DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records

DeepPhe - A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records

Precise phenotype information is needed to understand the effects of genetic and epigenetic changes on tumor behavior and responsiveness. Extraction and representation of cancer phenotypes is currently mostly performed manually, making it difficult to correlate phenotypic data to genomic data. In addition, genomic data are being produced at an increasingly faster pace, exacerbating the problem....

Natural language processing methods for extracting information from mathematical texts

FASTUS: A System for Extracting Information from Natural-Language Text

FASTUS is a system for extracting information from free text in English, and potentially other languages as well, for entry into a database, and potentially for other applications. It works essentially as a cascaded, nondeterministic finite state automaton. There are four steps in the operation of FASTUS. In Step 1 sentences are scanned for certain trigger words to determine whether further pro...

Natural Language Processing, Electronic Health Records, and Clinical Research

R.L. Richesson, J.E. Andrews (eds.), Clinical Research Informatics, Health Informatics, DOI 10.1007/978-1-84882-448-5_16, © Springer-Verlag London Limited 2012 Abstract Electronic health records (EHR) capture “real-world” disease and care processes and hence offer richer and more generalizable data for comparative effectiveness research than traditional randomized clinical trial studies. With t...

A common type system for clinical natural language processing

UNLABELLED BACKGROUND One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowab...