AIMC Topic: Biological Ontologies

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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
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...

Ontology-Based Healthcare Named Entity Recognition from Twitter Messages Using a Recurrent Neural Network Approach.

International journal of environmental research and public health
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...

Wikidata: A large-scale collaborative ontological medical database.

Journal of biomedical informatics
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...

Ontology based mining of pathogen-disease associations from literature.

Journal of biomedical semantics
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...

Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective.

Yearbook of medical informatics
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...

Architecture and usability of OntoKeeper, an ontology evaluation tool.

BMC medical informatics and decision making
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...

ROBOT: A Tool for Automating Ontology Workflows.

BMC bioinformatics
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...

Large-Scale Coarse-to-Fine Object Retrieval Ontology and Deep Local Multitask Learning.

Computational intelligence and neuroscience
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...

PhenPath: a tool for characterizing biological functions underlying different phenotypes.

BMC genomics
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...