AIMC Topic: Biological Ontologies

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

Journal of biomedical informatics Mar 14, 2016
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...
Quality Control Biological Ontologies
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Extracting drug-enzyme relation from literature as evidence for drug drug interaction.

Journal of biomedical semantics Mar 7, 2016
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....
Drug Interactions Data Mining Biological Ontologies Enzymes Protein Binding Pharmaceutical Preparations Machine Learning
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Vaccine and Drug Ontology Studies (VDOS 2014).

Journal of biomedical semantics Feb 25, 2016
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 (...
Biological Ontologies Pharmaceutical Preparations Vaccines
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OntoCR: A CEN/ISO-13606 clinical repository based on ontologies.

Journal of biomedical informatics Feb 18, 2016
OBJECTIVE: To design a new semantically interoperable clinical repository, based on ontologies, conforming to CEN/ISO 13606 standard.
Software Algorithms Humans Information Storage and Retrieval Semantics Systems Integration Systematized Nomenclature of Medicine Forms and Records Control Biological Ontologies Electronic Health Records Internet Programming Languages
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Ten Simple Rules for Selecting a Bio-ontology.

PLoS computational biology Feb 11, 2016
Humans Databases, Factual Computational Biology Biological Ontologies
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Semantic representation of reported measurements in radiology.

BMC medical informatics and decision making Jan 22, 2016
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...
Semantics Biological Ontologies Models, Theoretical Radiology Medical Informatics Applications Humans Image Processing, Computer-Assisted
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A Natural Language Interface Concordant with a Knowledge Base.

Computational intelligence and neuroscience Jan 21, 2016
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...
Biological Ontologies Geography Information Storage and Retrieval Semantics Knowledge Bases Humans Language Algorithms Natural Language Processing Databases, Factual
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Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

PloS one Dec 28, 2015
Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, al...
Semantics Biological Ontologies Vocabulary, Controlled Algorithms Heuristics Information Storage and Retrieval
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OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research.

Journal of biomedical semantics Dec 18, 2015
BACKGROUND: The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct representation of their metadata...
Biological Ontologies Data Curation Biostatistics Humans Software Epidemiologic Studies
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Special issue on bio-ontologies and phenotypes.

Journal of biomedical semantics Dec 17, 2015
The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems for Molecular Biology) conference in Bos...
Phenotype Humans Biological Ontologies
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