References

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

    OpenURL

  2. Ferrucci D, Lally A: Building an example application with the unstructured information management architecture.

    IBM Systems Journal 2004, 43(3):455-475. OpenURL

  3. 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. OpenURL

  4. Apache UIMA [http://incubator.apache.org/uima/]

    OpenURL

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

    OpenURL

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

    OpenURL

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

    OpenURL

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

    OpenURL

  9. Hirschman L, Yeh A, Blaschke C, Valencia A: Overview of BioCreAtIvE: critical assessment of information extraction for biology.

    BMC Bioinformatics 2005., 6: OpenURL

  10. Hirschman L, Krallinger M, Valencia A, (Eds):

    Proceedings of the Second BioCreative Challenge Evaluation Workshop. 2007. OpenURL

  11. Yeast Gene Nomenclature [http://www.yeastgenome.org/help/yeastGeneNomenclature.shtml]

    OpenURL

  12. 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. OpenURL

    [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. OpenURL

  14. Tanabe L, Wilbur JW: Tagging gene and protein names in biomedical text.

    Bioinformatics 2002, 18(8):1124-1132. PubMed Abstract | Publisher Full Text OpenURL

  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. PubMed Abstract | Publisher Full Text OpenURL

  16. 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. OpenURL

  17. 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 OpenURL

  18. Carpenter B, Baldwin B: LingPipe. [http://www.alias-i.com/lingpipe/]

    OpenURL

  19. 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 OpenURL

  20. Kinoshita S, Cohen KB, Ogren PV, Hunter L: BioCreAtIvE Task1A: entity identification with a stochastic tagger.

    BMC Bioinformatics 2005., 6(Suppl 1): OpenURL

  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. OpenURL

  22. Bio1 corpus [http://research.nii.ac.jp/~collier/resources/bio1.1.xml]

    OpenURL

  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. OpenURL

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

    OpenURL

  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. PubMed Abstract | Publisher Full Text OpenURL

  26. iProLink Corpus [http://pir.georgetown.edu/iprolink/]

    OpenURL

  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. PubMed Abstract | Publisher Full Text OpenURL

  28. Texas Corpus [http://www.cs.utexas.edu/users/ml/index.cgi?page=resourcesrepo]

    OpenURL

  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. OpenURL

  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. PubMed Abstract | Publisher Full Text OpenURL

  31. Yapex Corpus (Reference Set) [http://www.sics.se/humle/projects/prothalt]

    OpenURL

  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. OpenURL

  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. PubMed Abstract OpenURL

  34. 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 OpenURL

  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. OpenURL

  36. Yeh A, Morgan A, Colosimo M, Hirschman L: BioCreatve task1A: gene mention finding evaluation.

    BMC Bioinformatics 2005., 6(Suppl 1): OpenURL

  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. OpenURL

  38. Hirschman L, Blaschke C: Evaluation of text mining in biology. Volume 9. Norwood, MA: Artech House; 2006:213-245. OpenURL

  39. Hirschman L: MUC-7 Coreference Task Defintion.

    1997. OpenURL

  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. OpenURL

  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. OpenURL