AIMC Topic: 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...
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...
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...
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 ...
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...
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...
Evaluation of an ontology-based system for computerized cognitive rehabilitation.
International journal of medical informatics
Apr 21, 2018
OBJECTIVES: This paper describes the results of a randomized clinical trial about the effectiveness of a computerized rehabilitation treatment on a sample of 31 patients affected by Parkinson disease.
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
A critical issue in the usage of cancer drugs is its association with various adverse events (AEs) in some, but not all, patients. The National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE) is a controlled terminology ...
ProvCaRe Semantic Provenance Knowledgebase: Evaluating Scientific Reproducibility of Research Studies.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
Scientific reproducibility is critical for biomedical research as it enables us to advance science by building on previous results, helps ensure the success of increasingly expensive drug trials, and allows funding agencies to make informed decisions...
Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use ...
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