A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

Bioinformatics

Volumn 29, Issue 13, 2013, Pages

  Miwa, Makoto ^a   Ohta, Tomoko ^a   Rak, Rafal ^a   Rowley, Andrew ^a   Kell, Douglas B ^a   Pyysalo, Sampo ^a   Ananiadou, Sophia ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTIFICIAL INTELLIGENCE; BIOCHEMISTRY; DATA MINING; MEDLINE; PROCEDURES; SUPPORT VECTOR MACHINE; ARTICLE; METHODOLOGY;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BIOCHEMICAL PROCESSES; DATA MINING; MEDLINE; SUPPORT VECTOR MACHINES;

EID: 84879895059     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt227     Document Type: Conference Paper

References (47)

1. Ananiadou, S. et al. (2006) Text mining and its potential applications in systems biology. Trends Biotechnol., 24, 571-579.
2. Ananiadou, S. et al. (2010) Event extraction for systems biology by text mining the literature. Trends Biotechnol., 28, 381-390.
3. Courtot, M. et al. (2011) Controlled vocabularies and semantics in systems biology. Mol. Syst. Biol., 7, 543.
4. Demir, E. et al. (2010) The BioPAX community standard for pathway data sharing. Nat. Biotechnol., 28, 935-942.
5. Drucker, H. et al. (1996) Support vector regression machines. In: NIPS'96. MIT Press, Cambridge, MA, USA, pp. 155-161.
6. Funahashi, A. et al. (2003) Celldesigner: A process diagram editor for generegulatory and biochemical networks. Biosilico, 1, 159-162.
7. He, C. et al. (2011) A weighted curve fitting method for result merging in federated search. In: Proceedings of SIGIR'11. ACM, New York, NY, USA, pp. 1177-1178.
8. Herrgård, M.J. et al. (2008) A consensus yeast metabolic network obtained from a community approach to systems biology. Nat. Biotechnol., 26, 1155-1160.
9. Hucka, M. et al. (2003) The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
10. Järvelin, K. and Kekäläinen, J. (2002) Cumulated gain-based evaluation of ir techniques. ACM Trans. Inf. Syst., 20, 422-446.
11. Joachims, T. (2002) Optimizing search engines using clickthrough data. In: Proceedings of the 8th ACM SIGKDD. ACM, New York, NY, USA, pp. 133-142.
12. Kemper, B. et al. (2010) PathText: A text mining integrator for biological pathway visualizations. Bioinformatics, 26, i374-i381.
13. Kim, J.D. et al. (2008) Corpus annotation for mining biomedical events from literature. BMC Bioinformatics, 9, 10.
14. Kitano, H. (2002) Systems biology: A brief overview. Science, 295, 1662-1664.
15. Le Novre, N. et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol., 23, 1509-1515.
16. Li, C. et al. (2010) Biomodels database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol., 4, 92.
17. Lu, Z. (2011) Pubmed and beyond: A survey of web tools for searching biomedical literature. Database, 2011, baq036.
18. Mi, H. et al. (2007) PANTHER version 6: Protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res., 35(Suppl. 1), D247-D252.
19. Mi, H. et al. (2011) BioPAX support in CellDesigner. Bioinformatics, 27, 3437-3438.
20. Miwa, M. et al. (2012) Boosting automatic event extraction from the literature using domain adaptation and coreference resolution. Bioinformatics, 28, 1759-1765.
21. Miyao, Y. et al. (2006) Semantic retrieval for the accurate identification of relational concepts in massive textbases. In: Proceedings of ACL'06. ACL, Sydney, Australia, pp. 1017-1024.
22. Miyao, Y. and Tsujii, J. (2008) Feature forest models for probabilistic HPSG parsing. Comput. Linguist., 34, 35-80.
23. Nobata, C. et al. (2008) Kleio: A knowledge-enriched information retrieval system for biology. In: Proceedings of SIGIR'08. ACM, New York, NY, USA, pp. 787-788.
24. Novere, L. et al. (2006) Biomodels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res., 34(Suppl. 1), D689-D691.
25. Ohta, T. et al. (2011) From pathways to biomolecular events: Opportunities and challenges. In: Proceedings of BioNLP'11. ACL, Portland, OR, USA, pp. 105-113.
26. Okanohara, D. et al. (2006) Improving the scalability of semi-markov conditional random fields for named entity recognition. In: Proceedings of ACL'06. ACL, Sydney, Australia, pp. 465-472.
27. Okazaki, N. and Ananiadou, S. (2006) Building an abbreviation dictionary using a term recognition approach. Bioinformatics, 22, 3089-3095.
28. Okazaki, N. et al. (2010) Building a high-quality sense inventory for improved abbreviation disambiguation. Bioinformatics, 26, 1246-1253.
29. Park, J. et al. (2001) Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar. Pac. Symp. Biocomput., 6, 396-407.
30. Rajagopalan, D. and Agarwal, P. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793.
31. Robertson, S.E. et al. (1999)Okapi at trec-7: Automatic ad hoc, filtering, vlc and interactive track. In: Proceedings of The Seventh Text REtrieval Conference (TREC-7). NIST Special Publication 500-242, Gaithersburg, MD, pp. 253-264.
32. Rzhetsky, A. et al. (2004) Geneways: A system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Inform., 37, 43-53.
33. Sasaki, Y. et al. (2008) How to make the most of ne dictionaries in statistical NER. BMC Bioinformatics, 9(Suppl. 11), S5.
34. Shokouhi, M. and Si, L. (2011) Federated search. Found. Trends Inf. Retr., 5, 1-102.
35. Shokouhi, M. and Zobel, J. (2009) Robust result merging using sample-based score estimates. ACM Trans. Inf. Syst., 27, 14:1-14:29.
36. Si, L. and Callan, J. (2003) A semisupervised learning method to merge search engine results. ACM Trans. Inf. Syst., 21, 457-491.
37. Smoot, M.E. et al. (2011) Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics, 27, 431-432.
38. Strömbäck, L. and Lambrix, P. (2005) Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX. Bioinformatics, 21, 4401-4407.
39. Swainston, N. et al. (2011) The subliminal toolbox: Automating steps in the reconstruction of metabolic networks. Integr. Bioinformatics, 8, 186.
40. Thiele, I. and Palsson, B.O. (2010) Reconstruction annotation jamborees: A community approach to systems biology. Mol. Syst. Biol., 6, 361.
41. Tsuruoka, Y. et al. (2007) Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics, 23, 2768-2774.
42. Tsuruoka, Y. et al. (2011) Discovering and visualizing indirect associations between biomedical concepts. Bioinformatics, 27, i111-i119.
43. Vapnik, V.N. (1998) Statistical Learning Theory. Wiley-Interscience, New York.
44. Wang, X. et al. (2010) Disambiguating the species of biomedical named entities using natural language parsers. Bioinformatics, 26, 661-667.
45. Yao, D. et al. (2004) Pathwayfinder: Paving the way towards automatic pathway extraction. In: Proceedings of APBC'04. Australian Computer Society, Inc., Darlinghurst, Australia, pp. 53-62.
46. Yuryev, A. et al. (2006) Automatic pathway building in biological association networks. BMC Bioinformatics, 7, 171.
47. Zhang, L. et al. (2009) Pathbinder-text empirics and automatic extraction of biomolecular interactions. BMC Bioinformatics, 10(Suppl. 11), S18.