AIMC Topic: Biological Ontologies

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Discovering associations between adverse drug events using pattern structures and ontologies.

Journal of biomedical semantics Aug 22, 2017
BACKGROUND: Patient data, such as electronic health records or adverse event reporting systems, constitute an essential resource for studying Adverse Drug Events (ADEs). We explore an original approach to identify frequently associated ADEs in subgro...
Biological Ontologies Pattern Recognition, Automated Drug-Related Side Effects and Adverse Reactions Humans Electronic Health Records Phenotype
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Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies.

Artificial intelligence in medicine Aug 14, 2017
OBJECTIVE: Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an on...
Software Humans Biological Ontologies Programming Languages Gene Ontology
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An ontology-driven tool for structured data acquisition using Web forms.

Journal of biomedical semantics Aug 1, 2017
BACKGROUND: Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decisio...
Information Storage and Retrieval Biological Ontologies Internet Software
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Towards a more molecular taxonomy of disease.

Journal of biomedical semantics Jul 27, 2017
BACKGROUND: Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understanding the degree to which we ca...
Disease Reproducibility of Results Humans Medical Subject Headings Biological Ontologies
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Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals.

Journal of medical Internet research Jul 24, 2017
BACKGROUND: Social networking services (SNSs) contain abundant information about the feelings, thoughts, interests, and patterns of behavior of adolescents that can be obtained by analyzing SNS postings. An ontology that expresses the shared concepts...
Data Mining Biological Ontologies Social Media Social Networking Adult Adolescent Depression Humans Young Adult
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Lightweight predicate extraction for patient-level cancer information and ontology development.

BMC medical informatics and decision making Jul 5, 2017
BACKGROUND: Knowledge engineering for ontological knowledgebases is resource and time intensive. To alleviate these issues, especially for novices, automated tools from the natural language domain can assist in the development process of ontologies. ...
Neoplasms Public Health Humans Biological Ontologies Natural Language Processing MedlinePlus
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Ontological interpretation of biomedical database content.

Journal of biomedical semantics Jun 26, 2017
BACKGROUND: Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambig...
Biological Ontologies Databases, Factual
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Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques.

Journal of biomedical semantics Jun 19, 2017
BACKGROUND: Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are r...
Biological Ontologies Semantic Web Computer Graphics Humans Disease
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NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

Journal of biomedical semantics Jun 7, 2017
BACKGROUND: Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across dispara...
United States Semantics National Institutes of Health (U.S.) Biological Ontologies
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Literature evidence in open targets - a target validation platform.

Journal of biomedical semantics Jun 6, 2017
BACKGROUND: We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-disease associations in docum...
Molecular Targeted Therapy Documentation Biological Ontologies Data Mining Reproducibility of Results Publications
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