AIMC Topic: Biological Ontologies
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OntoTiger: a platform of ontology-based application tools for integrative biomedical exploration.
Nucleic acids research
Jul 7, 2025
Biomedical ontologies, such as Gene Ontology (GO), Disease Ontology (DO), and the Human Phenotype Ontology (HPO), have been extensively applied to characterize molecular roles and their semantic relationships in biomedical research and clinical pract...
Unveiling differential adverse event profiles in vaccines via LLM text embeddings and ontology semantic analysis.
Journal of biomedical semantics
May 23, 2025
BACKGROUND: Vaccines are crucial for preventing infectious diseases; however, they may also be associated with adverse events (AEs). Conventional analysis of vaccine AEs relies on manual review and assignment of AEs to terms in terminology or ontolog...
Adopting Ontologies: Sustainable Research Reusing the Biomedical Resource Ontology.
Studies in health technology and informatics
May 15, 2025
The FAIR principles have been adopted across scientific disciplines to promote sustainable use of data. Ontologies play a crucial role in facilitating data interoperability and reusability. However, existing ontologies may become outdated or redundan...
[Analysis of the ontology construction approach to acupoint anatomy].
Zhongguo zhen jiu = Chinese acupuncture & moxibustion
May 12, 2025
Through the investigation of relevant literature, the concepts, methods, languages and tools of ontology were explored, and the suitable methods and tools for the ontology construction of acupoint anatomy were selected. The current mainstream anatomi...
OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem.
Bioinformatics (Oxford, England)
May 6, 2025
SUMMARY: The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently, there has be...
Enrichment Analysis and Deep Learning in Biomedical Ontology: Applications and Advancements.
Chinese medical sciences journal = Chung-kuo i hsueh k'o hsueh tsa chih
Mar 31, 2025
Biomedical big data, characterized by its massive scale, multi-dimensionality, and heterogeneity, offers novel perspectives for disease research, elucidates biological principles, and simultaneously prompts changes in related research methodologies. ...
Post-composing ontology terms for efficient phenotyping in plant breeding.
Database : the journal of biological databases and curation
Mar 21, 2025
Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on...
The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.
Genetics
Mar 17, 2025
Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype...
A change language for ontologies and knowledge graphs.
Database : the journal of biological databases and curation
Jan 22, 2025
Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new ...
The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization.
Journal of veterinary internal medicine
Jan 1, 2025
BACKGROUND: Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support advancement in...
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