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Related Concept Videos

Inflammatory Bowel Disease III: Diagnostic Studies and Management I-Nutritional Therapy01:30

Inflammatory Bowel Disease III: Diagnostic Studies and Management I-Nutritional Therapy

Various diagnostic tests are employed in the diagnostic process for Inflammatory Bowel Disease (IBD), particularly to differentiate between Crohn's disease and ulcerative colitis.
Diagnostic studies
A colonoscopy is the definitive screening test, distinguishing ulcerative colitis from other colon diseases with similar symptoms. During a colonoscopy test, inflamed mucosa with exudate ulcerations can be observed, and biopsies are taken to determine the histologic characteristics of the colonic...
Inflammatory Bowel Disease II: Crohn's Disease01:30

Inflammatory Bowel Disease II: Crohn's Disease

Introduction
Inflammatory bowel disease, commonly known as IBD, refers to a collection of disorders that lead to persistent inflammation of the gastrointestinal tract. The two types of IBD are ulcerative colitis, which impacts the colon, and Crohn's disease, which can involve any part of the gastrointestinal segment.
Crohn's disease
Crohn's disease is a chronic, systemic inflammatory bowel disease (IBD) that predominantly affects the gastrointestinal tract. It is marked by transmural...
Inflammatory Bowel Disease IV: Clinical Manifestations01:20

Inflammatory Bowel Disease IV: Clinical Manifestations

Inflammatory bowel disease (IBD) encompasses two major chronic disorders—ulcerative colitis and Crohn’s disease—each characterized by relapsing episodes of gastrointestinal inflammation. Although they share certain clinical features, their patterns of involvement and manifestations differ in ways that aid diagnosis and guide management.Ulcerative ColitisUlcerative colitis is limited to the colon and rectum and involves continuous inflammation of the mucosal layer. The disease course is marked...
Inflammatory Bowel Disease III: Crohn's Disease01:25

Inflammatory Bowel Disease III: Crohn's Disease

Crohn’s disease is a chronic, relapsing form of inflammatory bowel disease characterized by segmental, transmural inflammation that can affect any part of the gastrointestinal tract. Its pathogenesis arises from a combination of genetic susceptibility, environmental exposures, epithelial barrier dysfunction, and immune dysregulation. Together, these factors lead to an exaggerated immune response against components of the gut microbiome.Genetic and Environmental InfluencesMultiple genetic...
Inflammatory Bowel Disease I: Introduction01:26

Inflammatory Bowel Disease I: Introduction

Inflammatory bowel disease is a group of chronic disorders marked by recurrent inflammation of the gastrointestinal tract due to an abnormal immune response against gut microflora. This leads to tissue damage. The two main forms are Crohn’s disease and ulcerative colitis.Crohn’s DiseaseCrohn’s disease is a relapsing inflammatory disorder that can affect any part of the GI tract, from the mouth to the anus. It involves all layers of the bowel wall (transmural) and shows “skip lesions” in which...
Inflammatory Bowel Disease I: Ulcerative Colitis01:27

Inflammatory Bowel Disease I: Ulcerative Colitis

Introduction
Inflammatory bowel disease, or IBD, encompasses a group of disorders characterized by chronic inflammation or ulceration of the gastrointestinal tract.
Risk Factors
The exact cause of IBD remains unclear, although it is believed to be due to a mix of genetic, environmental, microbial, and immune factors. Genetic factors are significant in determining susceptibility to IBD, with family history being a critical risk factor. Individuals with a first-degree relative who has IBD are at...

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Multimodal Quantitative Phase Imaging with Digital Holographic Microscopy Accurately Assesses Intestinal Inflammation and Epithelial Wound Healing
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Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel

Brett R South1, Shuying Shen, Makoto Jones

  • 1VA Salt Lake City Health Care System, IDEAS Center, Salt Lake City, Utah 84148, USA. brett.south@hsc.utah.edu

BMC Bioinformatics
|September 19, 2009
PubMed
Summary

Manual annotation of clinical notes for Natural Language Processing (NLP) is time-consuming. Focusing on specific document types and sections, like those for Inflammatory Bowel Disease (IBD), improves efficiency and data yield for research.

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Multimodal Quantitative Phase Imaging with Digital Holographic Microscopy Accurately Assesses Intestinal Inflammation and Epithelial Wound Healing
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Published on: February 14, 2021

Area of Science:

  • Biomedical Informatics
  • Clinical Data Science
  • Natural Language Processing

Background:

  • Natural Language Processing (NLP) systems aid in extracting phenotypic data from electronic medical records (EMR) for translational research.
  • Manual annotation of clinical text is crucial for training NLP models but is resource-intensive.
  • Developing efficient annotation strategies is key to advancing NLP in healthcare.

Purpose of the Study:

  • To identify challenges and opportunities in manual annotation for clinical information extraction.
  • To demonstrate methods for annotation using a specific use case (Inflammatory Bowel Disease - IBD).
  • To evaluate annotator agreement and concept yield in a clinical corpus.

Main Methods:

  • Utilized a set of VA EMR clinical documents for an Inflammatory Bowel Disease (IBD) use case.
  • Employed an open-source annotation tool and a customized annotation schema.
  • Assessed annotator agreement at document, concept, and concept attribute levels, and estimated concept yield.

Main Results:

  • High document-level annotator agreement (Kappa = 0.87) was observed for IBD-related concepts.
  • Concept-level F-measure ranged from 0.61 to 0.83, with variability at the attribute level.
  • GI clinic and primary care notes yielded the highest concept density, particularly in assessment and history sections.

Conclusions:

  • Key challenges include schema design, annotator training, and defining annotation granularity.
  • Focusing NLP information extraction on use-case-specific note types and sections enhances efficiency.
  • Optimizing annotation efforts can accelerate the extraction of valuable data from large clinical note repositories.