A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature

BMC Bioinformatics

Volumn 12, Issue SUPPL. 8, 2011, Pages

  Lourenço, Anália ^a   Conover, Michael ^b,c   Wong, Andrew ^d   Nematzadeh, Azadeh ^b,c   Pan, Fengxia ^d   Shatkay, Hagit ^d,e,f,g,h   Rocha, Luis M ^b,c  

^a UNIVERSITY OF MINHO   (Portugal)

^b INDIANA UNIVERSITY   (United States)

^c INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^d QUEEN S UNIVERSITY   (Canada)

^e MICROSOFT   (United States)

^f Faculty of Computing   (Canada)

^g University of Delaware   (United States)

^h UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION PERFORMANCE; CORRELATION COEFFICIENT; INTERACTION DETECTION; NAMED ENTITY RECOGNITION; NATURAL LANGUAGE PROCESSING; PRECISION AND RECALL; PROTEIN-PROTEIN INTERACTIONS; STATISTICAL APPROACH;

EXTRACTION; INFORMATION RETRIEVAL SYSTEMS; NATURAL LANGUAGE PROCESSING SYSTEMS; PATTERN MATCHING; PIPELINES; TOOLS;

PROTEINS;

PROTEIN;

ARTICLE; DATA MINING; HUMAN; METABOLISM; NATURAL LANGUAGE PROCESSING; PUBLICATION;

DATA MINING; HUMANS; NATURAL LANGUAGE PROCESSING; PERIODICALS AS TOPIC; PROTEINS;

EID: 80053392223     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S8-S12     Document Type: Article

References (29)

1. Krallinger M, Valencia A. BioCreative III, PPI Task. 2010, , http://www.biocreative.org/tasks/biocreative-iii/ppi/
2. Settles B. ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics 2005, 21:3191-3192. 10.1093/bioinformatics/bti475, 15860559.
3. Abi-Haidar A, Kaur J, Maguitman A, Radivojac P, Retchsteiner A, Verspoor K, Wang Z, Rocha LM. Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. Genome Biology 2008,
4. 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 Trans Comput Biol Bioinform 2010, 7:400-411.
5. Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A. An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform 2010, 7:385-399.
6. Wang X, Rafal Rak R, Restificar A, Nobata C, Rupp C, Batista-Navarro R, Nawaz R, Ananiadou S. Detecting Experimental Techniques and Selecting Relevant Documents for Protein-Protein Interactions from Biomedical Literature. BMC Bioinformatics 2011, 12(BioCreative Supplement):S6. 3111592, 21658293.
7. Rinaldi F, Schneider G, Clematide S, Romacker M, Vachon T. Detection of Interaction Articles and Experimental Methods in Biomedical Literature. BMC Bioinformatics 2011, 12(BioCreative Supplement):S9. 3044317, 21342592.
8. Krallinger M, Vasquez 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 LM, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Islamaj Dogan R, Fontaine J, 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. BMC Bioinformatics 2011, 12(BioCreative Supplement):S15. 3044269, 21342544.
9. Porter MF. An algorithm for suffix stripping. Program 1980, 14:130-137.
10. Settles B. Biomedical Named Entity Recognition Using Conditional Random Fields and Rich Feature Sets. International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA) 2004, 104-107.
11. Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res 2004, 32:W634-W637. 10.1093/nar/gkh427, 441565, 15215466.
12. Batchelor C, Corbett P. Semantic enrichment of journal articles using chemical named entity recognition. the 45th Annual Meeting of the Association for Computational Linguistics 2007, 45-48. Association for Computational Linguistics.
13. Corbett P, Batchelor C, Teufel S. Annotation of chemical named entities. BioNLP 2007: Biological, translational, and clinical language processing 2007, 57-64.
14. Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res 2007, 35:D511-D514. 10.1093/nar/gkl972, 1899097, 17202167.
15. Schomburg I, Chang A, Schomburg D. BRENDA, enzyme data and metabolic information. Nucleic Acids Research 2002, 30:47-49. 10.1093/nar/30.1.47, 99121, 11752250.
16. Degtyarenko K, De Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcantara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Research 2008, 36:D344-D350. 2238832, 17932057.
17. Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H. MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol 2008, 9(Suppl 2):S5. 10.1186/gb-2008-9-s2-s5, 2559989, 18834496.
18. Breitling R, Armengaud P, Amtmann A, Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. Febs Letters 2004, 573:83-92. 10.1016/j.febslet.2004.07.055, 15327980.
19. Kim S, Wilbur WJ. Classifying protein-protein interaction articles using word and syntactic features. BMC Bioinformatics 2011, 12(BioCreative Supplement):S16. 3044270, 21342545.
20. Shatkay H, Pan FX, Rzhetsky A, Wilbur WJ. Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. Bioinformatics 2008, 24:2086-2093. 10.1093/bioinformatics/btn381, 2530883, 18718948.
21. Wilbur WJ, Rzhetsky A, Shatkay H. New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinformatics 2006, 7:356. 10.1186/1471-2105-7-356, 1559725, 16867190.
22. Chang C, Lin C. LIBSVM: A Library for Support Vector Machines. 2001, , http://www.csie.ntu.edu.tw/~cjlin/libsvm
23. Yona S. CPAN module Lingua-EN-Sentence. 2010, , http://search.cpan.org/~shlomoy/Lingua-EN-Sentence 0.25/lib/Lingua/EN/Sentence.pm
24. HUPO Proteomics Standards Initiatives (PSI), Molecular Interaction (MI). 2010, , http://psidev.sourceforge.net/mi/rel25/data/psi-mi25.obo
25. Antezana E. CPAN module ONTO-PERL. 2010, , http://search.cpan.org/~easr/ONTO-PERL-1.23/
26. Franz B. CPAN module Lingua-Stem. 2010, , http://search.cpan.org/~snowhare/Lingua-Stem-0.84/
27. Kubina J. CPAN module Text-Ngramize. 2010, , http://search.cpan.org/~kubina/Text-Ngramize-1.03/lib/Text/Ngramize.pm
28. Simões A. CPAN module Text-RewriteRules. 2010, , http://search.cpan.org/~ambs/Text-RewriteRules-0.23/lib/Text/RewriteRules.pm
29. Humphrey M. CPAN module Lingua::StopWords. 2010, , http://search.cpan.org/dist/Lingua-StopWords/