Extension:PubmedParser

The PubmedParser extension provides a parser keyword ( ) to fetch article information by unique ID from the [http://www.pubmed.gov 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 , 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  extension.

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

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

This will produce the following output:

However, you will never get to see this output, since  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:



You will get this:

Template variables
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).

Example template "pubmed"


(When copying this into your own Wiki, make sure to have the entire text on one line.)

Formatted example:

Note: This template requires the ParserFunctions extension (which provides ) to link the DOI only if it is contained in the Pubmed data.

Alternative with collapsible abstract:

.  . PMID:.

Adding   tags automatically
You may add an additional parameter to the #PMID call to make the PubmedParser automatically insert  tags. The Cite extension will use these tags to build your bibliography. To reuse the reference, simply insert.

Example:

This will produce the following output:

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

Customization
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".

Configuration
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:
 * Forcing reload from Pubmed

or

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

Alternatively, have a look at NEWS.md.

Code
https://github.com/bovender/PubmedParser