Combining contextual and lexical features to classify UMLS concepts.

AMIA Annu Symp Proc

Department of Biomedical Informatics, Columbia University, New York, NY, USA.

Published: October 2007

Semantic classification is important for biomedical terminologies and the many applications that depend on them. Previously we developed two classifiers for 8 broad clinically relevant classes to reclassify and validate UMLS concepts. We found them to be complementary, and then combined them using a manual approach. In this paper, we extended the classifiers by adding an "other" class to categorize concepts not belonging to any of the 8 classes. In addition, we focused on automating the method for combining the two classifiers by training a meta-classifier that performs dynamic combination to exploit the strength of each classifier. The automated method performed as well as manual combination, achieving classification accuracy of about 0.81.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655898PMC

Publication Analysis

Top Keywords

umls concepts
8
combining contextual
4
contextual lexical
4
lexical features
4
features classify
4
classify umls
4
concepts semantic
4
semantic classification
4
classification biomedical
4
biomedical terminologies
4

Similar Publications

Analysis of longitudinal social media for monitoring symptoms during a pandemic.

J Biomed Inform

January 2025

School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058 China; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address:

Objective: Current studies leveraging social media data for disease monitoring face challenges like noisy colloquial language and insufficient tracking of user disease progression in longitudinal data settings. This study aims to develop a pipeline for collecting, cleaning, and analyzing large-scale longitudinal social media data for disease monitoring, with a focus on COVID-19 pandemic.

Materials And Methods: This pipeline initiates by screening COVID-19 cases from tweets spanning February 1, 2020, to April 30, 2022.

View Article and Find Full Text PDF

Background And Objective: Despite significant investments in the normalization and the standardization of Electronic Health Records (EHRs), free text is still the rule rather than the exception in clinical notes. The use of free text has implications in data reuse methods used for supporting clinical research since the query mechanisms used in cohort definition and patient matching are mainly based on structured data and clinical terminologies. This study aims to develop a method for the secondary use of clinical text by: (a) using Natural Language Processing (NLP) for tagging clinical notes with biomedical terminology; and (b) designing an ontology that maps and classifies all the identified tags to various terminologies and allows for running phenotyping queries.

View Article and Find Full Text PDF

ATC-to-RxNorm mappings - A comparison between OHDSI Standardized Vocabularies and UMLS Metathesaurus.

Int J Med Inform

December 2024

Amsterdam UMC location University of Amsterdam, Department of Medical Informatics, Amsterdam, the Netherlands; Methodology, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.

Introduction: The World Health Organization global standard for representing drug data is the Anatomical Therapeutic Chemical (ATC) classification. However, it does not represent ingredients and other drug properties required by clinical decision support systems. A mapping to a terminology system that contains this information, like RxNorm, may help fill this gap.

View Article and Find Full Text PDF

In traditional medicine (TM), blood stasis syndrome (BSS) is characterized by insufficient blood flow, resulting in a group of symptoms such as fixed pain, a dark complexion, bleeding, and an astringent pulse. While BSS pathology has been previously explored, its molecular mechanisms remain elusive owing to challenges in linking TM symptoms to genes. Our study aimed to elucidate the mechanisms underlying BSS using a phenotype-genotype association approach.

View Article and Find Full Text PDF

This study suggests a way to utilize the existing medical ontology and natural language processing techniques to extract major medical concepts from lay vocabularies of health consumers on social media and group them based on the defined semantic types in the ontology. Diabetes-related discussions on Tumblr was used to test the efficiency of SpaCy and the Markov-Viterbi algorithm to map lay medical terms to the defined medical concepts in the UMLS. The system discussed in this paper can better analyze free texts, take care of word ambiguity and extract the lifestyle indicators from the daily life discussions of diabetic people on Tumblr.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!