AIMC Topic: Biological Ontologies

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Biomedical ontology alignment: an approach based on representation learning.

Journal of biomedical semantics Aug 15, 2018
BACKGROUND: While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering...
Machine Learning Biological Ontologies
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EAPB: entropy-aware path-based metric for ontology quality.

Journal of biomedical semantics Aug 10, 2018
BACKGROUND: Entropy has become increasingly popular in computer science and information theory because it can be used to measure the predictability and redundancy of knowledge bases, especially ontologies. However, current entropy applications that e...
Biological Ontologies Entropy Humans Communicable Diseases
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Evaluating semantic relations in neural word embeddings with biomedical and general domain knowledge bases.

BMC medical informatics and decision making Jul 23, 2018
BACKGROUND: In the past few years, neural word embeddings have been widely used in text mining. However, the vector representations of word embeddings mostly act as a black box in downstream applications using them, thereby limiting their interpretab...
Unified Medical Language System Biological Ontologies Natural Language Processing Knowledge Bases Data Mining Semantics
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CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.

BMC bioinformatics Jul 16, 2018
BACKGROUND: Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associated repositories, leading to a ...
Humans Internet Metadata Software Algorithms Biological Ontologies
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Toward a standard ontology of surgical process models.

International journal of computer assisted radiology and surgery Jul 13, 2018
PURPOSE: The development of common ontologies has recently been identified as one of the key challenges in the emerging field of surgical data science (SDS). However, past and existing initiatives in the domain of surgery have mainly been focussing o...
Models, Anatomic Minimally Invasive Surgical Procedures Humans Biological Ontologies Europe Pattern Recognition, Automated International Cooperation
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From lexical regularities to axiomatic patterns for the quality assurance of biomedical terminologies and ontologies.

Journal of biomedical informatics Jun 14, 2018
Ontologies and terminologies have been identified as key resources for the achievement of semantic interoperability in biomedical domains. The development of ontologies is performed as a joint work by domain experts and knowledge engineers. The maint...
Computational Biology Cluster Analysis Natural Language Processing Quality Control Software Biological Ontologies Language Reproducibility of Results Medical Informatics Pattern Recognition, Automated Algorithms Terminology as Topic Programming Languages Systematized Nomenclature of Medicine
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Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs.

Journal of biomedical semantics Jun 7, 2018
BACKGROUND: Adverse drug reactions (ADRs), also called as drug adverse events (AEs), are reported in the FDA drug labels; however, it is a big challenge to properly retrieve and analyze the ADRs and their potential relationships from textual data. Pr...
Biological Ontologies Peripheral Nervous System Diseases Data Mining Drug-Related Side Effects and Adverse Reactions
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Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.

Journal of biomedical informatics May 28, 2018
In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of "complex") in an ontology are more likely to exhibit errors than other concepts. Thus, such complex concepts often ...
Electronic Data Processing Systematized Nomenclature of Medicine United States National Cancer Institute (U.S.) Vocabulary, Controlled Biological Ontologies
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Querying archetype-based EHRs by search ontology-based XPath engineering.

Journal of biomedical semantics May 11, 2018
BACKGROUND: Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that le...
Data Mining Software Electronic Health Records Biological Ontologies
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Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.

Journal of biomedical semantics May 9, 2018
BACKGROUND: Prompted by the frequency of concomitant use of prescription drugs with natural products, and the lack of knowledge regarding the impact of pharmacokinetic-based natural product-drug interactions (PK-NPDIs), the United States National Cen...
Biological Ontologies Biological Products Drug Interactions
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