Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus

BioC is a new format and associated code libraries for sharing text and annotations. We have implemented BioC natural language preprocessing pipelines in two popular programming languages: C++ and Java. The current implementations interface with the well-known MedPost and Stanford natural language processing tool sets. The pipeline functionality includes sentence segmentation, tokenization, part-of-speech tagging, lemmatization and sentence parsing. These pipelines can be easily integrated along with other BioC programs into any BioC compliant text mining systems. As an application, we converted the NCBI disease corpus to BioC format, and the pipelines have successfully run on this corpus to demonstrate their functionality. Code and data can be downloaded from http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net