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DokuWiki plugins

There are DokuWiki plugins for research & education which I developed. All plugins are under GPL2 license, so feel free to use them in your DokuWiki.

Dokuwiki Official

Scientific plugins

DokuWiki plugins for bioscience and biotechnology.

General plugins

start

Symplus Wiki

This wiki contains information about source codes for DokuWiki plugin.

  • PubMed plugin
  • PubChem Plugin
  • Chem plugin
  • PDB plugin

PubMed plugin

This is a plugin for DokuWiki that retrieves the information from PubMed widh PMID. The plugin stores NCBI ESummary XML file in /data/media/ncbi_esummary directory.

Functions

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

Command item function
short link Show a short pubmed link from NCBI Structure database
long link Show a detailed pubmed link from NCBI Structure database
summaryXML xml Show a XML summary data from the NCBI database using Entrez Utilities
clear_summary - Clear cached XML files in /data/media/ncbi_esummary
remove_dir - Clear cached files and remove cache directory

Examples

short

{{pubmed>short:9039911}}
Wilmut Iet al.Nature385p810-3(1997 Feb 27)

long

{{pubmed>long:9039911}}
Viable offspring derived from fetal and adult mammalian cells.
Wilmut I, Schnieke AE, McWhir J, Kind AJ, Campbell KH
Nature385p810-3(1997 Feb 27)

summaryXML

{{pubmed>summaryXML:9039911}}

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">
<eSummaryResult>
<DocSum>
	<Id>9039911</Id>
	<Item Name="PubDate" Type="Date">1997 Feb 27</Item>
	<Item Name="EPubDate" Type="Date"></Item>
	<Item Name="Source" Type="String">Nature</Item>
	<Item Name="AuthorList" Type="List">
		<Item Name="Author" Type="String">Wilmut I</Item>
		<Item Name="Author" Type="String">Schnieke AE</Item>
		<Item Name="Author" Type="String">McWhir J</Item>
		<Item Name="Author" Type="String">Kind AJ</Item>
		<Item Name="Author" Type="String">Campbell KH</Item>
	</Item>
	<Item Name="LastAuthor" Type="String">Campbell KH</Item>
	<Item Name="Title" Type="String">Viable offspring derived from fetal and adult mammalian cells.</Item>
	<Item Name="Volume" Type="String">385</Item>
	<Item Name="Issue" Type="String">6619</Item>
	<Item Name="Pages" Type="String">810-3</Item>
	<Item Name="LangList" Type="List">
		<Item Name="Lang" Type="String">English</Item>
	</Item>
	<Item Name="NlmUniqueID" Type="String">0410462</Item>
	<Item Name="ISSN" Type="String">0028-0836</Item>
	<Item Name="ESSN" Type="String">1476-4687</Item>
	<Item Name="PubTypeList" Type="List">
		<Item Name="PubType" Type="String">Journal Article</Item>
	</Item>
	<Item Name="RecordStatus" Type="String">PubMed - indexed for MEDLINE</Item>
	<Item Name="PubStatus" Type="String">ppublish</Item>
	<Item Name="ArticleIds" Type="List">
		<Item Name="pubmed" Type="String">9039911</Item>
		<Item Name="doi" Type="String">10.1038/385810a0</Item>
		<Item Name="eid" Type="String">9039911</Item>
		<Item Name="rid" Type="String">9039911</Item>
	</Item>
	<Item Name="DOI" Type="String">10.1038/385810a0</Item>
	<Item Name="History" Type="List">
		<Item Name="pubmed" Type="Date">1997/02/27 00:00</Item>
		<Item Name="medline" Type="Date">1997/02/27 00:01</Item>
		<Item Name="entrez" Type="Date">1997/02/27 00:00</Item>
	</Item>
	<Item Name="References" Type="List">
		<Item Name="Comment in" Type="String">Nature. 1997 Mar 13;386(6621):119. PMID: 9062180</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Apr 3;386(6624):431. PMID: 9087390</Item>
		<Item Name="Comment in" Type="String">Nature. 2006 Apr 27;440(7088):1112. PMID: 16641972</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Jun 19;387(6635):754. PMID: 9194550</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Feb 27;385(6619):753. PMID: 9039891</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Mar 6;386(6620):12. PMID: 9052771</Item>
		<Item Name="Comment in" Type="String">Nature. 1997 Apr 3;386(6624):431. PMID: 9087392</Item>
		<Item Name="Erratum in" Type="String">Nature 1997 Mar 13;386(6621):200</Item>
	</Item>
	<Item Name="HasAbstract" Type="Integer">1</Item>
	<Item Name="PmcRefCount" Type="Integer">460</Item>
	<Item Name="FullJournalName" Type="String">Nature</Item>
	<Item Name="ELocationID" Type="String"></Item>
	<Item Name="SO" Type="String">1997 Feb 27;385(6619):810-3</Item>
</DocSum>

</eSummaryResult>

When you want to create a link, use [[pubmed>9039911]]. → 9039911

History

  • 2016.10.24
    • URLs in code were changed to https according to changes in Web API of NCBI database.
  • 2008.3.22
  • 2008.3.7
    • Bug fix of incorrect permission of cache files
  • 2008.2.26
    • Cache ESummary XML file in /data/media/ncbi_esummary directory
  • 2007.12.08
    • Fix around directory creation & ACL
    • Append an icon image

Installation

Recent version of DokuWiki has Extention manager that can download and install plugin automatically. Use the manager.

In very old dokuwiki

  1. Install bio plugin and cache plugin if not installed.
  2. Download pubmed.zip and extract.
  3. Upload the folder to /lib/plugins/ directory.

Translations of this page:
start.txt · Last modified: 2016/10/31 09:08 by swadmin