Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions

BMC Bioinformatics

Volumn 12, Issue SUPPL. 8, 2011, Pages

  Agarwal, Shashank ^a   Liu, Feifan ^b   Yu, Hong ^a,b  

^a University of Wisconsin Milwaukee   (United States)

^b UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINARY CLASSIFICATION; DOMAIN INDEPENDENTS; EXPERIMENTAL METHODS; IDENTIFYING METHODS; INTERACTION METHODS; LEARNING FRAMEWORKS; PROTEIN-PROTEIN INTERACTIONS; RELEVANT DOCUMENTS;

DATA MINING; LEARNING SYSTEMS; MOLECULAR BIOLOGY;

PROTEINS;

PROTEIN;

ARTICLE; ARTIFICIAL INTELLIGENCE; DATA MINING; HUMAN; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEOMICS;

ARTIFICIAL INTELLIGENCE; DATA MINING; HUMANS; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS;

EID: 80053432028     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S8-S10     Document Type: Article

References (47)

1. Hashizume R, Fukuda M, Maeda I, Nishikawa H, Oyake D, Yabuki Y, Ogata H, Ohta T. The RING Heterodimer BRCA1-BARD1 Is a Ubiquitin Ligase Inactivated by a Breast Cancer-derived Mutation. Journal of Biological Chemistry 2001, 276(18):14537-14540. 10.1074/jbc.C000881200, 11278247.
2. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R. IntAct: an open source molecular interaction database. Nucleic acids research 2004, 32(Database issue):D452-D455. 308786, 14681455., http://dx.doi.org/10.1093/nar/gkh052
3. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Research 2006, 34(suppl 1):D535-D539. 1347471, 16381927.
4. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G. MINT: the Molecular INTeraction database. 2007, , http://nar.oxfordjournals.org/cgi/content/short/35/suppl_1/D572
5. Krallinger M. Importance of negations and experimental qualifiers in biomedical literature. Proceedings of the Workshop on Negation and Speculation in Natural Language Processing, NeSp-NLP '10 2010, 46-49. Morristown, NJ, USA: Association for Computational Linguistics., http://portal.acm.org/citation.cfm?id=1858959.1858967
6. Orchard S, Montecchi-palazzi L, Hermjakob H, Apweiler R, Orchard S, Montecchi-palazzi L, Hermjakob H, Apweiler R. The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. 2005, , http://citeseerx.ist.psu.edu/viewdoc/summary?doi=?doi=10.1.1.111.1176
7. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nature biotechnology 2004, 22(2):177-183. 10.1038/nbt926, 14755292.
8. Garcia FC, Puertas E, Hidalgo JMG, Mana M, Mata J. Attribute analysis in biomedical text classification. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 113-118. CNIO.
9. Cohen AM. Automatically Expanded Dictionaries with Exclusion Rules and Support Vector Machine Text Classifiers: Approaches to the BioCreAtIve 2 GN and PPI-IAS Tasks. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 169-174. CNIO.
10. Lan M, Tan CL, Su J. A term investigation and majority voting for protein interaction article sub-task 1 (IAS). Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 183-185. CNIO.
11. Shin SY, Kim S, Eom JH, Zhang BT, Sriram R. Identifying Protein-Protein Interaction Sentences Using Boosting and Kernel Methods. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 187-192. CNIO.
12. Figueroa A, Neumann G. Identifying Protein-Protein interactions in Biomedical publications. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 217-225. CNIO.
13. Huang M, Ding S, Wang H, Zhu X. Mining Physical Protein-Protein Interactions by Exploiting Abundant Features. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 237-245. CNIO.
14. Abi-Haider A, Kaur J, Maguitman A, Radivojac P, Retchsteiner A, Verspoor K, Wang Z, Rocha LM. Uncovering Protein-Protein Interactions in the Bibliome. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 247-255. CNIO.
15. Kolchinsky A, Abi-Haidar A, Kaur J, Hamed AA, Rocha LM. Classification of Protein-Protein Interaction Full-Text Documents Using Text and Citation Network Features. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010, 7:400-411.
16. Lan M, Su J. Empirical Investigations into Full-Text Protein Interaction Article Categorization Task (ACT) in the BioCreative II.5 Challenge. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010, 7:421-427.
17. Cao Y, Li Z, Liu F, Agarwal S, Zhang Q, Yu H. An IR-Aided Machine Learning Framework for the BioCreative II.5 Challenge. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010, 7:454-461.
18. Fontaine JF, Andrade-Navarro MA. Fast classification of scientific abstracts related to protein-protein interaction using a naïve Bayesian linear classifier. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 67-72. CNIO.
19. Matos S, Campos D, Oliveira JL. Vector-space models and terminologies in gene normalization and document classification. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 119-124. CNIO.
20. Dai HJ, Hung HC, Tsai RTH, Hsu WL. IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 69-76. CNIO.
21. Ehrler F, Gobeill J, Tbahriti I, Ruch P. GeneTeam Site Report for BioCreative II: Customizing a Simple Toolkit for Text Mining in Molecular Biology. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 199-207. CNIO.
22. Nakov P, Divoli A. BioText Report for the Second BioCreAtIvE Challenge. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 297-306. CNIO.
23. Rinaldi F, Schneider G, Clematide S, Jegen S, Parisot P, Romacker M, Vachon T. OntoGene (Team 65): preliminary analysis of participation in BioCreative III. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 131-136. CNIO.
24. Wang X, Rak R, Restificar A, Nobata C, Rupp C, Batista-Navarro RTB, Nawaz R, Ananiadou S. NaCTeM Systems for BioCreative III PPI Tasks. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 151-156. CNIO.
25. Grover C, Haddow B, Klein E, Matthews M, Neilsen LA, Tobin R, Wang X. Adapting a Relative Extraction Pipeline for the BioCreAtIvE II Tasks. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 273-286. CNIO.
26. Dogan RI, Yang Y, Neveol A, Huang M, Lu Z. Identifying protein-protein interactions in biomedical text articles. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 61-66. CNIO.
27. Greenwood MA, Stevenson M. A Semi-Supervised Approach To Learning Relevant Protein-Protein Interaction Articles. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 175-177. CNIO.
28. Chen YH, Ramampiaro H, Laegreid A, Saetre R. ProtIR prototype: abstract relevance for Protein-Protein Interaction in BioCreAtIvE2 Challenge, PPI-IAS subtask. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 179-181. CNIO.
29. Kim S, Wilbur WJ. Improving Protein-Protein Interaction Article Classification Performance by Utilizing Grammatical Relations. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 83-88. CNIO.
30. Rinaldi F, Kappeler T, Kaljurand K, Schneider G, Klenner M, Hess M, von Allmen JM, Romacker M, Vachon T. OntoGene in Biocreative II. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 193-198. CNIO.
31. Lourenco A, Conover M, Wong A, Pan F, Abi-Haider A, Nematzadeh A, Shatkay H, Rocha LM. Testing Extensive Use of NER tools in Article Classification and a Statistical Approach for Method Interaction Extraction in the Protein-Protein Interaction Literature. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 113-117. CNIO.
32. Leaman R, Sullivan R, Gonzalez G. A top-down approach for finding interaction detection methods. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 99-103. CNIO.
33. Krallinger M, Valencia A. Evaluating the Detection and Ranking of Protein Interaction relevant Articles: the BioCreative Challenge Interaction Article Sub-task (IAS). Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 29-39. CNIO.
34. Krallinger M, Leitner F, Valencia A. Assessment of the Second BioCreative PPI task: Automatically Extraction of Protein-Protein Interactions. Proceedings of the BioCreative II workshop; Madrid, Spain 2007, 41-54. CNIO.
35. Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A. An Overview of BioCreative II.5. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010, 7:385-399.
36. Krallinger M, Vazquez M, Leitner F, Valencia A. Results of the BioCreative III Interaction Method Task. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 9-16. CNIO.
37. Krallinger M, Vazquez M, Leitner F, Valencia A. Results of the BioCreative III Interaction Method Task. Proceedings of the BioCreative III workshop; Bethesda MA, USA 2010, 17-23. CNIO.
38. Krallinger M, Vazquez M, Leitner F, Salgado D, Chatraryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, Leaman R, Gonzalez G, Matos S, Kim S, Wilbur WJ, Rocha L, Tendulkar AV, Rangrej A, Raut V, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. Manuscript in review
39. Platt JC. Fast training of support vector machines using sequential minimal optimization. 1999, 185-208., http://portal.acm.org/citation.cfm?id=299105
40. Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten I. The WEKA data mining software: an update. Special Interest Group on Knowledge Discovery and Data Mining Explorer Newsletter 2009, 11:10-18., http://dx.doi.org/10.1145/1656274.1656278
41. van rijsbergen CJ, Robertson SE, Porter MF. New models in probabilistic information retrieval. British Library Research and Development Report, no. 5587 1980, London: British Library.
42. Porter MF. An algorithm for suffix stripping. Program 1980, 14(3):130-137., http://portal.acm.org/citation.cfm?id=275705
43. Breiman L. Random Forests. Machine Learning 2001, 45:5-32., http://dx.doi.org/10.1023/A:1010933404324
44. RandomCommittee. , http://weka.sourceforge.net/doc/weka/classifiers/meta/RandomCommittee.html
45. Kohavi R. Scaling Up the Accuracy of Naive-Bayes Classifiers: a Decision-Tree Hybrid. Proceedings of the Second International Conference on Knowledge Discovery and Data Mining 1996, 202-207., http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.57.4952
46. Quinlan JR. C4.5: Programs for Machine Learning (Morgan Kaufmann Series in Machine Learning). 1993, Morgan Kaufmann, 1., http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/1558602380
47. Vitali R, Cesi V, Tanno B, Ferrari-Amorotti G, Dominici C, Calabretta B, Raschella G. Activation of p53-dependent responses in tumor cells treated with a PARC-interacting peptide. Biochemical and biophysical research communications 2008, 368(2):350-356. 10.1016/j.bbrc.2008.01.093, 18230339.