Corpus refactoring: A feasibility study

Journal of Biomedical Discovery and Collaboration

Volumn 2, Issue 1, 2007, Pages

  Johnson, Helen L ^a   Baumgartner Jr , William A ^a   Krallinger, Martin ^b   Bretonnel, K Bretonnel ^a   Hunter, Lawrence ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 36048945461     PISSN: None     EISSN: 17475333     Source Type: Journal    
DOI: 10.1186/1747-5333-2-4     Document Type: Article

References (69)

1. Tsuruoka Y Tateishi Y Kim JD Ohta T Mcnaught J Ananiadou S Tsujii J Developing a robust part-of-speech tagger for biomedical text Proceedings of the 10th Panhellenic Conference on Informatics 2005:382-392.
2. Cohen KB Tanabe L Kinoshita S Hunter L A resource for constructing customized test suites for molecular biology entity identification systems HLT-NAACL 2004 Workshop: BioLINK Linking Biological Literature, Ontologies and Databases Association for Computational Linguistics 2004:1-8.
3. Cohen KB Fox L Ogren P Hunter L Empirical data on corpus design and usage in biomedical natural language processing American Medical Informatics Association Symposium 2005:156-160.
4. Cohen KB Fox L Ogren PV Hunter L Corpus design for biomedical natural language processing Proceedings of the ACL-ISMB workshop on linking biological literature, ontologies and databases Association for Computational Linguistics 2005:38-45.
5. Ide N Brew C Requirements, tools, and architectures for annotated corpora Proceedings of the Data Architectures and Software Support for Large Corpora European Languages Resources Association 2000:1-5.
6. Erjavec T Tateisi Y Kim J Ohta T Tsujii J Encoding biomedical resources in TEI: The case of the GENIA Corpus Proceedings of the ACL 2003 workshop on natural language processing in biomedicine Association for Computational Linguistics 2003, 13:97-104.
7. Smith L Tanabe L Rindflesch T Wilbur W MedTag: A collection of biomedical annotations BioLINK 2005:32-37.
8. Fowler M Beck K Brant J Opdyke W Roberts D Refactoring: Improving the design of existing code Addison-Wesley 1999.
9. Blaschke C Andrade MA Ouzounis C Valencia A Automatic extraction of biological information from scientific text: Protein-protein interactions Proc Int Conf Intell Syst Mol Biol 1999:60-67. 10786287
10. McEnery T Wilson A Corpus Linguistics Edinburgh University Press 1996.
11. WordFreak http://venom.ldc.upenn.edu/_resources/info/wordfreak_ann.html
12. Kulick S Bies A Liberman M Mandel M McDonald R Palmer M Schein A Ungar L Integrated annotation for biomedical information extraction Proc BioLINK 2004 Association for Computational Linguistics 2004:61-68.
13. Kim JD Ohta T Tateisi Y Mima H Tsujii J XML-based linguistic annotation of corpus Proceedings of The First NLP and XML Workshop 2001:47-53.
14. Center for Computational Pharmacology BioNLP SourceForge Homepage http://bionlp.sourceforge.net
15. Kann M Ofran Y Punta M Radivojac P Protein interactions and disease Pacific Symposium on Biocomputing World Scientific Publishing Company 2006:351-353.
16. NCBI Utils MEDLINE UI/PubMed ID Matcher http://eutils.ncbi.nlm.nih.gov/ entrez/publisher/uidpmid.cgi
17. Roberts A jTokeniser Java package http://www.andy-roberts.net/software/ jTokeniser/index.html
18. IBM UIMA Java Framework http://uima-framework.sourceforge.net/
19. Ferrucci D Lally A Building an example application with the unstructured information management architecture IBM Systems Journal 2004, 43(3):455-475.
20. Mack R Mukherjea S Soffer A Uramoto N Brown E Coden A Cooper J Inokuchi A Iyer B Mass Y Matsuzawa H Subramaniam LV Text analytics for life science using the unstructured information management architecture IBM Systems Journal 2004, 43(3):490-515.
21. Cohen KB Corpus Usage Survey http://compbio.uchsc.edu/ccp/corpora/ survey.shtml
22. Kim JD Tsujii J Corpora and their annotation Text Mining for Biology and Biomedicine, Artech House 2006:179-212.
23. Alex B Nissim M Grover C The impact of annotation on the performance of protein tagging in biomedical text Proceedings of the 5th International Conference on Language Resources and Evaluation, LREC 2006:595-600.
24. Tsai RTH Chou WC Lin YC Sung CL Ku W Su YS Sung TY Hsu WL BIOSMILE: adapting semantic role labeling for biomedical verbs: An exponential model coupled with automatically generated template features Proceedings of the BioNLP Workshop on Linking Natural Language Processing and Biology Association for Computational Linguistics 2006:57-64.
25. Olsson F Eriksson G Franzén K Asker L Lidén P Notions of correctness when evaluating protein name taggers Proceedings of the 19th international conference on computational linguistics (COLING 2002) 2002:765-771.
26. Tanabe L Xie N Thom L Matten W Wilbur W GENETAG: A tagged corpus for gene/protein named entity recognition BMC Bioinformatics 2005, 6(Suppl 1):S3. 1869017 15960837
27. Lu Z Bada M Ogren P Cohen KB Hunter L Improving biomedical corpus annotation guidelines The Joint BioLINK and 9th Bio-Ontologies Meeting 2006.
28. Yeh A Morgan A Colosimo M Hirschman L BioCreAtIvE task 1A: Gene mention finding evaluation BMC Bioinformatics 2005, 6(Suppl 1):S2. 1869012 15960832
29. Palmer M Gildea D Kingsbury P The Proposition Bank: An annotated corpus of semantic roles Computational Linguistics 2005, 31:71-105.
30. Meyers A Reeves R Macleod C Szekely R Zielinska V Young B Grishman R Annotating noun argument structure for NomBank Proceedings of Language Resources and Evaluation, LREC 2004.
31. Ogren P Knowtator: A Protege plug-in for annotated corpus construction Proceedings of the Human Language Technology Conference of the NAACL Association of Computational Linguistics 2006:273-275.
32. Cohen KB Corpora for biomedical natural language processing http://compbio.uchsc.edu/ccp/corpora/obtaining.shtml
33. Hakenberg J Benchmarks and Corpora for BioNLP http://www2.informatik.hu-berlin.de/~hakenber/links/benchmarks.html
34. Rinaldi F Schneider G Kaljurand K Hess M Andronis C Konstandi O Persidis A Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach Artif Intell Med 2007, 39(2):127-136. 17052900
35. Takeuchi K Collier N Bio-Medical entity extraction using support vector machines Proc ACL 2003 Workshop on NLP in Biomedicine 2003, 33(2):125-137.
36. Hirschman L Colosimo M Morgan A Yeh A Overview of BioCreative Task 1B: normalized gene lists BMC Bioinformatics 2005, 6(Suppl 1):S11. 1869004 15960823
37. Blaschke C Leon EA Krallinger M Valencia A Evaluation of BioCreative assessment of task 2 BMC Bioinformatics 2005, 6(Suppl 1):S16. 1869008 15960828
38. Smith L Tanabe L Johnson nee Ando R Kuo CJ Chung IF Hsu CN Lin YS Klinger R Friedrich C Ganchev K Torii M Liu H Haddow B Struble C Povinelli R Vlachos A Baumgartner WA Jr Hunter L Carpenter B Tsai RTH Dai HJ Liu F Chen Y Sun C Katrenko S Adriaans P Blaschke C Perez RT Neves M Nakov P Divoli A Mana M Mata-Vazquez J Wilber w Overview of BioCreative II gene mention recognition Genome Biology to appear
39. Morgan A Hirschmann L Overview of BioCreative II gene normalization task Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007.
40. Krallinger M Leitner F Valencia A Assessment of the second BioCreative PPI task: Automatic extraction of protein-protein interactions Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007.
41. Pyysalo S Ginter F Heimonen J Bjorne J Boberg J Jarvinen J Salakoski T BioInfer: A corpus for information extraction in the biomedical domain BMC Bioinformatics 2007, 8:50. 1808065 17291334
42. Schwartz A Hearst M A simple algorithm for identifying abbreviation definitions in biomedical text Pacific Symposium on Biocomputing 2003, 8:451-462.
43. Rosario B Hearst M Multi-way relation classification: Application to protein-protein interactions Proceedings of the HLT-NAACL 2005, 5.
44. Rosario B Hearst MA Classifying semantic relations in bioscience texts Proceedings of ACL 2004 2004:430-437.
45. Lease M Charniak E Parsing biomedical literature Second International Joint Conference on Natural Language Processing 2005:58-69.
46. Rinaldi F Schneider G Kaljurand K Dowdall J Andronis C Persidis A Konstanti O Mining relations in the GENIA corpus Proceedings of the Second European Workshop on Data Mining and Text Mining for Bioinformatics 2004:61-68.
47. Madkour A Darwish K Hassan H Hassan A Emam O BioNoculars: Extracting Protein-Protein Interactions from Biomedical Text Proceedings of the Workshop on BioNLP, Association for Computational Linguistics 2007:89-96.
48. Rindflesch T Tanabe L Weinstein J Hunter L EDGAR: Extraction of drugs, genes and relations from the biomedical literature Pacific Symposium on Biocomputing 2000 2000:515-524.
49. Kim JD Ohta T Tateisi Y Tsujii J GENIA corpus - a semantically annotated corpus for bio-textmining Bioinformatics 2003, 19(Suppl 1):i180-i182. 12855455
50. Tateisi Y Tsujii J Part-of-speech annotation of biology research abstracts Proceedings of LREC04 2004.
51. The FetchProt Corpus: Documentation and annotation guidelines http://fetchprot.sics.se
52. Ding J Berleant D Nettleton D Wurtele E Mining MEDLINE: Abstracts, sentences, or phrases Pacific Symposium on Biocomputing 2002, 7:326-337.
53. Hu ZZ Mani I Hermoso V Liu H Wu CH iProLINK: An integrated protein resource for literature mining Comput Biol Chem 2004, 28(5-6):409-416. 15556482
54. Pustejovsky J Castaño J Cochran B Kotecki M Morrell M Rumshisky A Linguistic knowledge extraction from MEDLINE: Automatic construction of an acronym database 10th World Congress on Health and Medical Informatics (MEDINFO) 2001.
55. Pustejovsky J Castaño J Saurí R Zhang J Luo W Medstract: creating large-scale information servers for biomedical libraries Natural language processing in the biomedical domain Association for Computational Linguistics 2002:85-92.
56. Hersh W Buckley C Leone T Hickam D OHSUMED: An interactive retrieval evaluation and new large test collection for research Proceedings of the 17th annual international ACM SIGIR conference on research and development in information retrieval, Springer-Verlag 1994:192-201.
57. Hersh W Hickam D Use of a multi-application computer workstation in a clinical setting Bull Med Libr Assoc 1994, 82(4):382-389. 225961 7841907
58. Wattarujeekrit T Shah PK Collier N PASBio: Predicate-argument structures for event extraction in molecular biology BMC Bioinformatics 2004, 5:155. 535924 15494078
59. Demetriou G Gaizauskas R Utilizing text mining results: The PastaWeb system Proceedings of the ACL-02 workshop on natural language processing in the biomedical domain Association for Computational Linguistics 2002, 3:77-84.
60. Ding J Viswanathan K Berleant D Hughes L Wurtele E Ashlock D Dickerson J Fulmer A Schnable P Using the biological taxonomy to access biological literature with PathBinderH Bioinformatics 2005, 21(10):2560-2562. 15769838
61. Kabiljo R Stoycheva D Shepherd AJ ProSpecTome: A new tagged corpus for protein named entity recognition Proceedings of The ISMB BioLINK, Special Interest Group on Text Data Mining 2007:24-27.
62. 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 Artificial Intelligence in Medicine 2005, 33(2):139-155. 15811782
63. Hersh WR Bhuptiraju RT Ross L Johnson P Cohen AM Kraemer DF TREC Genomics track overview The thirteenth Text Retrieval Conference, TREC 2004 National Institute of Standards and Technology 2004:132-150.
64. Hersh WR Cohen AM Yang J Bhupatiraju RT Roberts P Hearst M TREC 2005 Genomics track overview Proceedings of the 14th Text Retrieval Conference National Institute of Standards and Technology 2005.
65. Hersh W Cohen AM Roberts P Rekapalli HK TREC 2006 Genomics Track Overview TREC Notebook National Institute of Standards and Technology 2006.
66. Craven M Kumlien J Constructing biological knowledge bases by extracting information from text sources Intelligent Systems for Molecular Biology 1999:77-86.
67. Weeber M Mork J Aronson A Developing a test collection for biomedical word sense disambiguation Proc AMIA Symp 2001, 746:50.
68. Eriksson G Franzén K Olsson F Asker L Lidén P Using heuristics, syntax and a local dynamic dictionary for protein name tagging Human Language Technology Conference 2002.
69. Franzen K Eriksson G Olsson F Asker L Liden P Coster J Protein names and how to find them International Journal of Medical Informatics 2002, 67(1-3):49-61. 12460631