Project goals

• to adapt and develop text mining tools to evaluate the basis in the literature for the structure of biochemical and signalling models in systems biology
• to integrate text mining techniques with visualisation technologies for better understanding of the evidence for biochemical and signalling pathways
• to enrich models encoded in the Systems Biology Markup Language (SBML) with information derived from text mining
• to evaluate in conjunction with domain experts the effectiveness of using models of pathways augmented with evidence derived from text mining

Project members

• Douglas Kell
• Sophia Ananiadou
• Jun'ichi Tsujii
• Duncan Hull
• Yoshimasa Tsuruoka

Funding

The REFINE project is funded by the Biotechnology and Biological Sciences Research Council (BBSRC): grant code BB/E004431/1

Project publications

• Sophia Ananiadou, Douglas B. Kell and Jun'ichi Tsujii (2006) Text Mining and its Potential Applications in Systems Biology Trends in Biotechnology Volume 24, Issue 12, Pages 571-579 DOI:10.1016/j.tibtech.2006.10.002, pubmed.gov/17045684, citeulike 907397

Other references

• Yoshimasa Tsuruoka, John McNaught, Jun'ichi Tsujii and Sophia Ananiadou (2007) Learning string similarity measures for gene/protein name dictionary look-up using logistic regression Bioinformatics 23(20):2768-2774; DOI:10.1093/bioinformatics/btm393, pubmed.gov/17698493, citeulike 1626506
• Sophia Ananiadou (2008) Selected bibliography: Text-mining for Biomedicine

Relevant software

• Utopia
• Taverna workflows
• Enju
• GENIA tagger
• Machine learning

Relevant web sites

• DBK Group
• The National Centre for Text Mining (NaCTeM)
• Tsujii laboratory