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pubmed_result.txt
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PMID- 25665127
OWN - NLM
STAT- In-Data-Review
DA - 20150210
LR - 20150219
IS - 1932-6203 (Electronic)
IS - 1932-6203 (Linking)
VI - 10
IP - 2
DP - 2015
TI - Knowledge Retrieval from PubMed Abstracts and Electronic Medical Records with the
Multiple Sclerosis Ontology.
PG - e0116718
LID - 10.1371/journal.pone.0116718 [doi]
AB - 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 Protege 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.
FAU - Malhotra, Ashutosh
AU - Malhotra A
AD - Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, 53754, Sankt Augustin, Germany.
FAU - Gundel, Michaela
AU - Gundel M
AD - Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, 53754, Sankt Augustin, Germany.
FAU - Rajput, Abdul Mateen
AU - Rajput AM
AD - Merck KGaA, Darmstadt, Germany.
FAU - Mevissen, Heinz-Theodor
AU - Mevissen HT
AD - Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, 53754, Sankt Augustin, Germany.
FAU - Saiz, Albert
AU - Saiz A
AD - MS Center, Department of Neurology, Hospital Clinic of Barcelona, Barcelona,
Spain; Center of Neuroimmunology, Institut d'investigacions Biomediques August Pi
i Sunyer (IDIBAPS), Barcelona, Spain.
FAU - Pastor, Xavier
AU - Pastor X
AD - Department of Medical Informatics, Hospital Clinic of Barcelona-University of
Barcelona, Barcelona, Spain.
FAU - Lozano-Rubi, Raimundo
AU - Lozano-Rubi R
AD - Department of Medical Informatics, Hospital Clinic of Barcelona-University of
Barcelona, Barcelona, Spain.
FAU - Martinez-Lapsicina, Elena H
AU - Martinez-Lapsicina EH
AD - Center of Neuroimmunology, Institut d'investigacions Biomediques August Pi i
Sunyer (IDIBAPS), Barcelona, Spain.
FAU - Zubizarreta, Irati
AU - Zubizarreta I
AD - Center of Neuroimmunology, Institut d'investigacions Biomediques August Pi i
Sunyer (IDIBAPS), Barcelona, Spain.
FAU - Mueller, Bernd
AU - Mueller B
AD - Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, 53754, Sankt Augustin, Germany.
FAU - Kotelnikova, Ekaterina
AU - Kotelnikova E
AD - Center of Neuroimmunology, Institut d'investigacions Biomediques August Pi i
Sunyer (IDIBAPS), Barcelona, Spain.
FAU - Toldo, Luca
AU - Toldo L
AD - Merck KGaA, Darmstadt, Germany.
FAU - Hofmann-Apitius, Martin
AU - Hofmann-Apitius M
AD - Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific
Computing, 53754, Sankt Augustin, Germany.
FAU - Villoslada, Pablo
AU - Villoslada P
AD - Center of Neuroimmunology, Institut d'investigacions Biomediques August Pi i
Sunyer (IDIBAPS), Barcelona, Spain.
LA - eng
PT - Journal Article
DEP - 20150209
PL - United States
TA - PLoS One
JT - PloS one
JID - 101285081
SB - IM
PMC - PMC4321837
OID - NLM: PMC4321837
EDAT- 2015/02/11 06:00
MHDA- 2015/02/11 06:00
CRDT- 2015/02/10 06:00
PHST- 2015 [ecollection]
PHST- 2014/05/18 [received]
PHST- 2014/12/13 [accepted]
PHST- 2015/02/09 [epublish]
AID - 10.1371/journal.pone.0116718 [doi]
AID - PONE-D-14-22133 [pii]
PST - epublish
SO - PLoS One. 2015 Feb 9;10(2):e0116718. doi: 10.1371/journal.pone.0116718.
eCollection 2015.
PMID- 25663561
OWN - NLM
STAT- Publisher
DA - 20150209
LR - 20150211
IS - 1612-4790 (Electronic)
DP - 2015 Feb 7
TI - How different spatial representations interact in virtual environments: the role
of mental frame syncing.
AB - This experiment is aimed at understanding how egocentric experiences, allocentric
viewpoint-dependent representations, and allocentric viewpoint-independent
representations interact when encoding and retrieving a spatial environment.
Although several cognitive theories have highlighted the interaction between
reference frames, it is less clear about the role of a real-time presentation of
allocentric viewpoint-dependent representation on the spatial organization of
information. Sixty participants were asked to navigate in two virtual cities to
memorize the position of one hidden object. Half of the participants had the
possibility to visualize the virtual city with an interactive aerial view. Then,
they were required to find the position of the object in three different
experimental conditions ("retrieval with an interactive aerial view" vs.
"retrieval on a map" vs. "retrieval without an interactive aerial view"). Results
revealed that participants were significantly more precise in retrieving the
position of the object when immersed in an egocentric experience with the
interactive aerial view. The retrieval of spatial information is facilitated by
the presence of the interactive aerial view of the city, since it provides a
real-time allocentric viewpoint-dependent representation. More participants with
high preference for using cardinal points tend to be more accurate when they were
asked to retrieve the position of the object on the map. As suggested by the
mental frame syncing hypothesis, the presence of an allocentric
viewpoint-dependent representation during the retrieval seems to ease the
imposition on a specific viewpoint on the stored abstract allocentric
viewpoint-independent representation. Our findings represent another significant
step toward the comprehension of the organization of spatial representations of
our environment.
FAU - Serino, Silvia
AU - Serino S
AD - Applied Technology for Neuro-Psychology Lab, IRCCS Istituto Auxologico Italiano,
Via Magnasco, 2, 20149, Milan, MI, Italy, [email protected].
FAU - Riva, Giuseppe
AU - Riva G
LA - ENG
PT - JOURNAL ARTICLE
DEP - 20150207
TA - Cogn Process
JT - Cognitive processing
JID - 101177984
EDAT- 2015/02/11 06:00
MHDA- 2015/02/11 06:00
CRDT- 2015/02/10 06:00
PHST- 2014/07/24 [received]
PHST- 2015/01/28 [accepted]
PHST- 2015/02/07 [aheadofprint]
AID - 10.1007/s10339-015-0646-4 [doi]
PST - aheadofprint
SO - Cogn Process. 2015 Feb 7.