AIMC Topic: Biological Ontologies

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Construction and application of SARS-CoV-2 protein ontology (CoVPO).

PloS one Jan 1, 2025
The emergence of the SARS-CoV-2 virus and the resulting COVID-19 pandemic brought forth an urgent need for an in-depth molecular understanding, organization, and data integration to expedite therapeutic and preventive strategies. An essential approac...
Humans Pandemics Biological Ontologies Viral Proteins COVID-19 SARS-CoV-2
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Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology.

Database : the journal of biological databases and curation Dec 5, 2024
Atherosclerotic cerebrovascular disease could result in a great number of deaths and disabilities. However, it did not acquire enough attention. Less information, statistics, or data on the disease has been revealed. Thus, no systematic concept datas...
Cerebrovascular Disorders Humans Biological Ontologies Atherosclerosis
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The text2term tool to map free-text descriptions of biomedical terms to ontologies.

Database : the journal of biological databases and curation Nov 28, 2024
There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types-such as disease names, cell types, or chemicals-that are used in metadata associated with biomedical data. W...
Software Metadata Humans Biological Ontologies
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Enhancing Arden-Syntax-Based Clinical Reasoning with Ontologies.

Studies in health technology and informatics Nov 22, 2024
We present a new methodological approach based on integrating Arden-Syntax-based clinical decision support (CDS) with an upstream ontology service. Incoming linguistic patient data, such as single reports about detected germs or viruses, shall be ide...
Artificial Intelligence Electronic Health Records Humans Biological Ontologies Clinical Reasoning Decision Support Systems, Clinical Natural Language Processing Semantics
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Fine-tuning large language models for rare disease concept normalization.

Journal of the American Medical Informatics Association : JAMIA Sep 1, 2024
OBJECTIVE: We aim to develop a novel method for rare disease concept normalization by fine-tuning Llama 2, an open-source large language model (LLM), using a domain-specific corpus sourced from the Human Phenotype Ontology (HPO).
Vocabulary, Controlled Rare Diseases Natural Language Processing Biological Ontologies Humans Phenotype
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CoRTEx: contrastive learning for representing terms via explanations with applications on constructing biomedical knowledge graphs.

Journal of the American Medical Informatics Association : JAMIA Sep 1, 2024
OBJECTIVES: Biomedical Knowledge Graphs play a pivotal role in various biomedical research domains. Concurrently, term clustering emerges as a crucial step in constructing these knowledge graphs, aiming to identify synonymous terms. Due to a lack of ...
Natural Language Processing Biological Ontologies Terminology as Topic Unified Medical Language System Biomedical Research Cluster Analysis Humans Algorithms Machine Learning
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Merging Biomedical Ontologies with BioSTransformers.

Studies in health technology and informatics Aug 22, 2024
Ontologies play a key role in representing and structuring domain knowledge. In the biomedical domain, the need for this type of representation is crucial for structuring, coding, and retrieving data. However, available ontologies do not encompass al...
Biological Ontologies Unified Medical Language System Neural Networks, Computer Humans Semantics
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Dementia Ontology Development to Facilitate Collection of High-Quality Dementia Data.

Studies in health technology and informatics Aug 22, 2024
The population of dementia patients is on the rise, as society undergoes rapid aging. This led to an expansion of dementia-related data. This study aims to develop a comprehensive dementia ontology to facilitate the collection and analysis of high-qu...
Biological Ontologies Humans Electronic Health Records Dementia
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OntoBridge Versus Traditional ETL: Enhancing Data Standardization into CDM Formats Using Ontologies Within the DATOS-CAT Project.

Studies in health technology and informatics Aug 22, 2024
Common Data Models (CDMs) enhance data exchange and integration across diverse sources, preserving semantics and context. Transforming local data into CDMs is typically cumbersome and resource-intensive, with limited reusability. This article compare...
Humans Information Storage and Retrieval Semantics Software Electronic Health Records Biological Ontologies
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Active Learning Pipeline to Identify Candidate Terms for a CDSS Ontology.

Studies in health technology and informatics Aug 22, 2024
Ontology is essential for achieving health information and information technology application interoperability in the biomedical fields and beyond. Traditionally, ontology construction is carried out manually by human domain experts (HDE). Here, we e...
Biological Ontologies Terminology as Topic Vocabulary, Controlled Problem-Based Learning Humans Supervised Machine Learning
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