====== Pubmed Plugin ======

---- plugin ----
description: Plugin that integrates informations of scientific journals articles from PubMed with PMID.
author     : Eric Maeker and Ikuo Obataya
email      : eric[at]maeker.fr
type       : syntax
lastupdate : 2016-08-22
compatible : 2016-06-26 "Elenor Of Tsort", 2015-08-10a "Detritus"
depends    : 
conflicts  : 
similar    : 
tags       : biology chemistry medical science references
downloadurl: https://github.com/EricMaeker/dokuwiki-plugin-pubmed/archive/master.zip
bugtracker : https://github.com/EricMaeker/dokuwiki-plugin-pubmed/issues
sourcerepo : https://github.com/EricMaeker/dokuwiki-plugin-pubmed/

screenshot_img : https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_long_abstract.png
----

======Functions======

This plugin is based on the Ikuo Obataya <I.Obataya@gmail.com> code base (from 2013). It integrates informations scientific journal articles from PubMed using its PubMed identifiant: //PMID//. The plugin downloads and stores the summary of each articles in an XML file in // /data/media/ncbi_esummary // directory.

**%%{{pubmed>[Command]:[PubMed ID]}}%%**

^  Command        ^  item  ^  function  |
^[[#short]]        |link |Show a short pubmed link|
^[[#long]]         |link |Show a detailed pubmed link|
^[[#long_abstract]]|link |Show a detailed pubmed link and the complete abstract of the article (if available)|
^[[#search]]       |link |Create a link to a search query over PubMed (you can use MeSH terms, wildcards...)|
^summaryXML        |xml  |Show the XML data retreived from the NCBI database (usefull for debugging)|
^clear_summary     |  -  |Clear cached XML files in /data/media/ncbi_esummary|
^remove_dir       |  -  |Remove the XML output dir: /data/media/ncbi_esummary (by default)|

======Examples (code followed by a screenshot of the result)======
=====short=====

  {{pubmed>short:9039911}}
{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_short.png}}

=====long=====

  {{pubmed>long:9039911}}
{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_long.png}}

=====long_abstract=====

  {{pubmed>long_abstract:9039911}}
{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_long_abstract.png}}

======search======

  {{pubmed>search:"Empathy"[Mesh] AND "Communication"[Mesh] AND "Aged"[Mesh]}}
{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/search.png}}


====== History ======

  * See [[https://github.com/EricMaeker/dokuwiki-plugin-pubmed/commits/dokuwiki-web-site]]

====== Discussion ======