AIMC Topic: Biological Ontologies

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A prototype ETL pipeline that uses HL7 FHIR RDF resources when deploying pure functions to enrich knowledge graph patient data.

Journal of biomedical semantics
BACKGROUND: For clinical care and research, knowledge graphs with patient data can be enriched by extracting parameters from a knowledge graph and then using them as inputs to compute new patient features with pure functions. Systematic and transpare...

Semantic web-based ontology: a comprehensive framework for cardiovascular knowledge representation.

BMC cardiovascular disorders
In the healthcare industry, the Semantic Web offers to manage a huge amount of medical data which is machine-readable and machine-understandable as well. This domain incorporates ontologies, linked data, and semantic web technologies to promote healt...

A fourfold pathogen reference ontology suite.

Journal of biomedical semantics
BACKGROUND: Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus I...

Jackalope Plus tool for post-coordination, ontology development, and precise mapping in observational health studies.

Scientific reports
Accurate mapping of complex health data to the OMOP CDM while preserving clinical nuance remains a challenge. We introduce Jackalope Plus, a novel tool leveraging SNOMED CT post-coordination and a GPT-4o mini LLM, to significantly enhance the precisi...

Ontology enrichment using a large language model: Applying lexical, semantic, and knowledge network-based similarity for concept placement.

Journal of biomedical informatics
OBJECTIVE: Ontologies are essential for representing the knowledge of a domain. To make ontologies useful, they must encompass a comprehensive domain view. To achieve ontology enrichment, there is a need to discover new concepts to be added, either b...

Enhancing the Accuracy of Human Phenotype Ontology Identification: Comparative Evaluation of Multimodal Large Language Models.

Journal of medical Internet research
BACKGROUND: Identifying Human Phenotype Ontology (HPO) terms is crucial for diagnosing and managing rare diseases. However, clinicians, especially junior physicians, often face challenges due to the complexity of describing patient phenotypes accurat...

Development and evaluation of the COntextualised and Personalised Physical activity and Exercise Recommendations (COPPER) Ontology.

The international journal of behavioral nutrition and physical activity
BACKGROUND: Personalised recommendations for action and coping plans for physical activity (PA) may reduce user burden and increase plan quality. Ontologies are a promising alternative to existing black-box approaches for creating such personalised r...

Ontology accelerates few-shot learning capability of large language model: A study in extraction of drug efficacy in a rare pediatric epilepsy.

International journal of medical informatics
OBJECTIVE: Dravet Syndrome (DS) is a developmental and epileptic encephalopathy that is characterized by severe, prolonged motor seizures and high resistance to multiple antiseizure medications (ASMs) with multiple comorbidities. Evaluating the effic...

Knowledge Representation and Management: 2023 Highlights and the Rise of Knowledge Graph Embeddings.

Yearbook of medical informatics
OBJECTIVES: We aim to identify, select, and summarize the best papers published in 2023 for the Knowledge Representation and Management (KRM) section of the International Medical Informatics Association (IMIA) Yearbook.

Human Phenotype Ontology Annotations for Rare Congenital Conditions: Application to Arthrogryposis Multiplex Congenita.

American journal of medical genetics. Part A
Arthrogryposis multiplex congenita (AMC) represents a large, rare group of congenital conditions. This study addressed major challenges in AMC research posed by the lack of systematic frameworks for data collection and the use of inconsistent termino...