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Title: | Knowledge Retrieval from PubMed Abstracts and Electronic Medical Records with the Multiple Sclerosis Ontology |
Author: | Malhotra, Ashutosh Gündel, Michaela Rajput, Abdul Mateen Mevissen, Heinz-Theodor Saiz Hinarejos, Albert Pastor Durán, Xavier Lozano Rubí, Raimundo Martínez Lapiscina, Elena H. Zubizarreta, Irati Mueller, Bernd Kotelnikova, Ekaterina Toldo, Luca Hofmann Apitius, Martin Villoslada, Pablo |
Keywords: | MEDLINE Recursos electrònics en xarxa Esclerosi múltiple Informació científica i tècnica MEDLINE Computer network resources Multiple sclerosis Science and technical information |
Issue Date: | 9-Feb-2015 |
Publisher: | Public Library of Science (PLoS) |
Abstract: | Background In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS). Methods The 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, drug) into the text-mining tool SCAIView. We analyzed the EMRs from 624 patients with MS using the MS ontology dictionary in order to identify drug usage and comorbidities in MS. Testing competency questions and functional evaluation using F statistics further validated the usefulness of MS ontology. Results Validation of the lexicalized ontology by means of named entity recognition-based methods showed an adequate performance (F score = 0.73). The MS Ontology retrieved 80% of the genes associated with MS from scientific abstracts and identified additional pathways targeted by approved disease-modifying drugs (e.g. apoptosis pathways associated with mitoxantrone, rituximab and fingolimod). The analysis of the EMR from patients with MS identified current usage of disease modifying drugs and symptomatic therapy as well as comorbidities, which are in agreement with recent reports. Conclusion The MS Ontology provides a semantic framework that is able to automatically extract information from both scientific literature and EMR from patients with MS, revealing new pathogenesis insights as well as new clinical information. |
Note: | Reproducció del document publicat a: http://dx.doi.org/10.1371/journal.pone.0116718 |
It is part of: | PLoS One, 2015, vol. 10, num. 2 |
URI: | http://hdl.handle.net/2445/65484 |
Related resource: | http://dx.doi.org/10.1371/journal.pone.0116718 |
ISSN: | 1932-6203 |
Appears in Collections: | Articles publicats en revistes (Medicina) |
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