2015
DOI: 10.1371/journal.pone.0116718
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Knowledge Retrieval from PubMed Abstracts and Electronic Medical Records with the Multiple Sclerosis Ontology

Abstract: BackgroundIn order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS).MethodsThe MS Ontology was created using scientific literature and expert review under the Protégé OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining EMR. The MS Ontology was integrated with other ontologies and dictionaries (diseases/comorbidities, gene/protein, pathways,… Show more

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Cited by 29 publications
(21 citation statements)
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“…In order to screen out the kidney-tonifying herbal medicines with anti-aging effect, the names for the medicines of herbal data sets and the term “aging” were combined as the search terms in the field of theme, title and keywords in the two literature databases: Pubmed (http://www.ncbi.nlm.nih.gov) [18] and CBM (Chinese biomedical literature database, http://www.sinomed.ac.cn) [19], respectively. Kidney-tonifying herbal medicines with anti-aging effect were confirmed further by reading the research literatures, and then the base kidney-tonifying herbal medicines data sets (TKADS) with anti-aging effect were generated.…”
Section: Methodsmentioning
confidence: 99%
“…In order to screen out the kidney-tonifying herbal medicines with anti-aging effect, the names for the medicines of herbal data sets and the term “aging” were combined as the search terms in the field of theme, title and keywords in the two literature databases: Pubmed (http://www.ncbi.nlm.nih.gov) [18] and CBM (Chinese biomedical literature database, http://www.sinomed.ac.cn) [19], respectively. Kidney-tonifying herbal medicines with anti-aging effect were confirmed further by reading the research literatures, and then the base kidney-tonifying herbal medicines data sets (TKADS) with anti-aging effect were generated.…”
Section: Methodsmentioning
confidence: 99%
“…An ontology is a formal expression of the relationship between a set of concepts and their relationships in a specific field. As a method of expressing knowledge, ontologies have been widely used in various application fields, among which biomedicine is one of the most active areas of ontology applications [21,23]. PROTEGE [4] is a free and open-source ontology editor and a knowledge-based framework developed by the Stanford BioMedical Informatics Research Center.…”
Section: Clustering Analysis On Inspection Data In Text Formatmentioning
confidence: 99%
“…Whereas incorporating existing EMR variables is not informative for deriving brain volume measures, incorporation of NLP‐extracted variables is highly informative for deriving the Multiple Sclerosis Severity Score, a commonly used score in MS research . An MS ontology providing a semantic framework capable of automatically extract information from MS patients EMR has also been published …”
Section: Emr Research In the Era Of Big Datamentioning
confidence: 99%
“…34 An MS ontology providing a semantic framework capable of automatically extract information from MS patients EMR has also been published. 35 When developing algorithms to extract variables from unstructured data, it is important to carry out a validation step by manually reviewing a subset of notes. It is a laborious, but mandatory, process that will inform the researcher about the accuracy of the data that they are going to use.…”
Section: Automatic Data Extraction From Emrmentioning
confidence: 99%