BioC implementations in Go, Perl, Python and Ruby

Wanli Liu; Rezarta Islamaj Doğan; Dongseop Kwon; Hernani Marques; Fabio Rinaldi; W John Wilbur; Donald C Comeau

doi:10.1093/database/bau059

BioC implementations in Go, Perl, Python and Ruby

Database (Oxford). 2014 Jun 23:2014:bau059. doi: 10.1093/database/bau059. Print 2014.

Authors

Wanli Liu¹, Rezarta Islamaj Doğan¹, Dongseop Kwon¹, Hernani Marques¹, Fabio Rinaldi¹, W John Wilbur¹, Donald C Comeau²

Affiliations

¹ 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.
² 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.

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/

Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Publication types

Research Support, N.I.H., Intramural

MeSH terms

Algorithms
Data Mining / methods*
Databases as Topic
Programming Languages*
User-Computer Interface

Grants and funding

Intramural NIH HHS/United States