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REFINE Project

Representing Evidence For Interacting Network Elements

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

• Sophia Ananiadou
• Jun'ichi Tsujii
• Pedro Mendes
• Steve Pettifer
• Yoshimasa Tsuruoka
• Mashhuda Glencross
• Alice Villeger
• Brian Kemper

Funding

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

Publications

• Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou. 2009. Stochastic Gradient Descent Training for L1-regularized Log-linear Models with Cumulative Penalty, In Proceedings of ACL-IJCNLP, pp. 477-485.
• Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou. 2009. Fast Full Parsing by Linear-Chain Conditional Random Fields. In Proceedings of EACL, pp. 790-798
• Duncan Hull, Steve Pettifer and Douglas B. Kell. 2008. Defrosting the digital library: Bibliographic tools for the next generation web. PLoS Computational Biology, 4(10):e1000204+. DOI:10.1371/journal.pcbi.1000204, pmid:18974831
• Duncan Hull. 2008. GO faster ChEBI with Reasonable Biochemistry, Proceedings of OWL: Experiences and Directions (OWLED 2008) Fifth International Workshop, Karlsruhe, Germany, October 26-27, 2008. Available from Nature Precedings DOI:10101/npre.2008.2329.1
• Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou. 2008. Accelerating the annotation of sparse named entities by dynamic sentence selection, BMC Bioinformatics, 9(Suppl 11):S8. DOI:10.1186/1471-2105-9-S11-S8, pmid:19025694
• Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou. 2008. FACTA: a text search engine for finding associated biomedical concepts, Bioinformatics, Vol. 24, No. 21, pp. 2559-2560. pmid:18772154, DOI:10.1093/bioinformatics/btn469.
• 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, pmid:17045684

Other references

• Yoshimasa Tsuruoka, John McNaught, and Sophia Ananiadou. 2008. Normalizing biomedical terms by minimizing ambiguity and variability, BMC Bioinformatics 2008, 9(Suppl 3):S2. pmid:18426547, DOI:10.1186/1471-2105-9-S3-S2
• Yutaka Sasaki, Yoshimasa Tsuruoka, John McNaught, and Sophia Ananiadou. 2008. How to make the most of NE dictionaries in statistical NER, BMC Bioinformatics, 9(Suppl 11):S5. pmid:19025691, DOI:10.1186/1471-2105-9-S11-S5
• 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,pmid:17698493
• Chikashi Nobata, Philip Cotter, Naoaki Okazaki, Brian Rea, Yutaka Sasaki, Yoshimasa Tsuruoka, Jun-ichi Tsujii, and Sophia Ananiadou (2008) Kleio: a knowledge-enriched information retrieval system for biology, Proceedings of SIGIR, pp. 787-788
• Sophia Ananiadou (2008) Selected bibliography: Text-mining for Biomedicine

Relevant software

• GUI
  • Utopia
  • Arcadia
  • Taverna workflows
  • PathText
• Text Mining
  • FACTA+
  • Enju
  • GENIA tagger
  • Maximum entropy learning

Relevant web sites

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