BMC medical informatics and decision making
Jun 15, 2015
BACKGROUND: Phenotypic information locked away in unstructured narrative text presents significant barriers to information accessibility, both for clinical practitioners and for computerised applications used for clinical research purposes. Text mini...
Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are s...
UNLABELLED: Nationwide Children's Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system sh...
Many text mining applications in the biomedical domain benefit from automatic clustering of relational phrases into synonymous groups, since it alleviates the problem of spurious mismatches caused by the diversity of natural language expressions. Mos...
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...