AIMC Topic: Biological Ontologies

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Representing vision and blindness.

Journal of biomedical semantics
BACKGROUND: There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a variety of reasons. Blindness has ...

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.

Journal of biomedical semantics
BACKGROUND: The Centre for Therapeutic Target Validation (CTTV - https://www.targetvalidation.org/) was established to generate therapeutic target evidence from genome-scale experiments and analyses. CTTV aims to support the validity of therapeutic t...

Transitive closure of subsumption and causal relations in a large ontology of radiological diagnosis.

Journal of biomedical informatics
The Radiology Gamuts Ontology (RGO)-an ontology of diseases, interventions, and imaging findings-was developed to aid in decision support, education, and translational research in diagnostic radiology. The ontology defines a subsumption (is_a) relati...

Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

Journal of biomedical informatics
An Abstraction Network is a compact summary of an ontology's structure and content. In previous research, we showed that Abstraction Networks support quality assurance (QA) of biomedical ontologies. The development of an Abstraction Network and its a...

Extracting drug-enzyme relation from literature as evidence for drug drug interaction.

Journal of biomedical semantics
BACKGROUND: Information about drug-drug interactions (DDIs) is crucial for computational applications such as pharmacovigilance and drug repurposing. However, existing sources of DDIs have the problems of low coverage, low accuracy and low agreement....

Vaccine and Drug Ontology Studies (VDOS 2014).

Journal of biomedical semantics
The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat human and animal diseases. Work in both (...

Semantic representation of reported measurements in radiology.

BMC medical informatics and decision making
BACKGROUND: In radiology, a vast amount of diverse data is generated, and unstructured reporting is standard. Hence, much useful information is trapped in free-text form, and often lost in translation and transmission. One relevant source of free-tex...

A Natural Language Interface Concordant with a Knowledge Base.

Computational intelligence and neuroscience
The discordance between expressions interpretable by a natural language interface (NLI) system and those answerable by a knowledge base is a critical problem in the field of NLIs. In order to solve this discordance problem, this paper proposes a meth...