AIMC Topic: Biological Ontologies

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Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Rare diseases, although individually rare, collectively affect one in ten Americans. Because of their rarity, patients with rare diseases are typically left misdiagnosed or undiagnosed, which leads to a prolonged medical journey. The diagnosis pathwa...

Mining Disease-Symptom Relation from Massive Biomedical Literature and Its Application in Severe Disease Diagnosis.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Disease-symptom relation is an important biomedical relation that can be used for clinical decision support including building medical diagnostic systems. Here we present a study on mining disease-symptom relation from massive biomedical literature a...

Shared Decision-Making Ontology for a Healthcare Team Executing a Workflow, an Instantiation for Metastatic Spinal Cord Compression Management.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Regardless of potential benefits and better outcomes, adoption of shared decision-making between a patient and providers involved in his/her care is still in its infancy. This paper intends to fill this gap by formalizing shared decision-making, situ...

How Sustainable are Biomedical Ontologies?

AMIA ... Annual Symposium proceedings. AMIA Symposium
BioPortal is widely regarded to be the world's most comprehensive repository of biomedical ontologies. With a coverage of many biomedical subfields by 716 ontologies (June 27, 2018), BioPortal is an extremely diverse repository. BioPortal maintains e...

Ontology-based semantic mapping of chemical toxicities.

Toxicology
This study was undertaken to evaluate the use of ontology-based semantic mapping (OS-Mapping) in chemical toxicity assessment. Nineteen chemical-species phenotypic profiles (CSPPs) were constructed by ontologically annotating the toxicity responses r...

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes.

BMC bioinformatics
BACKGROUND: Despite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet a majority of natural language processing or semantic tools as well as domain terminologies or ont...

ProvCaRe: Characterizing scientific reproducibility of biomedical research studies using semantic provenance metadata.

International journal of medical informatics
OBJECTIVE: Reproducibility of research studies is key to advancing biomedical science by building on sound results and reducing inconsistencies between published results and study data. We propose that the available data from research studies combine...

Using Compact Coevolutionary Algorithm for Matching Biomedical Ontologies.

Computational intelligence and neuroscience
Over the recent years, ontologies are widely used in various domains such as medical records annotation, medical knowledge representation and sharing, clinical guideline management, and medical decision-making. To implement the cooperation between in...

Ontoserver: a syndicated terminology server.

Journal of biomedical semantics
BACKGROUND: Even though several high-quality clinical terminologies, such as SNOMED CT and LOINC, are readily available, uptake in clinical systems has been slow and many continue to capture information in plain text or using custom terminologies. Th...

Linked open data-based framework for automatic biomedical ontology generation.

BMC bioinformatics
BACKGROUND: Fulfilling the vision of Semantic Web requires an accurate data model for organizing knowledge and sharing common understanding of the domain. Fitting this description, ontologies are the cornerstones of Semantic Web and can be used to so...