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plugin:pubmed2020

PubMed2020 Plugin

Compatible with DokuWiki

  • rc2020-06-01 "Hogfather" unknown
  • 2018-04-22 "Greebo" yes
  • 2017-02-19 "Frusterick Manners" yes
  • 2016-06-26 "Elenor Of Tsort" yes

plugin Retrieves and creates publication citations from NCBI PubMed

Last updated on
2020-05-26
Provides
Syntax, Render
Repository
Source

Similar to pubmed

Tagged with citation, medical, pubmed, references, science

Description

This plugin retrieves the MedLine description of articles and books recorded in the NCBI PubMed and the PMC database and allow users to easily include article citation into their DokuWiki pages. The MedLine content is cached in the media directory of your wiki. This plugin is 100% compatible with the new citation interface of PubMed (as of 05/2020).

This plugin is perfectly adapted to dokuwiki farms and works with PHP 5.6+.

Authors and licence

  • Ikuo Obataya wrote the pubmed plugin in 2007-2016
  • Eric Maeker improved this first plugins (without integrating new Ikuo code) from 2016 to 2019
  • Code was rewritten in 2020 due to PubMed new API (see updateCtx)
  • License : Public Domain
  • Current version : 2020-06-05

Examples/Usage

Installation

Install the plugin using the Plugin Manager and the download URL above, which points to latest version of the plugin. Refer to Plugins on how to install plugins manually. The local plugin directory must have the same name as the plugin is named, otherwise the plugin won't work properly.

Syntax

Basic syntax

  • The plugin basic syntax architecture is the following:
    • {{pmid>___}} for the PubMed database
    • {{pmcid>___}} for the PMC database (please note carrefully the c in pmcid)
  • Following the database declaration, after the >, you can add
    • specific commands. Eg with the long command: {{pmid>long:012345678}} (see below)
    • or simply the ID of the publications. Eg {{pmcid>0123456}}

Including article citation into your pages

  • The syntax is quite easy:
    • {{pmid>01234567}} / {{pmcid>01234567}}
    • or {{pmid>command:01234567}} / {{pmcid>command:01234567}}
  • Using the default options:
    • {{pmid>24073682}} where 24073682 is the PMID of the article as notified by pubmed.
    • {{pmcid>7241351}} where 7241351 is the PCMID of the article as notified by pubmed PMC.
    • {{pmid>user:24073682}} where 24073682 is the PMID of the article as notified by pubmed and the default user parameter (see configuration) will be used to create the article citation.
  • Using specific format:
    • {{pmid>long:24073682}} where 24073682 is the PMID of the article as notified by pubmed and long is the selected article citation format.
    • Many predefined citation format are available. You can define yours in the configuration panel and call it using the user command.
  • You can require multiple citations at once (creating a nice HTML list):
    • For example this list uses the citations used as examples in the Vancouver referencing paper {{pmid>vancouver:19171717,12142303,12028325,12084862,12166575,15857727}}
  • Including links to pubmed search page
    • You can also use this plugin to create pubmed search URL.
{{pmid>search:"Inappropriate Prescribing"[Mesh]}}
{{pmid>search:"Drug-Related Side Effects and Adverse Reactions"[Mesh] AND (Review[ptyp] AND "loattrfree full text"[sb])}}

Options

Citation format

  • The article citation can be automatically included using pre-formatted outputs:
    • vancouver : Full Vancouver citation see Vancouver for more information.
    • short : ISO citation in a short way.
    • long : full ISO citation including all authors, article title, journal title, volume, year, month, pages.
    • long_tt : same as long but with translated title (if exists)
    • long_pdf : full ISO citation including all authors, article title, journal title, volume, year, month, pages. If you own the PDF file a link will show.
    • long_tt_pdf : same as long_pdf but with translated title (if exists)
    • long_abstract : append the full abstract to the long citation. The abstract can toggled and is hidden by default.
    • long_tt_abstract : same as long_tt_abstract but with translated title (if exists)
    • long_abstract_pdf : append the full abstract to the long citation. The abstract can toggled and is hidden by default. If you own the PDF file a link will show.
    • long_tt_abstract_pdf : same as long_tt_abstract_pdf but with translated title (if exists)
    • or user defined : you can define you own citation format (see below).
  • Provides by default a link to the PubMed page and to the free full text in PMC if exists.

User defined citation

You can define in the configuration a simple string to define your own citation format. The following tokens are available.

Token Content
%pmid% PMID with a link to pubmed citation
%pmcid% PMCID with a link to pubmed PMC citation
%type% Type of the citation (“article”, “book”)
%authors% All authors (complete lastname)
%authorsVancouver% All authors (initials lastname)
%first_author% Only first author +/- “et al”
%corporate_author% Author collective
%title% Title of the article
%title_tt% Translated title in the original language of the publication
%book_title% Title of the Book
%collection_title% Title of the collection
%copyright% Copyright
%country% Country
%lang% Language of the article
%journal_iso% ISO Journal title (abbrev)
%journal_title% Full Journal title
%journal_id% Journal ID
%iso% Self computed ISO citation
%so% Medline ISO citation
%vol% Volume
%issue% Issue
%year% Year
%month% Month
%pages% Pages
%abstract% Abstract (togglable)
%doi% DOI of the publication
%pii% PII of the publication
%journal_url% Link to Journal web site using the DOI
%pmc_url% If available, link to free PDF of the article.
%abstractFr% Show french translated abstract (see specific doc)
%localpdf% Add link to local PDF file (see specific doc)
Hard coded format Content
short %first_author%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url%
long %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url%
long_pdf %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %localpdf%
long_abstract %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr%
long_abstract_pdf %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr% %localpdf%
long_tt %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url%
long_tt_pdf %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %localpdf%
long_tt_abstract %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr%
long_tt_abstract_pdf %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr% %localpdf%

Styling

  • You can change the style of your citation. Please take a look at the style.css file for further information.

Using local PDF

  • You get a direct link to your media PDF files of publications. You have to save the PDF files in the media directory: media/pubmed/pmid_pdf or media/pubmed/doi_pdf. Just use the PMID or DOI as file name. It is recommanded to use the PMID mode.

Specific commands

  • Some more commands are available:
    • test only for devs
    • raw_medline show the retrieved MedLine code. summaryxml:24073682
    • clear_raw_medline : clear all cached Medline files
    • remove_dir : remove the cache directory (by default /data/media/pubmed)
    • recreate_cross_refs : recreate the crossref (DOI ↔ PMID)
    • full_pdf_list : show all available PDF (see specific doc)
  • To use these commands, use this syntax:
    • {{pmid>cmd:0123456789}}
    • {{pmcid>cmd:01234567}}

Configuration and Settings

  • This plugin comes with some configuration parameters:
    • Default citation format.
    • Default user defined format.
    • Default authors limitation in Vancouver format
    • Default string replacement of authors over the Vancouver author limitation

Development

Change Log

Report Bugs and Issues

Please use the github repository to adress any comments, issues or wishes.

Roadmap

  • Get related using eftech
  • Show Mesh terms
  • Search Mesh terms extracted from a PMID

Discussion

plugin/pubmed2020.txt · Last modified: 2020-06-05 18:53 by eric.maeker@gmail.com