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Biological Ontologies

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Hypothesis generation for rare and undiagnosed diseases through clustering and classifying time-versioned biological ontologies.

PloS one
Rare diseases affect 1-in-10 people in the United States and despite increased genetic testing, up to half never receive a diagnosis. Even when using advanced genome sequencing platforms to discover variants, if there is no connection between the var...

Core reference ontology for individualized exercise prescription.

Scientific data
"Exercise is medicine" emphasizes personalized prescriptions for better efficacy. Current guidelines need more support for personalized prescriptions, posing scientific challenges. Facing those challenges, we gathered data from established guidelines...

An Automatic and End-to-End System for Rare Disease Knowledge Graph Construction Based on Ontology-Enhanced Large Language Models: Development Study.

JMIR medical informatics
BACKGROUND: Rare diseases affect millions worldwide but sometimes face limited research focus individually due to low prevalence. Many rare diseases do not have specific International Classification of Diseases, Ninth Edition (ICD-9) and Tenth Editio...

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...

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...

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 ...

Leveraging Transformers-based models and linked data for deep phenotyping in radiology.

Computer methods and programs in biomedicine
BACKGROUND AND OBJECTIVE: Despite significant investments in the normalization and the standardization of Electronic Health Records (EHRs), free text is still the rule rather than the exception in clinical notes. The use of free text has implications...

An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets.

Scientific data
Although rare diseases (RDs) affect over 260 million individuals worldwide, low data quality and scarcity challenge effective care and research. This work aims to harmonise the Common Data Set by European Rare Disease Registry Infrastructure, Health ...

GNOme, an ontology for glycan naming and subsumption.

Analytical and bioanalytical chemistry
While GlyTouCan provides stable identifiers for referencing glycan structures, they are not organized semantically. GNOme, a glycan naming and subsumption ontology and a member of the OBOFoundry, organizes GlyTouCan accessions for automated reasoning...

An Ontology for Digital Medicine Outcomes: Development of the Digital Medicine Outcomes Value Set (DOVeS).

JMIR medical informatics
BACKGROUND: Over the last 10-15 years, US health care and the practice of medicine itself have been transformed by a proliferation of digital medicine and digital therapeutic products (collectively, digital health tools [DHTs]). While a number of DHT...