2 Mar 2005 - Impressive new BioMinT text mining results

The BioMinT consortium, of which PharmaDM is a member since 2003, has recently impressed reviewers with "world class research".

• GPSDB -a new database for synonyms expansion of gene and protein names- has become publicly available; a paper on GPSDB will appear in an upcoming 2005 BioInformatics issue.


• at the November 2004 mid-term review meeting the EC reviewers were particularly enthusiastic about the close integration of state-of-the-art Data Mining and Language Technology to solve real problems in biology. As one of the experts pointed out: "I had not seen such a system working before".


• a paper on "Classifying Protein Fingerprints" won the PKDD-2004 best paper award.

All public BioMinT reports can be found here.

The EC project "BioMinT" (QLRI-CT-2002-02770, start date 1 January 2003) aims at the development of a generic text mining tool for the biological domain. More specifically, the goal of BioMinT is to:

1. semi-automate and therefore speed up the construction and update of SWISS-PROT , PRINTS and other protein databases while preserving their high standards of quality;
2. automate report generation from scientific abstracts and papers using the advanced information retrieval and -extraction features of the BioMinT text miner;
3. develop a semantic, concept-based information retrieval and extraction system for the biomedical literature.

Intended users are researchers at biotech & pharmaceutical companies, bench biologists and all bio-database curators.

BioMinT is a multidisciplinary project involving six partners: (key contribution between parentheses)

• SIB (Swissprot database)
• University of Manchester (Prints database and Precis, a tool producing protein reports based on Swissprot database annotations)
• University of Geneva (Info Retrieval/Info Extraction)
• University of Vienna (Info Retrieval/Info Extraction)
• University of Antwerp (Natural language processing)
• PharmaDM (Relational mining engines, AlphaDMax^TM)