Extension:PubmedParser

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PubmedParser

Release status:Extension status stable

ImplementationTemplate:Extension#type Parser function
DescriptionTemplate:Extension#description Adds a parser function #pmid to look up articles in pubmed.gov by ID.
Author(s)Template:Extension#username Daniel Kraus (Bovendertalk)
Latest versionTemplate:Extension#version 4.0.2 (2017-03-19)
MediaWikiTemplate:Extension#mediawiki 1.26+
Database changesTemplate:Extension#needs-updatephp Yes
LicenseTemplate:Extension#license GNU General Public License 2.0 or later
Download
README
CHANGELOG
ExampleTemplate:Extension#example
  • {{#pmid:19782018}}
  • {{#pmid:19782018|Alon2009}}
ParametersTemplate:Extension#parameters

$wgPubmedParserCache

Hooks usedTemplate:Extension#hook
ParserFirstCallInitManual:Hooks/ParserFirstCallInit

Translate the PubmedParser extension if it is available at translatewiki.net

Check usage and version matrix.

The PubmedParser extension provides a parser keyword (#pmid) to fetch article information by unique ID from the Pubmed database. It outputs the article information formatted as Wiki markup for a template. The template can be defined inside the Wiki and adjusted as needed.

Compared with the other, very useful extension Pubmed, this extension can be fully configured using Wiki messages (see the special page "Sytem Messages" in your wiki). It does not require editing configuration files on the server.

PubmedParser fetches information on a single article at a time only. If you would like to generate lists of article, please have a look at the Pubmed extension.

If the Cite extension is installed, you can add an additional parameter to the #pmid keyword, and PubmedParser will generate a <ref name="additional parameter">...</ref> structure for you. This makes it extremely easy to insert reusably references into your Wiki page.

Usage[edit]

To retrieve the article with PMID 19782018, insert the following into your page:

{{#pmid:19782018}}

This will produce the following output:

{{pubmed|pmid=19782018|authors=Alon|allauthors=Alon
 |title=How to choose a good scientific problem
 |journal=Molecular cell|journala=Mol. Cell.
 |year=2009|volume=35|pages=726-8|doi=10.1016/j.molcel.2009.09.013}}

However, you will never get to see this output, since {{pubmed|...}} represents a template, which is immediately processed by the MediaWiki software.

Notes:

  • The template "pubmed" must exist in your wiki; otherwise, "Template:pubmed" will be inserted in red into your displayed page (click on the red link to create the template).
  • You can fully customize the names of the template itself as well as the names of the parameters of the template (see below)).
  • Your template does not need to use all parameters; unused parameters will be discarded.
  • authors is an abbreviated list of the author names; use allauthors if you need all of the names.
  • journal is the full journal name as stored in Pubmed; use journala to get the ISO abbreviation.

Thus, if your template looks like this:

{{{authors}}}: {{{title}}}. {{{journala}}} {{{year}}};{{{volume}}}:{{{pages}}}.

You will get this:

Alon: How to choose a good scientific problem. Mol. Cell. 2009;35:726-8.

Template variables[edit]

You can use the following variables in your "pubmed" template. Note that you can edit all variable names (as well as the name of the template itself) according to your needs (see Customization below).

Parameter Description
{{{authors}}} Abbreviated list of author names. If there are only two authors, they will be concatenated by "&"; with three or more authors, an "et al." will be appended after the first author.
Note: You can edit the "&" and "et al." at Special:AllMessages (see below).
{{{authorsi}}} Abbreviated list of author names, just like above, but with initials appended.
Note: You can edit the separator between last name and first name as well as what to put after the initials (e.g., a period) at Special:AllMessages (see below).
{{{allauthors}}} List of all author names. The last author's name is appended with "&".
Note: You can edit the "&" and "et al." at Special:AllMessages (see below).
{{{allauthorsi}}} List of all author names, just like above, but with initials appended.
Note: You can edit the separator between last name and first name as well as what to put after the initials (e.g., a period) at Special:AllMessages (see below).
{{{title}}} The title of the article. A trailing period will be stripped.
{{{journal}}} The full name of the journal as stored in Pubmed. Capitalization is the same as in Pubmed.
{{{journalcaps}}} The full name of the journal as stored in Pubmed with all words capitalized.
{{{journala}}} The abbreviated name of the journal (ISO specification), e.g.: N. Engl. J. Med.
{{{journalanop}}} The abbreviated name of the journal (ISO specification) without periods, e.g.: N Engl J Med
{{{year}}} The year the article was published.
{{{volume}}} The volume of the journal.
{{{pages}}} The pagination as stored in Pubmed. Leading digits may be omitted in the last page number; for example, "1324 through 1336" is given as "1324-36".
{{{pmid}}} The PMID number (i.e., the same ID that was used to call #pmid).
{{{doi}}} The DOI (Digital Object Identifer) of the article that points to the full text. Not all Pubmed entries provide this information.
{{{abstract}}} The article's abstract. If you want to have a collapsible abstract in your template, consider using this code: {{#if:{{{abstract}}}|<span class="mw-collapsible mw-collapsed" data-expandtext="Abstract" data-collapsetext="Abstract">{{{abstract}}}</span>}} (NB: This only works in MediaWiki 1.18+).

Example template "pubmed"[edit]

{{{authors}}}: {{{title}}}. ''{{{journala}}}'' {{{year}}};{{#if:{{{volume|}}}|{{{volume|}}}:}}{{{pages|)}}}.
 PMID: [http://pubmed.gov/{{{pmid|}}} {{{pmid|}}}]. {{#if:{{{doi|}}}|[http://dx.doi.org/{{{doi|}}} DOI].}}

Formatted example:

Cumming et al.: Error bars in experimental biology. J. Cell Biol. 2007;177:7-11. PMID: 17420288. DOI.

Note: This template requires the ParserFunctions extension (which provides {{#if:test|then|else}}) to link the DOI only if it is contained in the Pubmed data.

Adding <ref></ref> tags automatically[edit]

You may add an additional parameter to the #PMID call to make the PubmedParser automatically insert <ref></ref> tags. The Cite extension will use these tags to build your bibliography. To reuse the reference, simply insert <ref name="yourparameter" />.

Example:

{{#pmid:19782018|Alon2009}}

This will produce the following output:

<ref name="Alon2009">{{pubmed|pmid=19782018|authors=Alon|allauthors=Alon|title=How to choose a good scientific problem|journal=Molecular cell|journala=Mol. Cell.|year=2009|volume=35|pages=726-8|doi=10.1016/j.molcel.2009.09.013}}</ref>

Since this output is immediately parsed again by MediaWiki, you will never get to see it this way; instead, you will see the footnote generated by the Cite extension, which contains whatever output your template "pubmed" produces from this.

To cite this same paper again, simply type <ref name="Alon2009" />

Customization[edit]

You can customize the name of the template as well as the names of the parameters by editing the system messages of your wiki: Go to Special:AllMessages and filter for "pubmedparser".

PubmedParser messages
Name Description Default value
pubmedparser-templatename Name of the MediaWiki template pubmed
pubmedparser-abstract Template parameter for the abstract abstract
pubmedparser-authors Template parameter for the abbreviated list of authors authors
pubmedparser-authorsi Template parameter for abbreviated list of authors with initials authorsi
pubmedparser-allauthors Template parameter for the complete list of authors allauthors
pubmedparser-allauthorsi Template parameter for the complete list of authors with initials allauthorsi
pubmedparser-journal Template parameter for the journal name (Pubmed style) journal
pubmedparser-journalcaps Template parameter for the journal name (capitalized) journalcaps
pubmedparser-journala Template parameter for the abbreviated journal name journala
pubmedparser-journalanop Template parameter for the complete list of authors without periods journalanop
pubmedparser-volume Template parameter for the volume volume
pubmedparser-pages Template parameter for the pagination pages
pubmedparser-firstpage Template parameter for the first page number firstpage
pubmedparser-year Template parameter for the year of publication year
pubmedparser-doi Template parameter for the digital object identifier (DOI) doi
pubmedparser-title Template parameter for the article title title
pubmedparser-and Concatenation symbol for the last author name (e.g., "and") &
pubmedparser-etal Abbreviation of the author list ''et al.''
pubmedparser-initialseparator Separator between last name and initials (e.g., ",") [empty]
pubmedparser-initialperiod Abbreviation symbol for the initials (e.g., "." or ". "). [empty]

Installation[edit]

  • Download and place the file(s) in a directory called PubmedParser in your extensions/ folder.
  • Add the following code at the bottom of your LocalSettings.php:
    wfLoadExtension( 'PubmedParser' );
    
  • Run the update script which will automatically create the necessary database tables that this extension needs.
  • YesY Done - Navigate to Special:Version on your wiki to verify that the extension is successfully installed.
Older versions of the extension required the PHP parameter allow_url_fopen to be able to fetch XML data from PubMed. Since there are security concerns over using this parameter, from version 1.0.0 on, PubmedParser will also work if this option is not set. In that case, it will require the Curl library. Many PHP servers are configured to work with Curl.

Configuration[edit]

Forcing reload from Pubmed

Occasionally, Pubmed article information is updated, e.g. when an article that was initially published online-only appears in print. When using the cache feature, you can force retrieval of information from Pubmed by adding a 'reload' parameter to your #pmid call:

{{#pmid:123456|reload}}

or

{{#pmid:123456|Miller2011|reload}}

It goes without saying that the updated information is stored in the cache folder.

Note that reloading only occurs when a page is edited but not when it is viewed. Therefore, you can leave the 'reload' parameter in your #pmid call without causing superfluous download requests from Pubmed. The next time you edit a page, you can remove the 'reload' option, and the article information will be retrieved from cache again.

Changelog[edit]

Please see the tag messages here: https://github.com/bovender/PubmedParser/releases

Alternatively, have a look at NEWS.md.

Code[edit]

https://github.com/bovender/PubmedParser

See also[edit]

Language:Project:Language policy English  • Deutsch