1====== Pubmed Plugin ======
2
3---- plugin ----
4description: Plugin that integrates informations of scientific journals articles from PubMed with PMID.
5author     : Eric Maeker and Ikuo Obataya
6email      : eric[at]maeker.fr
7type       : syntax
8lastupdate : 2016-08-22
9compatible : 2016-06-26 "Elenor Of Tsort", 2015-08-10a "Detritus"
10depends    :
11conflicts  :
12similar    :
13tags       : biology chemistry medical science references
14downloadurl: https://github.com/EricMaeker/dokuwiki-plugin-pubmed/archive/master.zip
15bugtracker : https://github.com/EricMaeker/dokuwiki-plugin-pubmed/issues
16sourcerepo : https://github.com/EricMaeker/dokuwiki-plugin-pubmed/
17
18screenshot_img : https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_long_abstract.png
19----
20
21======Functions======
22
23This 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.
24
25**%%{{pubmed>[Command]:[PubMed ID]}}%%**
26
27^  Command        ^  item  ^  function  |
28^[[#short]]        |link |Show a short pubmed link|
29^[[#long]]         |link |Show a detailed pubmed link|
30^[[#long_abstract]]|link |Show a detailed pubmed link and the complete abstract of the article (if available)|
31^[[#search]]       |link |Create a link to a search query over PubMed (you can use MeSH terms, wildcards...)|
32^summaryXML        |xml  |Show the XML data retreived from the NCBI database (usefull for debugging)|
33^clear_summary     |  -  |Clear cached XML files in /data/media/ncbi_esummary|
34^remove_dir       |  -  |Remove the XML output dir: /data/media/ncbi_esummary (by default)|
35
36======Examples (code followed by a screenshot of the result)======
37=====short=====
38
39  {{pubmed>short:9039911}}
40{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_short.png}}
41
42=====long=====
43
44  {{pubmed>long:9039911}}
45{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_long.png}}
46
47=====long_abstract=====
48
49  {{pubmed>long_abstract:9039911}}
50{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/pubmed_long_abstract.png}}
51
52======search======
53
54  {{pubmed>search:"Empathy"[Mesh] AND "Communication"[Mesh] AND "Aged"[Mesh]}}
55{{https://github.com/EricMaeker/dokuwiki-plugin-pubmed/raw/dokuwiki-web-site/site/search.png}}
56
57
58====== History ======
59
60  * See [[https://github.com/EricMaeker/dokuwiki-plugin-pubmed/commits/dokuwiki-web-site]]
61
62====== Discussion ======
63
64