Template talk:Pubmed

From Embryology

This is the new format for referencing on pages.

Alon U. (2009). How to choose a good scientific problem. Mol. Cell , 35, 726-8. PMID: 19782018 DOI.


This was original template format.


{{{allauthorsi}}}: {{{title}}}. {{{journala}}} {{{year}}};{{{volume}}}:{{{pages}}} PMID: [1]


here is the non production test page

https://embryology.nonprod.med.unsw.edu.au/embryology/index.php/PubmedParser_Test

APA Format

Journal

http://www.bibme.org/citation-guide/apa/journal-article/

http://www.easybib.com/reference/guide/apa/journal


Website

http://www.easybib.com/reference/guide/apa/website

Last, F. M. (Year, Month Date Published). Article title. Retrieved from URL

Satalkar, B. (2010, July 15). Water aerobics. Retrieved from http://www.buzzle.com

Hill, M.A. 2018 Embryology Main Page. Retrieved February 7, 2018, from https://embryology.med.unsw.edu.au/embryology/index.php/Main_Page

Hill, M.A. 2018 Embryology Main Page. Retrieved February 7, 2018, from https://embryology.med.unsw.edu.au/embryology/index.php/Main_Page

Original citation

Cite this page: Hill, M.A. 2019 Embryology Pubmed. Retrieved August 18, 2019, from https://embryology.med.unsw.edu.au/embryology/index.php/Template_talk:Pubmed

APA format

Cite this page: Hill, M.A. (2019, August 18) Embryology Pubmed. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Template_talk:Pubmed

Extension:PubmedParser

https://www.mediawiki.org/wiki/Extension:PubmedParser


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).

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"

{{{authors}}}: {{{title}}}. ''{{{journala}}}'' {{{year}}};{{#if:{{{volume|}}}|{{{volume|}}}:}}{{{pages|)}}}.
 PMID: [https://www.ncbi.nlm.nih.gov/pubmed/{{{pmid|}}} {{{pmid|}}}]. {{#if:{{{doi|}}}|[https://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

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

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

Template:TNT Template:TNT

Configuration

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.