An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

Journal of Biomedical Discovery and Collaboration

Volumn 3, Issue , 2008, Pages

  Baumgartner Jr , William A ^a   Bretonnel, K Cohen ^a   Hunter, Lawrence ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

EID: 41649118959     PISSN: None     EISSN: 17475333     Source Type: Journal    
DOI: 10.1186/1747-5333-3-1     Document Type: Article

References (41)

1. BioNLP UIMA Component Repository http://bionlp-uima.sourceforge.net/
2. Ferrucci D Lally A Building an example application with the unstructured information management architecture IBM Systems Journal 2004, 43(3):455-475.
3. Mack R Mukherjea S Soffer A Uramoto N Brown E Coden A Cooper J Inokuchi A Iyer B Mass Y Text analytics for life science using the unstructured information management architecture IBM Systems Journal 2004, 43(3):490-515.
4. Apache UIMA http://incubator.apache.org/uima/
5. Tsujii Lab UIMA Repository http://www-tsujii.is.s.u-tokyo.ac.jp/uima/
6. JULIE Lab tools http://www.julielab.de/content/view/117/174/
7. CMU UIMA Component Repository http://uima.lti.cs.cmu.edu:8080/UCR/ Welcome.do
8. UIMA Sandbox http://incubator.apache.org/uima/sandbox.html
9. Hirschman L Yeh A Blaschke C Valencia A Overview of BioCreAtIvE: critical assessment of information extraction for biology BMC Bioinformatics 2005, 6.
10. Hirschman L Krallinger M Valencia A (Eds) Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007.
11. Yeast Gene Nomenclature http://www.yeastgenome.org/help/ yeastGeneNomenclature.shtml
12. Kim J Ohta T Tsuruoka Y Tateisi Y Collier N Introduction to the bio-entity recognition task at JNLPBA Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), Geneva, Switzerland Collier N, Ruch P, Nazarenko A 2004, 70-75. [Held in conjunction with COLING'2004]
13. 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.
14. Tanabe L Wilbur JW Tagging gene and protein names in biomedical text Bioinformatics 2002, 18(8):1124-1132. 10.1093/bioinformatics/18.8.1124 12176836
15. 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
16. Talreja R Schein A Winters S Ungar L GeneTaggerCRF: An entity tagger for recognizing gene names in text Tech rep University of Pennsylvania 2004.
17. Fukuda K Tamura A Tsunoda T Takagi T Toward information extraction: identifying protein names from biological papers Pac Symp Biocomput 1998, 707-718. 9697224
18. Carpenter B Baldwin B LingPipe http://www.alias-i.com/lingpipe/
19. McDonald R Pereira F Identifying gene and protein mentions in text using conditional random fields BMC Bioinformatics 2005, 6(Suppl 1):S6. 1869020 15960840 10.1186/1471-2105-6-S1-S6
20. Kinoshita S Cohen KB Ogren PV Hunter L BioCreAtIvE Task1A: Entity identification with a stochastic tagger BMC Bioinformatics 2005, 6(Suppl 1).
21. Tateisi Y Ohta T Collier N Nobata C Tsujii J Building an Annotated Corpus from Biology Research Papers Proceedings COLING 2000 Workshop on Semantic Annotation and Intelligent Content 2000, 28-34.
22. Bio1 corpus http://research.nii.ac.jp/~collier/resources/bio1.1.xml
23. 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.
24. Penn BioIE Corpus http://bioie.ldc.upenn.edu
25. 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. 10.1016/j.compbiolchem.2004.09.010 15556482
26. iProLink Corpus http://pir.georgetown.edu/iprolink/
27. 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. 10.1016/j.artmed.2004.07.016 15811782
28. Texas Corpus http://www.cs.utexas.edu/users/ml/index.cgi?page= resourcesrepo
29. 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.
30. 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. 10.1016/S1386-5056(02)00052-7 12460631
31. Yapex Corpus (Reference Set) http://www.sics.se/humle/projects/prothalt
32. Baumgartner WA Jr Lu Z Johnson HL Caporaso JG Paquette J Lindemann A White EK Medvedeva O Cohen KB Hunter L An integrated approach to concept recognition in biomedical text Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007.
33. Morgan AA Wellner B Colombe JB Arens R Colosimo ME Hirschman L Evaluating the automatic mapping of human gene and protein mentions to unique identifiers Pacific Symposium on Biocomputing 2007, 281-291. 17990499
34. Maglott D Ostell J Pruitt KD Tatusova T Entrez Gene: Gene-centered information at NCBI Nucleic Acids Res 2007, 35: Database D26-D31. 1761442 17148475 10.1093/nar/gkl993
35. 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.
36. Yeh A Morgan A Colosimo M Hirschman L BioCreatve task1A: Gene mention finding evaluation BMC Bioinformatics 2005, 6(Suppl 1).
37. Jones KS Galliers JR (Eds) Evaluating Natural Language Processing Systems, An Analysis and Review, Volume 1083 of Lecture Notes in Computer Science Springer 1996.
38. Hirschman L Blaschke C Evaluation of text mining in biology Norwood, MA: Artech House 2006, 9:213-245.
39. Hirschman L MUC-7 Coreference Task Defintion 1997.
40. 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 2004, Linking Biological Literature, Ontologies and Databases, Association for Computational Linguistics 2004, 1-8.
41. Kano Y Nguyen N Sætre R Yoshida K Miyao Y Tsuruoka Y Matsubayashi Y Ananiadou S Tsujii J Filling the gaps between tools and users: A tool comparator, using protein-protein interactions as an example Pac Symp Biocomput 2008, 6:616-627.