AI Medical Compendium Journal:
Journal of biomedical semantics

Showing 1 to 10 of 193 articles

Unveiling differential adverse event profiles in vaccines via LLM text embeddings and ontology semantic analysis.

Journal of biomedical semantics
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...

Sentences, entities, and keyphrases extraction from consumer health forums using multi-task learning.

Journal of biomedical semantics
PURPOSE: Online consumer health forums offer an alternative source of health-related information for internet users seeking specific details that may not be readily available through articles or other one-way communication channels. However, the effe...

Digital evolution: Novo Nordisk's shift to ontology-based data management.

Journal of biomedical semantics
The amount of biomedical data is growing, and managing it is increasingly challenging. While Findable, Accessible, Interoperable and Reusable (FAIR) data principles provide guidance, their adoption has proven difficult, especially in larger enterpris...

New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern.

Journal of biomedical semantics
BACKGROUND: There is a new framework from the United States government for screening synthetic nucleic acids. Beginning in October of 2026, it calls for the screening of sequences 50 nucleotides or greater in length that are known to contribute to pa...

Annotation of epilepsy clinic letters for natural language processing.

Journal of biomedical semantics
BACKGROUND: Natural language processing (NLP) is increasingly being used to extract structured information from unstructured text to assist clinical decision-making and aid healthcare research. The availability of expert-annotated documents for the d...

An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology.

Journal of biomedical semantics
Automatic disease progression prediction models require large amounts of training data, which are seldom available, especially when it comes to rare diseases. A possible solution is to integrate data from different medical centres. Nevertheless, vari...

Concretizing plan specifications as realizables within the OBO foundry.

Journal of biomedical semantics
BACKGROUND: Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specification as a process in which a realizable entity that concretizes the plan specification, a "realizable concretizat...

Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models.

Journal of biomedical semantics
BACKGROUND: Vaccines have revolutionized public health by providing protection against infectious diseases. They stimulate the immune system and generate memory cells to defend against targeted diseases. Clinical trials evaluate vaccine performance, ...

Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis.

Journal of biomedical semantics
BACKGROUND: The exploration of cancer vaccines has yielded a multitude of studies, resulting in a diverse collection of information. The heterogeneity of cancer vaccine data significantly impedes effective integration and analysis. While CanVaxKB ser...

Explanatory argumentation in natural language for correct and incorrect medical diagnoses.

Journal of biomedical semantics
BACKGROUND: A huge amount of research is carried out nowadays in Artificial Intelligence to propose automated ways to analyse medical data with the aim to support doctors in delivering medical diagnoses. However, a main issue of these approaches is t...