MediaWiki Extension PubmedEx

This extension provides <pubmed>...</pubmed> tags to show article information fetched from PubMed.

This is forked from Pubmed Extension version 2.0 (2018-10-31).

Install

To install this extension, add the following to LocalSettings.php.

wfLoadExtension("PubmedEx");

Optional settings

• $wgPubmedApiKey
  • enables to use the E-utilities API key.
    • see more details
  • default: ""
• $wgPubmedCache
  • cache directory to store the PubMed responses and article data.
  • default: "${IP}/images/pubmed"
• $wgPubmedCacheExpires
  • enables to set cache expiration in sec. 0 means never expires.
  • default: 604800
• $wgPubmedProxyHost
  • set the proxy host for querying PubMed API.
  • default: ""
• $wgPubmedProxyPort
  • set the proxy port.
  • default: 8080
• $wgPubmedProxyUser
  • set the proxy user, if proxy requires authentication.
  • default: ""
• $wgPubmedProxyPass
  • set the proxy password.
  • default: ""
• $wgPubmedLimit
  • maximum number of the PubMed search query returns.
    • remember the PubMed limit of 500 articles.
  • default: 20
• $wgPubmedOffset
  • start offset of the PubMed search query returns.
  • default: 0
• $wgPubmedTemplateFile
  • template file to format PubMed articles. this file should be located under templates/ directory.
  • default: "default.php"

Usage

typical case.

<pubmed>15011281</pubmed>

search neuroinformatics and show related five and next five articles.

<pubmed limit="5">neuroinformatics</pubmed>
...
<pubmed limit="5" offset="5">neuroinformatics</pubmed>

override template file yetanother.php dynamically.

<pubmed templatefile="yetanother.php">15046238</pubmed>

Changes from the original version

• Reimplemented all sources.
  • new E-utilities client to support API key.
  • new PubMed xml parser to support PubmedBookArticle data.
  • new cache system to store each pubmed responses and parsed article data.
  • new template system for more flexible format support.
  • modern MediaWiki extention framework.
• Global variables
  • added: $wgPubmedApiKey, $wgCacheExpires and $wgPubmedTemplateFile
  • removed: $wgPubmedPath,$wgPubmedLayoutFile, $wgPubmedLayoutLinks, $wgPubmedSOAP, $wgNUSOAPencodinghack, $wgPubmedWDSLVersion and $wgPubmedDEBUG
• Tag parameters
  • added: templatefile.
  • removed: layoutfile, layoutlink and debug.

License

This software is licensed under the GNU General Public License 2.0 or later.

Authors

• Yoshihiro Okumura
• Andreas Bohne-Lang (Original Concept)

Usage examples

• https://bsd.neuroinf.jp Brain Science Dictionary project in Japanese.