AIMC Topic: Biological Ontologies

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Jointly Integrating VCF-Based Variants and OWL-Based Biomedical Ontologies in MongoDB.

IEEE/ACM transactions on computational biology and bioinformatics Nov 4, 2019
The development of the next-generation sequencing (NGS) technologies has led to massive amounts of VCF (Variant Call Format) files, which have been the standard formats developed with 1000 Genomes Project. At the same time, with the widespread use of...
Algorithms Genomics Humans High-Throughput Nucleotide Sequencing Semantics Biological Ontologies Databases, Genetic Programming Languages
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Analysis of risk factor domains in psychosis patient health records.

Journal of biomedical semantics Oct 31, 2019
BACKGROUND: Readmission after discharge from a hospital is disruptive and costly, regardless of the reason. However, it can be particularly problematic for psychiatric patients, so predicting which patients may be readmitted is critically important b...
Male Natural Language Processing Psychotic Disorders Data Mining Risk Factors Young Adult Electronic Health Records Female Biological Ontologies Humans Neural Networks, Computer
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Technical Note: Ontology-guided radiomics analysis workflow (O-RAW).

Medical physics Oct 25, 2019
PURPOSE: Radiomics is the process to automate tumor feature extraction from medical images. This has shown potential for quantifying the tumor phenotype and predicting treatment response. The three major challenges of radiomics research and clinical ...
Biological Ontologies Image Processing, Computer-Assisted Workflow
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Towards an ontology for soft robots: what is soft?

Bioinspiration & biomimetics Oct 25, 2019
The advent of soft robotics represents a profound change in the forms robots will take in the future. However, this revolutionary change has already yielded such a diverse collection of robots that attempts at defining this group do not reflect many ...
Elastic Modulus Humans Equipment Design Biological Ontologies Robotics
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Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung.

Journal of biomedical semantics Oct 24, 2019
BACKGROUND: Although the mouse is widely used to model human lung development, function, and disease, our understanding of the molecular mechanisms involved in alveolarization of the peripheral lung is incomplete. Recently, the Molecular Atlas of Lun...
Biological Ontologies Pulmonary Alveoli Humans Animals Mice
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Ontology patterns for the representation of quality changes of cells in time.

Journal of biomedical semantics Oct 16, 2019
BACKGROUND: Cell tracking experiments, based on time-lapse microscopy, have become an important tool in biomedical research. The goal is the reconstruction of cell migration patterns, shape and state changes, and, comprehensive genealogical informati...
Time Factors Biological Ontologies Cell Tracking
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PARS, a system combining semantic technologies with multiple criteria decision aiding for supporting antibiotic prescriptions.

Journal of biomedical informatics Oct 14, 2019
OBJECTIVE: Motivated by the well documented worldwide spread of adverse drug events, as well as the increased danger of antibiotic resistance (caused mainly by inappropriate prescribing and overuse), we propose a novel recommendation system for antib...
Decision Support Systems, Clinical Medical Informatics Machine Learning Anti-Bacterial Agents Drug Prescriptions Inappropriate Prescribing Semantics Biological Ontologies Humans
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Aggregating the syntactic and semantic similarity of healthcare data towards their transformation to HL7 FHIR through ontology matching.

International journal of medical informatics Oct 5, 2019
BACKGROUND AND OBJECTIVE: Healthcare systems deal with multiple challenges in releasing information from data silos, finding it almost impossible to be implemented, maintained and upgraded, with difficulties ranging in the technical, security and hum...
Vocabulary, Controlled Systems Integration Health Level Seven Semantics Electronic Health Records Biological Ontologies Information Dissemination Algorithms Humans Delivery of Health Care
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Ontology-Based Healthcare Named Entity Recognition from Twitter Messages Using a Recurrent Neural Network Approach.

International journal of environmental research and public health Sep 27, 2019
Named Entity Recognition (NER) in the healthcare domain involves identifying and categorizing disease, drugs, and symptoms for biosurveillance, extracting their related properties and activities, and identifying adverse drug events appearing in texts...
Information Storage and Retrieval Biological Ontologies Unified Medical Language System Algorithms Humans Social Media Neural Networks, Computer
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Wikidata: A large-scale collaborative ontological medical database.

Journal of biomedical informatics Sep 23, 2019
Created in October 2012, Wikidata is a large-scale, human-readable, machine-readable, multilingual, multidisciplinary, centralized, editable, structured, and linked knowledge-base with an increasing diversity of use cases. Here, we raise awareness of...
Internet Semantics Databases, Factual Electronic Health Records Humans Database Management Systems Biological Ontologies Multilingualism
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