PIMiner: A web tool for extraction of protein interactions from biomedical literature

International Journal of Data Mining and Bioinformatics

Volumn 7, Issue 4, 2013, Pages 450-462

  Chowdhary, Rajesh ^a   Zhang, Jinfeng ^b   Tan, Sin Lam ^a   Osborne, Daniel E ^b   Bajic, Vladimir B ^c   Liu, Jun S ^d  

^a MARSHFIELD CLINIC   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^d HARVARD UNIVERSITY   (United States)

Author keywords

Bioinformatics; Biological text mining; Complex biological networks; Data mining; Gene protein networks; Interactome mining; Literature mining; PI; Protein interactions; Protein protein interactions; Systems biology

Indexed keywords

EID: 84878775644     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2013.054232     Document Type: Article

References (24)

1. Bunescu, R. and Mooney, R. (2006) 'Subsequence kernels for relation extraction', in Weiss, Y., Scholkopf, B. and Platt, J. (Eds.): Advances in Neural Information Processing Systems, MIT Press, Cambridge, MA, Vol. 18, pp.171-178.
2. Chen, X.W., Han, B., Fang, J. and Haasl, R.J. (2008) 'Large-scale protein-protein interaction prediction using novel kernel methods', Int. J. Data Mining and Bioinformatics, Vol. 2, No. 2, pp.145-156.
3. Chowdhary, R., Zhang, J. and Liu, J.S. (2009) 'Bayesian inference of protein-protein interactions from biological literature', Bioinformatics, Vol. 25, No. 12, pp.1536-1542.
4. Dong, Q., Zhou, S. and Liu, X. (2010) 'Prediction of protein-protein interactions from primary sequences', Int. J. Data Mining and Bioinformatics, Vol. 4, No. 2, pp.211-227.
5. Fundel, K., Küffner, R. and Zimmer, R. (2007) 'RelEx - relation extraction using dependency parse trees', Bioinformatics, Vol. 23, No. 3, pp.365-371. (Pubitemid 46323160)
6. Giles, C.B. and Wren, J.D. (2008) 'Large-scale directional relationship extraction and resolution', BMC Bioinformatics, Vol. 9, No. 9, p. S11.
7. Hirschman, L., Yeh, A., Blaschke, C. and Valencia, A. (2005) 'Overview of Bio Creative: critical assessment of information extraction for biology', BMC Bioinformatics, Vol. 6, No. 1, p. S1.
8. Hoffmann, R. and Valencia, A. (2005) 'Implementing the iHOP concept for navigation of biomedical literature', Bioinformatics, Vol. 21, Suppl. 2, pp.ii252-ii258. (Pubitemid 41535458)
9. Hu, X., Zhang, X., Yoo, I., Wang, X. and Feng, J. (2010) 'Mining hidden connections among biomedical concepts from disjoint biomedical literature sets through semantic-based association rule', Intl. J. Intel. Sys., Vol. 25, pp.207-223.
10. Huang, M., Ding, S., Wang, H. and Zhu, X. (2008) 'Mining physical protein-protein interactions from the literature', Genome Biol., Vol. 9, No. 2, p. S12.
11. Hunter, L., Lu, Z., Firby, J., Baumgartner, W.A., Johnson, Jr, H.L., Ogren, p. V. and Cohen, K.B. (2008) 'Open DMAP: an open source, ontology-driven concept analysis engine, with application to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression', BMC Bioinformatics, Vol. 9, p. 78.
12. Jose, H., Vadivukarasi, T. and Devakumar, J. (2007) 'Extraction of protein interaction data: a comparative analysis of methods in use', EURASIP J. Bioinform. Syst. Biol., p. 53096.
13. Kabiljo, R., Clegg, A.B. and Shepherd, A.J. (2009) 'A realistic assessment of methods for extracting gene/protein interactions from free text', BMC Bioinformatics, Vol. 10, p. 233.
14. Leaman, R. and Gonzalez, G. (2008) 'BANNER: an executable survey of advances in biomedical named entity recognition', Pac. Symp. Biocomput., Vol. 13, pp.652-663.
15. Li, X.L., Tan, S.H. and Ng, S.K. (2006) 'Improving domain-based protein interaction prediction using biologically significant negative datasets', Int. J. Data Mining and Bioinformatics, Vol. 1, No. 2, pp.138-149.
16. Liu, H., Hu, Z.Z., Zhang, J. and Wu, C. (2006) 'Bio Thesaurus: a web-based thesaurus of protein and gene names', Bioinformatics, Vol. 22, No. 1, pp.103-105. (Pubitemid 43057014)
17. Maglott, D., Ostell, J., Pruitt, K.D. and Tatusova, T. (2005) 'Entrez gene: gene-centered information at NCBI', Nucleic Acids Res., Vol. 33, pp. D54-D58. (Pubitemid 40207830)
18. Rebholz-Schuhmann, D., Arregui, M., Gaudan, S., Kirsch, H. and Jimeno, A. (2008) 'Text processing through web services: calling whatiszit', Bioinformatics, Vol. 24, No. 2, pp. 296-298.
19. Saetre, R., Kenji, S. and Tsujii, J. (2007) 'Syntactic features for protein-protein interaction extraction', in Christopher, J.O. and Baker, S.J. (Eds.): Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine, Singapore, pp. 6.1-6.14.
20. Schmeier, S., Jankovic, B. and Bajic, V.B. (2011) 'Simplified method to predict mutual interactions of human transcription factors based on their primary structure', PLoS ONE, Vol. 6, No. 7, p. e21887.
21. Stark, C., Breitkreutz, B.J., Reguly, T., Boucher, L., Breitkreutz, A. and Tyers, M. (2006) 'Bio GRID: a general repository for interaction datasets', Nucleic Acids Res., Vol. 34, pp. D535-D539.
22. The UniProt Consortium (2010) 'The Universal Protein Resource (UniProt) in 2010', Nucleic Acids Res., pp. D142-D148.
23. Tikk, D., Thomas, p., Palaga, p., Hakenberg, J. and Leser, U. (2010) 'A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature', PLoS Comput. Biol., Vol. 6, p. e1000837.
24. Tsuruoka, Y., Tateishi, Y., Kim, J.D., Ohta, T., McNaught, J., Ananiadou, S. and Tsujii, J. (2005) 'Developing a robust part-of-speech tagger for biomedical text', Advances in Informatics - 10th Panhellenic Conference on Informatics, LNCS, Vol. 3746, pp. 382-392.