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Biological Ontologies

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Prioritising lexical patterns to increase axiomatisation in biomedical ontologies. The role of localisation and modularity.

Methods of information in medicine
INTRODUCTION: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".

Toward a view-oriented approach for aligning RDF-based biomedical repositories.

Methods of information in medicine
INTRODUCTION: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".

Enrichment Analysis and Deep Learning in Biomedical Ontology: Applications and Advancements.

Chinese medical sciences journal = Chung-kuo i hsueh k'o hsueh tsa chih
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
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
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
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 ...

Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology.

Database : the journal of biological databases and curation
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...

The text2term tool to map free-text descriptions of biomedical terms to ontologies.

Database : the journal of biological databases and curation
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...

Enhancing Arden-Syntax-Based Clinical Reasoning with Ontologies.

Studies in health technology and informatics
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...

Fine-tuning large language models for rare disease concept normalization.

Journal of the American Medical Informatics Association : JAMIA
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).