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DEXTER: Disease-Expression Relation Extraction from Text
2018
Database: The Journal of Biological Databases and Curation
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In this work, we describe an automated text-mining tool, Disease-Expression Relation Extraction from Text (DEXTER) to extract information from literature on gene and microRNA expression in the context ...
Also, to demonstrate the ability to extract rich expression information in different disease-related scenarios, we used DEXTER to extract information on differential V C The Author(s) expression information ...
In this work, we describe an automated text-mining tool, DEXTER to extract information on gene/microRNA expression in the context of diseases. ...
doi:10.1093/database/bay045
pmid:29860481
pmcid:PMC6007211
fatcat:fvq3m7lzlfgsva3q36t4actwlq
Data extraction for epidemiological research (DExtER): a novel tool for automated clinical epidemiology studies
2020
European Journal of Epidemiology
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The basis of DExtER relies on principles of extract, transform and load processes. ...
from datasets for research purposes. ...
and supervision provided by Dr Behzad Bordbar, previously a senior lecturer and Dr Ronan Ryan, previously a research fellow at University of Birmingham, during the initial phase of the development of DExtER ...
doi:10.1007/s10654-020-00677-6
pmid:32856160
fatcat:3m7fhzobgbbrljnsmy2jce4tvi
Deep functional synthesis: a machine learning approach to gene functional enrichment
[article]
2019
bioRxiv
pre-print
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Here we present an alternative machine learning approach, Deep Functional Synthesis (DeepSyn), which moves beyond gene function databases to dynamically infer the functions of a gene set from its associated ...
including drug target identification, gene set functional enrichment, and disease gene prediction. ...
DeepSyn is queried with a set of genes, from which it returns the most relevant functions, diseases, and drugs extracted from the knowledge graph. ...
doi:10.1101/824086
fatcat:yq2rx6qx2racbkv4fpvv3mavoe
GLAD4U: deriving and prioritizing gene lists from PubMed literature
2012
BMC Genomics
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Answering questions such as "Which genes are related to breast cancer?" ...
The quality of gene lists created by GLAD4U for three Gene Ontology (GO) terms and three disease terms was assessed using corresponding "gold standard" lists curated in public databases. ...
All performance values are expressed in the text as mean ± standard deviation.
Web implementation The GLAD4U user interface was developed in HTML and PHP languages. ...
doi:10.1186/1471-2164-13-s8-s20
pmid:23282288
pmcid:PMC3535723
fatcat:mxi3lpcl3fdwtbpg7si6bvmrlm
Large Scale Advanced Data Analytics on Skin Conditions from Genotype to Phenotype
2018
Informatics
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These conditions have been selected based on reasoning of big scale UCSF patient data of 527,273 females from 2011 to 2017, and related publications from 2000 to 2017 regarding skin conditions. ...
The selected conditions have been confirmed with experts in the field from different research centers and hospitals. ...
As a first step, we extracted a group of genes for each skin conditions from Gene expression Omnibus (GEO). ...
doi:10.3390/informatics5040039
fatcat:echtoi3d7jhejfiae3eehqdp6a
Untangling the complexity of multimorbidity with machine learning
2020
Mechanisms of Ageing and Development
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Understanding its determinants and impact is proving to be a challenge yet it offers new opportunities for research to go beyond the study of diseases in isolation. ...
We discuss the challenges and opportunities of machine learning to identify likely causal links between previously poorly understood disease associations while giving an estimate of the uncertainty on ...
In addition to disease clusters, a similar effect can exist for their expressions, i.e., the expression of a particular disease cluster in a patient, can reduce the risk of the expression of another disease ...
doi:10.1016/j.mad.2020.111325
pmid:32768443
pmcid:PMC7493712
fatcat:cztvlpkzozcizdi5lbbh4peny4
Whole genome expression profiling of the medial and lateral substantia nigra in Parkinson's disease
2006
Neurogenetics
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We have used brain tissue from clinically well-documented and neuropathologically confirmed cases of sporadic Parkinson's disease to establish the transcriptomic expression profile of the medial and lateral ...
A large number of differentially regulated expressed sequence tags were also identified. ...
This work was funded through a programme grant from the UK Parkinson's Disease Society. ...
doi:10.1007/s10048-005-0020-2
pmid:16344956
fatcat:a55cglgij5bf7ht3c4gyadutz4
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
[article]
2016
bioRxiv
pre-print
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Next, we identified network patterns that distinguish treatments from non-treatments. Then we predicted the probability of treatment for 209,168 compound–disease pairs (http://het.io/repurpose). ...
Data was integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects ...
Anatomy-expresses-Gene edges were extracted from Bgee and TISSUES [116] [117] [118] . ...
doi:10.1101/087619
fatcat:drln54if6baajkxj3knmc2b5cq
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
2017
eLife
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Next, we identified network patterns that distinguish treatments from non-treatments. Then, we predicted the probability of treatment for 209,168 compound–disease pairs (het.io/repurpose). ...
Data were integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects ...
DISEASES integrates evidence of association from text mining, curated catalogs, and experimental data . Associations from DISEASES with integrated scores ! ...
doi:10.7554/elife.26726
pmid:28936969
pmcid:PMC5640425
fatcat:4brx7dtpo5eznlgygn4a4aqz4m
Mitochondrial proteomics as a selective tool for unraveling Parkinson's disease pathogenesis
2010
Espert Review of Proteomics
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A related challenge, therefore, entails the extraction of meaningful information from the large datasets that mitochondrial proteomics continuously produce. ...
A u t h o r P r o o f Review Pienaar, Dexter & Burkhard Another MAO-B inhibitor, selegiline, differs from rasagiline molecularly and pharmacologically. ...
pathology related to sporadic Parkinson's disease. Neurobiol. Aging 24, 197-211 (2003 ...
doi:10.1586/epr.10.8
pmid:20377388
fatcat:3esc7j3dobdijfmah6wkvfv46q
Review of the effects of soft robotic gloves for activity-based rehabilitation in individuals with reduced hand function and manual dexterity following a neurological event
2020
Journal of Rehabilitation and Assistive Technologies Engineering
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Despite the heterogeneity across studies, soft robotic gloves stand out as a safe and promising technology to improve hand- and finger-related dexterity and functional performance. ...
A total of 272 titles, abstracts, and keywords were initially retrieved, and data were extracted out of 13 articles. ...
Acknowledgement CEP holds a scholarship from INSPIRE and the School of Rehabilitation (Universit e de Montr eal) and DHG holds a senior research salary award from the Fonds de la recherche du Qu ebec - ...
doi:10.1177/2055668320918130
pmid:32435506
pmcid:PMC7223210
fatcat:4rkaaxedozdxtc6pskiavkn3jy
Precision annotation of digital samples in NCBI's gene expression omnibus
2017
Scientific Data
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The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. ...
However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. ...
gene signatures of disease by meta-analysis of gene expression. ...
doi:10.1038/sdata.2017.125
pmid:28925997
pmcid:PMC5604135
fatcat:2bzcq5qvzfe3ffob3jhxniitem
DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx
2015
Journal of Biomedical Informatics
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Natural language processing (NLP) techniques have been developed to extract clinical information from free text. ...
In Electronic Health Records (EHRs), much of valuable information regarding patients' conditions is embedded in free text format. ...
Acknowledgments This work was supported in part by the agency for healthcare research and quality R01 HS19818-01, grant from the office of the vice president for research at IUPUI and a joint funding from ...
doi:10.1016/j.jbi.2015.02.010
pmid:25791500
pmcid:PMC5863758
fatcat:connw37ws5fdjp3kxmx3kvwija
On Crowd-verification of Biological Networks
2013
Bioinformatics and Biology Insights
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The resulting network models will represent the current status of biological knowledge within the defined boundaries, here processes related to human lung disease. ...
Web-based graphical interfaces allow visualization of causal and correlative biological relationships represented using Biological Expression Language (BEL). ...
Acknowledgements The authors express their gratitude to Vincenzo Belcastro, Mark Ciapka, and Ryan Todd for their invaluable input while discussing the challenge and for the design of the website, Filipe ...
doi:10.4137/bbi.s12932
pmid:24151423
pmcid:PMC3798292
fatcat:yrb7vcywhngz3ebqk3xmlnjke4
November Meeting. Gifts to the Cabinet; Morton Dexter; Contemporary Opinion on the Howes; Parliament and the Howes; The Mauduit Pamphlets; Hollis's "Tractate on Church Music"; Letters of John Bridge and Emmanuel Altham; Additional Belcher Papers, 1732-1749; Mrs. Stevenson to Thomas Sewall, 1837, 1840
1910
Proceedings of the Massachusetts Historical Society
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Kippis,
and adds extracts from their letters. ...
The following further extract from General Robertson's evi dence (p. 325) relates to the same topic: Q. You have said there was a great deal of plundering; will you ascertain where and when? A. ...
Clipping from the London Chronicle, July 3, 1779, signed "A. B.," in defence of Galloway. nerves. ...
fatcat:l5ybphdqzngbjgvzb72563ttdi
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