Bluima: a UIMA-based NLP Toolkit for Neuroscience

This paper describes Bluima, a natural language processing (NLP) pipeline focusing on the extraction of neuroscientific content and based on the UIMA framework. Bluima builds upon models from biomedical NLP (BioNLP) like specialized tokenizers and lemmatizers. It adds further models and tools specific to neuroscience (e.g. named entity recognizer for neuron or brain region mentions) and provides collection readers for neuroscientific corpora. Two novel UIMA components are proposed: the first allows configuring and instantiating UIMA pipelines using a simple scripting language, enabling non-UIMA experts to design and run UIMA pipelines. The second component is a common analysis structure (CAS) store based on MongoDB, to perform incremental annotation of large document corpora.