AIMC Topic: Biological Ontologies

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Ontology-based integration and querying of heterogeneous rare disease data sources - POLVAS perspective.

Computers in biology and medicine
The integration of rare disease medical databases belonging to different countries is an important problem, as a large number of observations are required for reliable statistical inference of patient data in order to facilitate clinical research. Su...

Definition of reproductive structures in Eucalyptus for phenological data collection.

International journal of biometeorology
In an era where global climate change is shifting plant phenology, global meta-analyses of multiple species are required more than ever. Common language or references for enhanced data compatibility are key for such analyses. Although the Plant Pheno...

simona: a comprehensive R package for semantic similarity analysis on bio-ontologies.

BMC genomics
BACKGROUND: Bio-ontologies are keys in structuring complex biological information for effective data integration and knowledge representation. Semantic similarity analysis on bio-ontologies quantitatively assesses the degree of similarity between bio...

Special supplement issue on quality assurance and enrichment of biological and biomedical ontologies and terminologies.

BMC medical informatics and decision making
Ontologies and terminologies serve as the backbone of knowledge representation in biomedical domains, facilitating data integration, interoperability, and semantic understanding across diverse applications. However, the quality assurance and enrichme...

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, ...

An ontology-based tool for modeling and documenting events in neurosurgery.

BMC medical informatics and decision making
BACKGROUND: Intraoperative neurophysiological monitoring (IOM) plays a pivotal role in enhancing patient safety during neurosurgical procedures. This vital technique involves the continuous measurement of evoked potentials to provide early warnings a...

Predicting Future Disorders via Temporal Knowledge Graphs and Medical Ontologies.

IEEE journal of biomedical and health informatics
Despite the vast potential for insights and value present in Electronic Health Records (EHRs), it is challenging to fully leverage all the available information, particularly that contained in the free-text data written by clinicians describing the h...

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...