A realistic assessment of methods for extracting gene/protein interactions from free text

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Kabiljo, Renata ^a   Clegg, Andrew B ^b   Shepherd, Adrian J ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED EXTRACTION; BIOMEDICAL TEXT MININGS; EXTRACTION METHOD; INTERACTION-MINING; PERCENTAGE POINTS; PROTEIN INTERACTION; REALISTIC EVALUATIONS; USER COMMUNITIES;

BENCHMARKING; DATA MINING; EXTRACTION; GENES; PROTEINS; TOOLS;

NATURAL LANGUAGE PROCESSING SYSTEMS;

ACCURACY; ARTICLE; AUTOMATION; BIOMEDICINE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA EXTRACTION; DATA MINING; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GENE INTERACTION; GOLD STANDARD; INFORMATION PROCESSING; INTERMETHOD COMPARISON; INTERNET; PROTEIN INTERACTION; QUALITY CONTROL; SCIENTIFIC LITERATURE; SCORING SYSTEM; BIOLOGY; CHEMISTRY; GENE; GENETIC DATABASE; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE;

PROTEIN;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; GENES; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 68649115793     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-233     Document Type: Article

References (38)

1. Pyysalo S Airola A Heimonen J Björne J Ginter F Salakoski T Comparative analysis of five protein-protein interaction corpora BMC Bioinformatics, special issue 2008, 9(Suppl 3):S6. 10.1186/ 1471-2105-9-S3-S6
2. Kabiljo R Stoycheva D Shepherd AJ ProSpecTome: A new tagged corpus for protein named entity recognition Proceedings of the Annual Meeting of the ISMB BioLINK Special Interest Group on Text Data Mining, 19 July 2007, Vienna 2007, 24-27.
3. Kabiljo R Shepherd AJ Protein Name Tagging in the Immunological Domain Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008) Turku, Finland, Turku Centre for Computer Science (TUCS) 2008, 141-144.
4. Fundel K Küffner R Zimmer R RelEx - relation extraction using dependency parse trees Bioinformatics 2007, 23(3):365-371. 10.1093/ bioinformatics/btl616 17142812
5. Nédellec C Learning language in logic - genic interaction extraction challenge Proceedings of LLL'05 2005, 31-37.
6. Krallinger M Rodriguez-Penagos C Valencia A Overview of the protein-protein interaction annotation extraction task of BioCreative II Genome Biol 2008, 9(Suppl 2):S4. 2559988 18834495 10.1186/gb-2008-9-s2-s4
7. Bunescu R Ge R Kate RJ Marcotte EM Mooney RJ Ramani AK Wong YW Comparative Experiments on Learning Information Extractors for Proteins and their Interactions Artif Intell Med, Summarization and Information Extraction from Medical Documents 2005, 33:139-155.
8. Pyysalo S Ginter F Heimonen J Björne J Boberg J Järvinen J Salakoski T BioInfer: A corpus for information extraction in the biomedical domain BMC Bioinformatics 2007, 8:50. 1808065 17291334 10.1186/1471-2105-8-50
9. Ding J Berleant D Nettleton D Wurtele E Mining MEDLINE: Abstracts, sentences, or phrases? Proceedings of PSB'02 2002, 326-337.
10. Fluck J Mevissen HT Dach H ProMiner: Recognition of human gene and protein names using regularly updated dictionaries Proceedings of Second BioCreative Challenge Evaluation Workshop Madrid, Spain: Fundación CNIO Carlos III 2007 149 151
11. Pyysalo S Ohta T Kim JD Tsujii J Static Relations: A Piece in the Biomedical Information Extraction Puzzle Proceedings of the Workshop on BioNLP, Boulder, Colorado 2009, 1-9.
12. Settles B ABNER: An open source tool for automatically tagging genes, proteins and other entity names in text Bioinformatics 2005, 21(14):3191-3192. 10.1093/bioinformatics/bti475 15860559
13. Yeh AS Morgan A Colosimo M Hirschman L BioCreAtIvE task 1A: Gene mention finding evaluation BMC Bioinformatics 2005, 6(Suppl 1):S2. 1869012 15960832 10.1186/1471-2105-6-S1-S2
14. Leaman R Gonzalez G BANNER: An executable survey of advances in biomedical named entity recognition Pacific Symposium on Biocomputing 2008, 13:652-663.
15. Franzén K Eriksson G Olsson F Asker L Lidén P Cöster J Protein names and how to find them International Journal of Medical Informatics 2002, 67(1-3):49-61. 10.1016/S1386-5056(02)00052-7 12460631
16. Kim JD Ohta T Tateisi Y Tsujii J GENIA corpus - a semantically annotated corpus for bio-textmining Bioinformatics 2003, 19(suppl 1):i180-i182. 10.1093/bioinformatics/btg1023 12855455
17. Jose H Vadivukarasi T Devakumar J Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use EURASIP J Bioinform Syst Biol 2007, 53096. 2233894 18274648
18. Cohen AM Hersh WR A survey of current work in biomedical text mining Briefings in Bioinformatics 2005, 6(1):57-71. 10.1093/bib/6.1.57 15826357
19. Hoffmann R Valencia A A Gene Network for Navigating the Literature Nature Genetics 2004, 36:664. 10.1038/ng0704-664 15226743
20. Sætre R Kenji S Tsujii J Syntactic features for protein-protein interaction extraction Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007) Christopher JO Baker, Su Jian 2008 ISSN 1613-0073319. Singapore, pp. 6.1-6.14, CEUR Workshop Proceedings (CEUR-WS.org), January 2008.
21. Hara T Miyao Y Tsujii J Evaluating Impact of Re-training a Lexical Disambiguation Model on Domain Adaptation of an HPSG Parser Proceedings of IWPT 2007 Prague, Czech Republic 2007.
22. Sagae K Tsujii J Dependency parsing and domain adaptation with LR models and parser ensembles In the CoNLL 2007 Shared Task, Joint Conferences on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL'07), Prague, Czech Republic 2007.
23. Moschitti A A study on Convolution Kernels for Shallow Semantic Parsing Proceedings of the 42-th Conference on Association for Computational Linguistic (ACL-2004), Barcelona, Spain 2004.
24. Hunter L Lu Z Firby J Baumgartner WA Jr Johnson HL Ogren PV Cohen KB OpenDMAP: 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 2008, 9:78. 2275248 18237434 10.1186/1471-2105-9-78
25. Baumgartner WA Lu Z Johnson HL Caporaso G Paquette J Lindemann A White EK Medvedeva O Cohen KB Hunter L Concept recognition for extracting protein interaction relations from biomedical text Genome Biology 2008, 9(Suppl 2):S9. 2559993 18834500 10.1186/gb-2008-9-s2-s9
26. Johnson HL Baumgartner WA Jr Krallinger M Cohen KB Hunter L Corpus Refactoring: A Feasibility Study Journal of Biomedical Discovery and Collaboration 2007, 13:2-4. 10.1186/1747-5333-2-4
27. Prodisen http://www.pdg.cnb.uam.es/martink/PRODISEN/
28. Rebholz-Schuhmann D Arregui M Gaudan S Kirsch H Jimeno A Text processing through Web services: Calling Whatizit Bioinformatics 2008 15;24 2 296 8
29. Protein Corral http://www.ebi.ac.uk/Rebholz-srv/pcorral/
30. Domedel-Puig N Wernisch L Applying GIFT, a Gene Interactions Finder in Text, to fly literature Bioinformatics 2005, 21(17):3582-3583. 10.1093/ bioinformatics/bti578 16014369
31. Clegg AB Shepherd AJ Syntactic pattern matching with GraphSpider and MPL The Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland Turku Centre for Computer Science (TUCS) 2008, 129-132.
32. FlyBase http://flybase.org/
33. Kim JD Ohta T Tsujii J Corpus annotation for mining biomedical events from literature. BMC Bioinformatics 2008, 9:10. 2267702 18182099 10.1186/ 1471-2105-9-10
34. Enju http://www-tsujii.is.s.u-tokyo.ac.jp/enju/
35. TinyXML download page http://sourceforge.net/projects/tinyxml
36. Tree kernels in SVM-light http://dit.unitn.it/~moschitt/Tree-Kernel.htm
37. Standoff Manager http://www-tsujii.is.s.u-tokyo.ac.jp/~satre/akane/ StandOffManager.tgz
38. Protégé http://protege.stanford.edu