title: BioC implementations in Go, Perl, Python and Ruby.
abstract: As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
authors: Wanli
authors: W
authors: Liu
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
authors: Rezarta
authors: R
authors: Islamaj Doğan
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
authors: Dongseop
authors: D
authors: Kwon
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
authors: Hernani
authors: H
authors: Marques
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
authors: Fabio
authors: F
authors: Rinaldi
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
authors: W John
authors: WJ
authors: Wilbur
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland comeau@ncbi.nlm.nih.gov.
authors: Donald C
authors: DC
authors: Comeau
mesh_terms: D000465:Algorithms; D057225:Data Mining / Q000379:methods*; D019992:Databases as Topic; D011381:Programming Languages; D014584:User-Computer Interface