The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on identifying risk factors for heart disease (specifically, Cardiac Artery Disease) in clinical narratives. For this track, we used a "light" annotation paradigm...
Clinical documents are rich free-text data sources containing valuable medication and symptom information, which have a great potential to improve health care. In this paper, we build an integrating system for extracting medication names and symptom ...
BMC medical informatics and decision making
May 20, 2015
BACKGROUND: The Entity Linking (EL) task links entity mentions from an unstructured document to entities in a knowledge base. Although this problem is well-studied in news and social media, this problem has not received much attention in the life sci...
BMC medical informatics and decision making
May 20, 2015
BACKGROUND: Alterations of a genome can lead to changes in protein functions. Through these genetic mutations, a protein can lose its native function (loss-of-function, LoF), or it can confer a new function (gain-of-function, GoF). However, when a mu...
BMC medical informatics and decision making
May 20, 2015
Narrative text is a useful way of identifying injury circumstances from the routine emergency department data collections. Automatically classifying narratives based on machine learning techniques is a promising technique, which can consequently redu...
Journal of the American Medical Informatics Association : JAMIA
May 14, 2015
OBJECTIVE: Many tasks in natural language processing utilize lexical pattern-matching techniques, including information extraction (IE), negation identification, and syntactic parsing. However, it is generally difficult to derive patterns that achiev...
OBJECTIVE: This paper describes the University of Michigan's nine-year experience in developing and using a full-text search engine designed to facilitate information retrieval (IR) from narrative documents stored in electronic health records (EHRs)....
Database : the journal of biological databases and curation
May 13, 2015
The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by...
UNLABELLED: PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of a database and a web interface supporting data...
One effective way to improve the state of the art is through competitions. Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by th...
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