Help talk:Reference Tutorial

From Embryology

PubMed Extensions

Currently using Pubmed extension, but this has not been maintained and has begun generating errors at the server end.

Note there is a update to PHP7 pending in 2017.

Need to test either PubmedParser or BiblioPlus as possible replacement.


The Pubmed extension can fetch literature data from scientific articles stored in PubMed (, and generate a reference list or box. The extension can create, in addition to the primary data like author, article title, journal, year, pages, etc., links like back to PubMed or to by ISSN or to the full text at the publisher's page (if a DOI is specified). Further links can be defined using the layout template.

NCBI - Possible Blocking

"Frequency, Timing and Registration of E-utility URL Requests

In order not to overload the E-utility servers, NCBI recommends that users post no more than three URL requests per second and limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays. Failure to comply with this policy may result in an IP address being blocked from accessing NCBI. If NCBI blocks an IP address, service will not be restored unless the developers of the software accessing the E-utilities register values of the tool and email parameters with NCBI. The value of tool should be a string with no internal spaces that uniquely identifies the software producing the request. The value of email should be a complete and valid e-mail address of the software developer and not that of a third-party end user. The value of email will be used only to contact developers if NCBI observes requests that violate our policies, and we will attempt such contact prior to blocking access. In addition, developers may request that the value of email be added to the E-utility mailing list that provides announcements of software updates, known bugs and other policy changes affecting the E-utilities. To register tool and email values, simply send an e-mail to vog.hin.mln.ibcn@seitilitue including the desired values along with the name of either a developer or the organization creating the software. Once NCBI establishes communication with a developer, receives values for tool and email and validates the e-mail address in email, the block will be lifted. Once tool and email values are registered, all subsequent E-utility requests from that software package should contain both values. Please be aware that merely providing values for tool and email in requests is not sufficient to comply with this policy; these values must be registered with NCBI. Requests from any IP that lack registered values for tool and email and that violate the above usage policies may be blocked. Software developers may register values of tool and email at any time, and are encouraged to do so."


4.0.1 (2016-11-09)

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.

Steps for updating from Pubmed to Parser extension code.

  1. Open original page in edit mode.
  2. In edit mode copy n paste into text editor.
  3. Find and replace <pubmed> with {{#pmid:PMIDno
  4. Find and replace </pubmed> with }}
  5. Copy n paste the new text back on the original page.
  6. Save.




Simple Referencing

Simply pasting the text of the PMID on the page is sufficient to generate a link to the PubMed reference.

PMID 18508724