AIMC Topic: Biological Ontologies

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Ontology based mining of pathogen-disease associations from literature.

Journal of biomedical semantics Sep 18, 2019
BACKGROUND: Infectious diseases claim millions of lives especially in the developing countries each year. Identification of causative pathogens accurately and rapidly plays a key role in the success of treatment. To support infectious disease researc...
Internet Data Mining Biological Ontologies Communicable Diseases
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Formal Medical Knowledge Representation Supports Deep Learning Algorithms, Bioinformatics Pipelines, Genomics Data Analysis, and Big Data Processes.

Yearbook of medical informatics Aug 16, 2019
OBJECTIVE: To select, present, and summarize the best papers published in 2018 in the field of Knowledge Representation and Management (KRM).
Genetic Association Studies Computational Biology Big Data Genomics Biological Ontologies Knowledge Management Data Mining Semantics Data Analysis Deep Learning Artificial Intelligence
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Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective.

Yearbook of medical informatics Aug 16, 2019
OBJECTIVES: There exists a communication gap between the biomedical informatics community on one side and the computer science/artificial intelligence community on the other side regarding the meaning of the terms "semantic integration" and "knowledg...
Humans Medical Informatics Common Data Elements Biological Ontologies Knowledge Management Semantic Web Interdisciplinary Communication Neoplasms Data Management Artificial Intelligence Biomedical Research
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Architecture and usability of OntoKeeper, an ontology evaluation tool.

BMC medical informatics and decision making Aug 8, 2019
BACKGROUND: The existing community-wide bodies of biomedical ontologies are known to contain quality and content problems. Past research has revealed various errors related to their semantics and logical structure. Automated tools may help to ease th...
Software Semantics Biological Ontologies Humans Knowledge
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ROBOT: A Tool for Automating Ontology Workflows.

BMC bioinformatics Jul 29, 2019
BACKGROUND: Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and appl...
Humans Programming Languages Software Biological Ontologies Workflow Disease
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Large-Scale Coarse-to-Fine Object Retrieval Ontology and Deep Local Multitask Learning.

Computational intelligence and neuroscience Jul 18, 2019
Object retrieval plays an increasingly important role in video surveillance, digital marketing, e-commerce, etc. It is facing challenges such as large-scale datasets, imbalanced data, viewpoint, cluster background, and fine-grained details (attribute...
Computer Simulation Biological Ontologies Humans Deep Learning Problem Solving Neural Networks, Computer Resource Allocation
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PhenPath: a tool for characterizing biological functions underlying different phenotypes.

BMC genomics Jul 16, 2019
BACKGROUND: Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For...
Biological Ontologies Disease Computational Biology Databases, Genetic Humans Phenotype
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Phenotype annotation with the ontology of microbial phenotypes (OMP).

Journal of biomedical semantics Jul 15, 2019
BACKGROUND: Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and conserved functions beyond m...
Phenotype Metadata Data Curation Microbiology Biological Ontologies
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HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology.

Journal of biomedical informatics Jun 27, 2019
BACKGROUND: In precision medicine, deep phenotyping is defined as the precise and comprehensive analysis of phenotypic abnormalities, aiming to acquire a better understanding of the natural history of a disease and its genotype-phenotype associations...
Rare Diseases Computer Simulation Semantics Humans Genetic Association Studies Machine Learning Databases, Genetic Precision Medicine Models, Statistical Algorithms Electronic Health Records Phenotype ROC Curve Area Under Curve Medical Informatics Biological Ontologies
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Predicting instances of pathway ontology classes for pathway integration.

Journal of biomedical semantics Jun 13, 2019
BACKGROUND: To improve the outcomes of biological pathway analysis, a better way of integrating pathway data is needed. Ontologies can be used to organize data from disparate sources, and we leverage the Pathway Ontology as a unifying ontology for or...
Neural Networks, Computer Biological Ontologies Supervised Machine Learning
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