining and information extraction applied to biology and biomedicine. Via this list we will basically announce events organized by the Special Interest Group (SIG) or things related to the general theme of text mining and information extraction that we think are of broader interest. So it will be basically a low-traffic list. This is a distribution list only and not open for free discussion among the subscribers. For any comments and inquiries please contact the list owner at BioLink-owner@listas.cnb.uam.es.
| |
| |
| |
| |
|
|
| |
| |
| |
| |
|
|
- Christian Blaschke, CNB/CSIC, Madrid, Spain.
- Ian Donaldson, Samuel Lunenfeld Research Institute, Canada
- Carol Friedman, Columbia University
- Rob Gaizauskas, University of Sheffield
- Lynette Hirschman, The MITRE Corporation
- Larry Hunter,University of Colorado
- Barend Mons,Erasmus Medical Center
- See-Kiong Ng,Institute for Infocomm Research, Singapore
- Andrey Rzhetsky ,Columbia Genome Center
- Alfonso Valencia, CNB/CSIC Madrid
|
| |
| |
|
|
|
