AIMC Topic: Biological Ontologies

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ontologyX: a suite of R packages for working with ontological data.

Bioinformatics (Oxford, England)
SUMMARY: Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three package...

Modeling a System for Generating Structured Reports.

Studies in health technology and informatics
The purpose of this research is to make the medical report generation process more practical, fast and reliable, both for the health professional and for the patient. We created an ontology and modeling of a structured report (SR) Standard DICOM SR.

Using an Ontology-Based Approach to Handle Author Affiliations in a Large Biomedical Citation Database.

Studies in health technology and informatics
To handle differences in affiliation names submitted with biomedical journal articles, we build an affiliation knowledge base named Authority File for Affiliations (AFA) based on ontology principles. There are currently 113,700 affiliation concepts w...

Summarizing an Ontology: A "Big Knowledge" Coverage Approach.

Studies in health technology and informatics
Maintenance and use of a large ontology, consisting of thousands of knowledge assertions, are hampered by its scope and complexity. It is important to provide tools for summarization of ontology content in order to facilitate user "big picture" compr...

Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation.

Studies in health technology and informatics
In this research we aim to demonstrate that an ontology-based system can categorize potential drug-drug interaction (PDDI) evidence items into complex types based on a small set of simple questions. Such a method could increase the transparency and r...

From Patient Discharge Summaries to an Ontology for Psychiatry.

Studies in health technology and informatics
Psychiatry aims at detecting symptoms, providing diagnoses and treating mental disorders. We developed ONTOPSYCHIA, an ontology for psychiatry in three modules: social and environmental factors of mental disorders, mental disorders, and treatments. T...

Application of Ontology Technology in Health Statistic Data Analysis.

Studies in health technology and informatics
UNLABELLED: Research Purpose: establish health management ontology for analysis of health statistic data. Proposed Methods: this paper established health management ontology based on the analysis of the concepts in China Health Statistics Yearbook, a...

An Ontology-Based Approach to Estimate the Frequency of Rare Diseases in Narrative-Text Radiology Reports.

Studies in health technology and informatics
This study sought to use ontology-based knowledge to identify patients with rare diseases and to estimate the frequency of those diseases in a large database of radiology reports. Natural language processing methods were applied to 12,377,743 narrari...

Expressing Biomedical Ontologies in Natural Language for Expert Evaluation.

Studies in health technology and informatics
We report on a study of our custom Hootation software for the purposes of assessing its ability to produce clear and accurate natural language phrases from axioms embedded in three biomedical ontologies. Using multiple domain experts and three discre...

Processual Reasoning over Sequences of Situations in Endoscopic Surgery.

Studies in health technology and informatics
Minimally invasive surgery is a highly complex and technically demanding alternative to open surgery. Surgical procedures based on this method are characterized by small incisions and allow for a fast recovery of the patient. Such techniques are chal...