BioC implementations in Go, Perl, Python and Ruby

• Published in: Database : the journal of biological databases and curation Vol. 2014; no. p.bau059-bau059; p. bau059
• Main Authors: Liu, W., Islamaj Do an, R., Kwon, D., Marques, H., Rinaldi, F., Wilbur, W. J., Comeau, D. C.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 2014
• Subjects: Algorithms; biomedical research; computer software; Data Mining - methods; Databases as Topic; information retrieval; Internet; Original; Programming Languages; User-Computer Interface
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/bau059

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/