Extension:Pubmed

What can this extension do?
The extension can fetch literature data from scientific articles stored in PubMed (www.pubmed.org) and generate a reference list/box. Next to the primary data like author, article title, journal, year, pages, etc - the extension can create links like back to PubMed or WorldCat.org by ISSN or the full text at publishers page (if a doi is specified). Other links can be defined with the layout template.

Usage
PubMed-ID or search string

Example:

15980568 will result:

 Andreas Bohne-Lang, Wolf-Dieter Groch, René Ranzinger

AISMIG--an interactive server-side molecule image generator. Nucleic Acids Res.: 2005, 33(Web Server issue);W705-9 [PubMed:15980568] [WorldCat.org] [DOI] (I p) Pubmed can be combined quite elegantly with the Cite extension to produce in-text citations and an automatically numbered list of PubMed references, like so:

==References== .
 * 1) place "Pubmed" directory in.

Note: $IP stands for the root directory of your MediaWiki installation, the same directory that holds LocalSettings.php.

Installation
To install this extension, add the following to LocalSettings.php:

Configuration parameters
$wgPubmedCache="/tmp/pubmedcache"; enables cacheing of the Pubmed article data in a directory

$wgPubmedLimit=0; means that you get all articles a search query returns (remember there is the Pubmed limit of 500 articles) $wgPubmedLimit=10 sets the global limit of max retrieved articles to ten / can override the global setting

$wgPubmedLayoutFile="layout_ext.def"; sets the global default layout file can override the default setting

$wgPubmedLayoutLinks="PMID,WORLDCAT,EZB,DOI"; sets default link includes

--

... set a limit of max data set that sould be listed if there are more than one

 ... sets an alternative layout template file

Version 1 - SOAP interface

 * 01.12.2008: small bugfix in SOAP class
 * 07.07.2009: Add ProxyUser and ProxyPassword to code area that handles a SOAP proxy connection
 * 28.04.2010: Try to code a work around for the mismatch encoding information in the SOAP-data comming from Pubmed. Adding 2 new variables: $wgPubmedSOAP="nusoap"; that can be "auto or nusoap" and $wgNUSOAPencodinghack=true; At the moment only $wgPubmedSOAP="nusoap" is working correctly.
 * 28.12.2010: Fix Pubmed changing in Title: Unfixed 'Array' occurs in titel. This is fixed in layout.inc.php now.
 * 08.02.2011: Fix Pubmed changing in ["MedlineCitation"]["PMID"]["_"]: Cache function was worry about...
 * 11.02.2011: Version is outdated and not longer suppported. Please update to version 2.

Version 2 - fcgi interface

 * 11 Feb 2011: Doing a complete redesign of the API. The SAOP-interface (used in Version 1) of Pubmed causes more problems than clouds in the sky. The redesigned extension uses the fcgi-interface and xml.

Contact
Andreas Bohne-Lang Medical Faculty Mannheim of the University Heidelberg Computational Center/Library Ludolf-Krehl-Str. 13-17 68167 Mannheim Germany eMail: andreas.bohne-lang@medma.uni-heidelberg.de