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/

BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language

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“…Data processing. Download the human General Transfer Format(hunman.gtf) from Ensemble(https://www.ensembl.org/index.html) [25] and annotate the TCGA data using Perl language [26]. The chip data le (GSE39582) was preprocessed using Perl language through the annotation le of the GPL570 platform.…”

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“…BioC is an XML-based format for embedding text, annotations and relations. Not only is BioC simple and straightforward, BioC programming libraries ( 1 , 3 ) are also freely available in multiple languages such as C ++, Java, Perl, Python, Go and Ruby. Moreover, there are a number of text mining and curation tools ( 4–8 ) that support BioC.…”