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DEXTER: Disease-Expression Relation Extraction from Text

Samir Gupta, Hayley Dingerdissen, Karen E Ross, Yu Hu, Cathy H Wu, Raja Mazumder, K Vijay-Shanker
2018 Database: The Journal of Biological Databases and Curation  
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

Krishna Margadhamane Gokhale, Joht Singh Chandan, Konstantinos Toulis, Georgios Gkoutos, Peter Tino, Krishnarajah Nirantharakumar
2020 European Journal of Epidemiology  
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]

Sheng Wang, Jianzhu Ma, Samson Fong, Stefano Rensi, Jiawei Han, Jian Peng, Dexter Pratt, Russ Altman, Trey Ideker
2019 bioRxiv   pre-print
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

Jérôme Jourquin, Dexter Duncan, Zhiao Shi, Bing Zhang
2012 BMC Genomics  
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

Maryam Panahiazar, Darya Fadavi, Jihad Aljabban, Laraib Safeer, Imad Aljabban, Dexter Hadley
2018 Informatics  
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

Abdelaali Hassaine, Gholamreza Salimi-Khorshidi, Dexter Canoy, Kazem Rahimi
2020 Mechanisms of Ageing and Development  
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

L. B. Moran, D. C. Duke, M. Deprez, D. T. Dexter, R. K. B. Pearce, M. B. Graeber
2006 Neurogenetics  
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]

Daniel S. Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L. Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E. Baranzini
2016 bioRxiv   pre-print
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

Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
2017 eLife  
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

Ilse Sanet Pienaar, David Trevor Dexter, Pierre Roland Burkhard
2010 Espert Review of Proteomics  
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

Camille E Proulx, Myrka Beaulac, Mélissa David, Catryne Deguire, Catherine Haché, Florian Klug, Mario Kupnik, Johanne Higgins, Dany H. Gagnon
2020 Journal of Rehabilitation and Assistive Technologies Engineering  
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

Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D. Azad, Mohamad O. Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran (+7 others)
2017 Scientific Data  
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

Saeed Mehrabi, Anand Krishnan, Sunghwan Sohn, Alexandra M. Roch, Heidi Schmidt, Joe Kesterson, Chris Beesley, Paul Dexter, C. Max Schmidt, Hongfang Liu, Mathew Palakal
2015 Journal of Biomedical Informatics  
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

Sam Ansari, Jean Binder, Stephanie Boue, Anselmo Di Fabio, William Hayes, Julia Hoeng, Anita Iskandar, Robin Kleiman, Raquel Norel, Bruce O'neel, Manuel C. Peitsch, Carine Poussin (+5 others)
2013 Bioinformatics and Biology Insights  
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

Franklin B. Dexter, Charles Francis Adams, Ford, Green, Jameson, Wendell, Greenough, Norcross
1910 Proceedings of the Massachusetts Historical Society  
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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