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BioNLP UIMA Component Repository
[http://bionlp-uima.sourceforge.net/]

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Ferrucci D, Lally A: Building an example application with the unstructured information management architecture.
IBM Systems Journal 2004, 43(3):455-475. 
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Mack R, Mukherjea S, Soffer A, Uramoto N, Brown E, Coden A, Cooper J, Inokuchi A, Iyer B, Mass Y, et al.: Text analytics for life science using the unstructured information management architecture.
IBM Systems Journal 2004, 43(3):490-515. 
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Apache UIMA
[http://incubator.apache.org/uima/]

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Tsujii Lab UIMA Repository
[http://www-tsujii.is.s.u-tokyo.ac.jp/uima/]

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JULIE Lab tools
[http://www.julielab.de/content/view/117/174/]

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CMU UIMA Component Repository
[http://uima.lti.cs.cmu.edu:8080/UCR/Welcome.do]

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UIMA Sandbox
[http://incubator.apache.org/uima/sandbox.html]

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Hirschman L, Yeh A, Blaschke C, Valencia A: Overview of BioCreAtIvE: critical assessment of information extraction for biology.
BMC Bioinformatics 2005., 6: 
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Hirschman L, Krallinger M, Valencia A, (Eds):
Proceedings of the Second BioCreative Challenge Evaluation Workshop. 2007. 
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Yeast Gene Nomenclature
[http://www.yeastgenome.org/help/yeastGeneNomenclature.shtml]

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Kim J, Ohta T, Tsuruoka Y, Tateisi Y, Collier N: Introduction to the bio-entity recognition task at JNLPBA. In 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]
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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. 
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Tanabe L, Wilbur JW: Tagging gene and protein names in biomedical text.
Bioinformatics 2002, 18(8):1124-1132. PubMed Abstract | Publisher Full Text 
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Settles B: ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text.
Bioinformatics 2005, 21(14):3191-3192. PubMed Abstract | Publisher Full Text 
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Talreja R, Schein A, Winters S, Ungar L: GeneTaggerCRF: An entity tagger for recognizing gene names in text. In Tech rep. University of Pennsylvania; 2004. 
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Fukuda K, Tamura A, Tsunoda T, Takagi T: Toward information extraction: identifying protein names from biological papers.
Pac Symp Biocomput 1998, 707-718. PubMed Abstract 
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Carpenter B, Baldwin B: LingPipe.
[http://www.alias-i.com/lingpipe/]

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McDonald R, Pereira F: Identifying gene and protein mentions in text using conditional random fields.
BMC Bioinformatics 2005, 6(Suppl 1):S6. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text 
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Kinoshita S, Cohen KB, Ogren PV, Hunter L: BioCreAtIvE Task1A: entity identification with a stochastic tagger.
BMC Bioinformatics 2005., 6(Suppl 1): 
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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. 
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Bio1 corpus
[http://research.nii.ac.jp/~collier/resources/bio1.1.xml]

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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. 
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Penn BioIE Corpus
[http://bioie.ldc.upenn.edu]

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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. PubMed Abstract | Publisher Full Text 
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iProLink Corpus
[http://pir.georgetown.edu/iprolink/]

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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. PubMed Abstract | Publisher Full Text 
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Texas Corpus
[http://www.cs.utexas.edu/users/ml/index.cgi?page=resourcesrepo]

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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. 
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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. PubMed Abstract | Publisher Full Text 
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Yapex Corpus (Reference Set)
[http://www.sics.se/humle/projects/prothalt]

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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. 
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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. PubMed Abstract 
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Maglott D, Ostell J, Pruitt KD, Tatusova T: Entrez Gene: gene-centered information at NCBI.
Nucleic Acids Res 2007, (35 Database):D26-D31. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
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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. 
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Yeh A, Morgan A, Colosimo M, Hirschman L: BioCreatve task1A: gene mention finding evaluation.
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Hirschman L, Blaschke C: Evaluation of text mining in biology. Volume 9. Norwood, MA: Artech House; 2006:213-245. 
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Hirschman L: MUC-7 Coreference Task Defintion.
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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. 
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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.
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