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EFetchPlugin

Extract and display content from PubMed in TWiki pages

Introduction

This plugin allows the user to display the abstract for a given PubMed ID. This is accomplished by either displaying the desired information on the current page or by displaying a link to the desired information on PubMed. The plugin utilizes EFetch, provided by Entrez. For more information, visit Entrez programming utilities.

Syntax Rules

  • There is one way to display the abstract for a given PubMed ID. In the example "number" is the desired PubMed ID.
    1. %PMID{number}%
  • There are three methods for calling the EFetchPlugin plugin to display a link to PubMed. In the following examples, "number" is the desired PubMed ID (an 8-digit number) and "link text" is the desired text to display for the link.
    1. %PMIDL{pmid="number" name="link text"}%
    2. %PMIDL{number}%
      This method defaults the link text to number.
    3. %PMIDC{number}%
      This method defaults the link text to the short citation provided by PubMed.

Examples

  • %PMID{15572332}%
%PMID{15572332}%

What you will see if installed:

1: Am J Sports Med. 2004 Dec;32(8):1986-95. 

Anterior cruciate ligament reconstruction autograft choice: bone-tendon-bone
versus hamstring: does it really matter? A systematic review.

Spindler KP, Kuhn JE, Freedman KB, Matthews CE, Dittus RS, Harrell FE Jr.

Vanderbilt University Medical Center, Nashville, Tennessee, USA.
kurt.spindler@vanderbilt.edu

Anterior cruciate ligament graft choice is controversial, with no evidence-based
consensus available to guide decision making. The study design was
evidence-based medicine systematic review of randomized controlled trials
evaluating patellar tendon versus hamstring tendon autografts. A literature
review identified 9 randomized controlled trials comparing patellar tendon and
hamstring tendon autografts. An evidence-based systematic review was performed.
Objective and subjective outcomes of interest included surgical technique,
rehabilitation, instrumented laxity, isokinetic strength, patellofemoral pain,
return to preinjury activity, and Tegner, Lysholm, Cincinnati, and International
Knee Documentation Committee-1991 scores. Additional surgery, graft failure, and
complications were reviewed. Slight increased laxity on arthrometer testing was
seen in the hamstring population in 3 of 7 studies. Pain with kneeling was
greater for the patellar tendon population in 4 of 4 studies. Only 1 of 9
studies showed increased anterior knee pain in the patellar tendon group.
Frequency of additional surgery seemed to be related to the fixation method and
not graft type. No study reported a significant difference in graft failure
between patellar tendon and hamstring tendon autografts. Objective differences
(range of motion, isokinetic strength, arthrometer testing) were not detected
between groups in the majority of studies, suggesting that their sensitivity to
detect clinical outcomes may be limited. Increased kneeling pain in the patellar
tendon group was seen consistently in the studies evaluated. Subjective
differences in anterior knee pain or return-to-activity level were not
consistently observed in these studies. With numbers available, failure rates
were not significantly different between groups. These findings suggest that
graft type may not be the primary determinant for successful outcomes after
anterior cruciate ligament surgery.

PMID: 15572332 [PubMed - in process]
  • %PMIDL{pmid="15572332" name="Here's a link to the abstract"}%
%PMIDL{pmid="15572332" name="Here's a link to the abstract"}%

What you will see if installed:

Here's a link to the abstract

  • %PMIDL{15572332}%
%PMIDL{15572332}%

What you will see if installed:

15572332

  • %PMIDC{15572332}%
%PMIDC{15572332}%

What you will see if installed:

Spindler KP, Kuhn JE, Freedman KB, Matthews CE, Dittus RS, Harrell FE Jr.  Anterior cruciate ligament reconstruction autograft choice: bone-tendon-bone versus hamstring: does it really matter? A systematic review.  Am J Sports Med 2004 Dec;32(8):1986-95.

Plugin Settings

Plugin settings are stored as preferences variables. To reference a plugin setting write %<plugin>_<setting>%, i.e. %INTERWIKIPLUGIN_SHORTDESCRIPTION%

  • One line description, is shown in the TextFormattingRules topic:
    • Set SHORTDESCRIPTION = Extract and display content from PubMed in TWiki pages

  • Debug plugin: (See output in data/debug.txt)
    • Set DEBUG = 0

Plugin Installation Instructions

Note: You do not need to install anything on your browser to use this plugin. The following instructions are for the administrator who installs the plugin on the server where TWiki is running.

  • Install the Perl module LWP::Simple
  • Download the ZIP file from the Plugin web (see below)
  • Unzip EFetchPlugin.zip in your twiki installation directory. Content:
    File: Description:
    data/TWiki/EFetchPlugin.txt Plugin topic
    lib/TWiki/Plugins/EFetchPlugin.pm Plugin Perl module
  • Visit configure in your TWiki installation, and enable the plugin in the {Plugins} section.
  • Test if the installation was successful:
    • Try one of the examples

Plugin Info

Plugin Author: TWiki:Main.ColeBeck
Copyright: © 2004 TWiki:Main.ColeBeck
© 2004-2013 TWiki:TWiki.TWikiContributor
Plugin Version: 2013-01-08
Change History:  
2013-01-13: TWikibug:Item7122: Caching of Efetch records -- TWiki:Main.IanHolmes
2010-12-12: TWikibug:Item6530: Doc improvements, changing TWIKIWEB to SYSTEMWEB -- TWiki:Main.PeterThoeny
28 Dec 2004: Initial version
TWiki Dependency: $TWiki::Plugins::VERSION 1.024
CPAN Dependencies: LWP::Simple
Other Dependencies: none
Perl Version: 5.005
TWiki:Plugins/Benchmark: GoodStyle 100%, FormattedSearch 100%, EFetchPlugin 100%
Plugin Home: http://twiki.org/cgi-bin/view/Plugins/EFetchPlugin
Feedback: http://twiki.org/cgi-bin/view/Plugins/EFetchPluginDev
Appraisal: http://twiki.org/cgi-bin/view/Plugins/EFetchPluginAppraisal

Related Topics: TWikiPreferences, TWikiPlugins

Topic attachments
I Attachment History Action Size Date Who Comment
Unknown file formatmd5 EFetchPlugin.md5 r4 r3 r2 r1 manage 0.2 K 2013-01-09 - 03:27 PeterThoeny  
Compressed Zip archivetgz EFetchPlugin.tgz r4 r3 r2 r1 manage 7.4 K 2013-01-09 - 03:27 PeterThoeny  
Compressed Zip archivezip EFetchPlugin.zip r6 r5 r4 r3 r2 manage 8.9 K 2013-01-09 - 03:27 PeterThoeny  
Unknown file formatEXT EFetchPlugin_installer r2 r1 manage 3.4 K 2013-01-09 - 03:27 PeterThoeny  
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Topic revision: r10 - 2013-10-16 - PeterThoeny
 
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