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Searching NCBI Databases Using Entrez

Gretchen Gibney, Andreas D. Baxevanis
2011 Current Protocols in Bioinformatics  
One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system.  ...  An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query.  ...  There are also interactive tutorials for various procedures related to DCC along the right-hand side of the page. 19. Scroll down the page to find the Clinical Trials section of the MedlinePlus page.  ... 
doi:10.1002/0471250953.bi0103s34 pmid:21633942 fatcat:mmv64x4lf5cutjlrkmme4d7aeu

Phylogeny for the faint of heart: a tutorial

Sandra L. Baldauf
2003 Trends in Genetics  
The main search engines for Keywords searching are Entrez (NCBI) and SRS (everywhere else); both have excellent online tutorials (Box 1).  ...  what difference it really makes.  ...  This publication and the individual contributions within it are protected by the copyright of Elsevier Science.  ... 
doi:10.1016/s0168-9525(03)00112-4 pmid:12801728 fatcat:zfoelr2tzbauljh2ixvzekl5fq

Revisão sistemática e meta-análise de estudos de diagnóstico e prognóstico: um tutorial

Marcos R. de Sousa, Antonio Luiz P. Ribeiro
2009 Arquivos Brasileiros de Cardiologia  
the statistical power of the primary research.  ...  References for the details of each statistical technique used were provided in the meta-analysis.  ...  Make it clear how the literature review process was made ( Figure 2 ).  ... 
doi:10.1590/s0066-782x2009000300013 pmid:19390713 fatcat:5xmssyun3bdz5f6ximu2u3tn5m

Defining, Identifying, and Evaluating Clinical Trials of Stuttering Treatments: A Tutorial for Clinicians

Mark Onslow, Mark Jones, Sue O'Brian, Ross Menzies, Ann Packman
2008 American Journal of Speech-Language Pathology  
For a report identified as such, a 10-item checklist is applied to verify its status as a clinical trial and to allocate it to 1 of 3 levels of clinical trials evidence.  ...  We define a clinical trial of a stuttering treatment and specify 3 levels of clinical trials evidence. We use this taxonomy to identify and evaluate clinical trials of stuttering treatment.  ...  Acknowledgments We acknowledge Martin Nevdahl's useful editing of the manuscript.  ... 
doi:10.1044/1058-0360(2008/07-0047) pmid:18840700 fatcat:3i4tfic2snhstkiw5g6gkrdq3e

Education resources of the National Center for Biotechnology Information

P. S. Cooper, D. Lipshultz, W. T. Matten, S. D. McGinnis, S. Pechous, M. L. Romiti, T. Tao, M. Valjavec-Gratian, E. W. Sayers
2010 Briefings in Bioinformatics  
public make use of the wealth of public data available at the NCBI.  ...  NCBI also offers training programs including the Discovery Workshops, webinars and tutorials at conferences.  ...  Acknowledgements We gratefully acknowledge the contributions of former members of the NCBI User Services group.  ... 
doi:10.1093/bib/bbq022 pmid:20570844 pmcid:PMC2984538 fatcat:qfweze4ipberbjfxro7ylo3ckm

Strategies to Explore Functional Genomics Data Sets in NCBI's GEO Database [chapter]

Stephen E. Wilhite, Tanya Barrett
2011 Msphere  
In addition to serving as a public archive for these data, GEO has a suite of tools that allow users to identify, analyze and visualize data relevant to their specific interests.  ...  The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies  ...  Funding This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.  ... 
doi:10.1007/978-1-61779-400-1_3 pmid:22130872 pmcid:PMC3341798 fatcat:uaxflq4iavbc5glxfrjazvkpii

Performance Evaluation Of Structured And Semi-Structured Bioinformatics Tools: A Comparative Study

Abdelsalam M. Maatuk Raja A. Moftah
2018 Zenodo  
We used Sequence Retrieval System (SRS) and Entrez search tools for structured data, while Perl and BioPerl search programs were used for semi-structured data to retrieve complex queries including a combination  ...  In this paper, we investigate and evaluate the performance of some of these methods in terms of their ability to efficiently access bioinformatics databases using webbased interfaces.  ...  The analysis of results of this study shows that its limitation makes Entrez unfit for its intended purpose.  ... 
doi:10.5281/zenodo.1453755 fatcat:h2uyatbi4jaqpeotn7atfsk4cu

Database resources of the National Center for Biotechnology Information

Richa Agarwala, Tanya Barrett, Jeff Beck, Dennis A Benson, Colleen Bollin, Evan Bolton, Devon Bourexis, J Rodney Brister, Stephen H Bryant, Kathi Canese, Mark Cavanaugh, Chad Charowhas (+61 others)
2017 Nucleic Acids Research  
The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system.  ...  Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets.  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.  ... 
doi:10.1093/nar/gkx1095 pmid:29140470 pmcid:PMC5753372 fatcat:v2wabu3mezcpnbvn7pnssppfdy

Molecular Biology Databases on the Internet, Part II

David M. Sander
1997 BioTechniques  
Seeking information on microsatellites in Arabidopsis, a Netter on bionet.genome. arabidopsiswas advised to search the "papers" section of the prototype Arabidopsis thalianadatabase, accessible through  ...  Concerned that a dramatic decrease in yield of PCR product accompanied by the appearance of artifactual bands may be due to freeze-thaw degradation of primers , a poster was advised to store primer stocks  ...  Good tutorials located at Prot-Web make the site very user friendly. Protein Motifs Another aspect of protein sequence analysis is the identification of protein motifs.  ... 
doi:10.2144/97221ir01 pmid:9081313 fatcat:nz7p43lxozgmfmofbzqc5qowzm

Analysis of viral diversity for vaccine target discovery

Asif M. Khan, Yongli Hu, Olivo Miotto, Natascha M. Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J. Thomas August
2017 BMC Medical Genomics  
identification of vaccine targets.  ...  A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets.  ...  Liang, Shweta Ramdas, Tan Thiam Joo, Ernesto Marques, Eduardo Nascimento, Keun-Ok Jung, and Paul Nordstrom August for their valuable suggestions, critique, and help in the development and application of  ... 
doi:10.1186/s12920-017-0301-2 pmid:29322922 pmcid:PMC5763473 fatcat:7su4xz5aqrcflpbvorswaitn6a

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+30 others)
2010 Nucleic Acids Research  
Formats: Artic le | PubR (150 K) | Citati Share Fac ebo o k Database resources of the national center for biotechnology information.  ...  Autho r info rma tio n ► Artic le no te s ► Co pyrig ht a nd Lic e nse info rma tio n ► Disc la ime r This a rtic le ha s be e n c ite d by o the r a rtic le s in PMC.  ...  The Table of Contents section in the upper right of the Gene full report now has subheadings, making it easier to jump to a subsection of the record in one click.  ... 
doi:10.1093/nar/gkq1172 pmid:21097890 pmcid:PMC3013733 fatcat:evc3u4jqubchjoqyvc3ff5qple

PubChem BioAssay: 2014 update

Yanli Wang, Tugba Suzek, Jian Zhang, Jiyao Wang, Siqian He, Tiejun Cheng, Benjamin A. Shoemaker, Asta Gindulyte, Stephen H. Bryant
2013 Nucleic Acids Research  
To this end, PubChem BioAssay is integrated into the National Center for Biotechnology Information retrieval system, making them searchable by Entrez queries and cross-linked to other biomedical information  ...  The mission of PubChem is to serve the community by providing free and easy access to all deposited data.  ...  ACKNOWLEDGEMENTS The authors thank all submitters who have contributed data to PubChem and the rest of the PubChem team for their support.  ... 
doi:10.1093/nar/gkt978 pmid:24198245 pmcid:PMC3965008 fatcat:57wu2puoovaevlpqtrp5pjsq7e

PILGRM: an interactive data-driven discovery platform for expert biologists

C. S. Greene, O. G. Troyanskaya
2011 Nucleic Acids Research  
This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner.  ...  This server is free, does not require registration and is available for use at  ...  PILGRM contains step-by-step tutorials that familiarize users with the system. Optional example input is provided for each tutorial.  ... 
doi:10.1093/nar/gkr440 pmid:21653547 pmcid:PMC3125802 fatcat:hcttvj62vnbc3jlwumtb4xaeza

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin (+18 others)
2007 Nucleic Acids Research  
Several tutorials are also offered under with the Training and Tutorials category link on the left side of the NCBI home page.  ...  GENSAT (www.ncbi.nlm.nih.gov/ projects/gensat/) catalogs images of histological sections of the mouse brain in which biochemical tags have been used to visualize local gene expression.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl1031 pmid:17170002 pmcid:PMC1781113 fatcat:pj7gnwwlpnbmza7c4ae7yatega

Database Resources of the National Center for Biotechnology Information

2016 Nucleic Acids Research  
Several tutorials are also offered under with the Training and Tutorials category link on the left side of the NCBI home page.  ...  GENSAT (www.ncbi.nlm.nih.gov/ projects/gensat/) catalogs images of histological sections of the mouse brain in which biochemical tags have been used to visualize local gene expression.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkw1071 pmid:27899561 pmcid:PMC5210554 fatcat:itaqk5uwv5bv7gm7f55zunbcwq
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