Template talk:Pubmed: Difference between revisions
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This is the new format for referencing on pages. | |||
{{#pmid:19782018}} | |||
This was original template format. | |||
{{{allauthorsi}}}: {{{title}}}. {{{journala}}} {{{year}}};{{{volume}}}:{{{pages}}} PMID: [https://www.ncbi.nlm.nih.gov/pubmed/{{{pmid|}}} {{{pmid|}}}] | |||
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. {{CURRENTYEAR}} '''Embryology''' <i>{{PAGENAME}}</i>. Retrieved {{CURRENTMONTHNAME}} {{CURRENTDAY}}, {{CURRENTYEAR}}, from https://embryology.med.unsw.edu.au/embryology/index.php/{{FULLPAGENAMEE}}<noinclude>[[Category:Template]][[Category:2018]]</noinclude> | |||
APA format | |||
Cite this page: Hill, M.A. ({{CURRENTYEAR}}, {{CURRENTMONTHNAME}} {{CURRENTDAY}}) '''Embryology''' <i>{{PAGENAME}}</i>. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/{{FULLPAGENAMEE}} | |||
==Extension:PubmedParser== | ==Extension:PubmedParser== | ||
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{{#pmid:19782018}} | ===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|Customization]] below). | |||
{| class="wikitable" | |||
! Parameter | |||
! Description | |||
|- | |||
| <code>{{{authors}}}</code> | |||
| 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. <br /> Note: You can edit the "&" and "et al." at Special:AllMessages (see [[#Customization|below]]). | |||
|- | |||
| <code>{{{authors'''i'''}}}</code> | |||
| Abbreviated list of author names, just like above, but with initials appended. <br /> 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 [[#Customization|below]]). | |||
|- | |||
| <code>{{{allauthors}}}</code> | |||
| List of all author names. The last author's name is appended with "&". <br /> Note: You can edit the "&" and "et al." at Special:AllMessages (see [[#Customization|below]]). | |||
|- | |||
| <code>{{{allauthors'''i'''}}}</code> | |||
| List of all author names, just like above, but with initials appended. <br /> 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 [[#Customization|below]]). | |||
|- | |||
| <code>{{{title}}}</code> | |||
| The title of the article. A trailing period will be stripped. | |||
|- | |||
| <code>{{{journal}}}</code> | |||
| The full name of the journal as stored in Pubmed. Capitalization is the same as in Pubmed. | |||
|- | |||
| <code>{{{journalcaps}}}</code> | |||
| The full name of the journal as stored in Pubmed with all words capitalized. | |||
|- | |||
| <code>{{{journal''a''}}}</code> | |||
| The abbreviated name of the journal (ISO specification), e.g.: N. Engl. J. Med. | |||
|- | |||
| <code>{{{journal''anop''}}}</code> | |||
| The abbreviated name of the journal (ISO specification) without periods, e.g.: N Engl J Med | |||
|- | |||
| <code>{{{year}}}</code> | |||
| The year the article was published. | |||
|- | |||
| <code>{{{volume}}}</code> | |||
| The volume of the journal. | |||
|- | |||
| <code>{{{pages}}}</code> | |||
| 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". | |||
|- | |||
| <code>{{{pmid}}}</code> | |||
| The PMID number (i.e., the same ID that was used to call #pmid). | |||
|- | |||
| <code>{{{doi}}}</code> | |||
| The DOI ([http://www.doi.org Digital Object Identifer]) of the article that points to the full text. Not all Pubmed entries provide this information. | |||
|- | |||
| <code>{{{abstract}}}</code> | |||
| The article's abstract. If you want to have a ''collapsible'' abstract in your template, consider using this code: <code><nowiki>{{#if:{{{abstract}}}|<span class="mw-collapsible mw-collapsed" data-expandtext="Abstract" data-collapsetext="Abstract">{{{abstract}}}</span>}}</nowiki></code> (NB: This only works in MediaWiki '''1.18+'''). | |||
|} | |||
=== Example template "pubmed" === | |||
<nowiki>{{{authors}}}: {{{title}}}. ''{{{journala}}}'' {{{year}}};{{#if:{{{volume|}}}|{{{volume|}}}:}}{{{pages|)}}}. | |||
PMID: [https://www.ncbi.nlm.nih.gov/pubmed/{{{pmid|}}} {{{pmid|}}}]. {{</nowiki>'''<nowiki>#if</nowiki>'''<nowiki>:{{{doi|}}}|[https://dx.doi.org/{{{doi|}}} DOI].}}</nowiki> | |||
Formatted example: | |||
{| class="wikitable" style="width:100%;" | |||
| Cumming ''et al.'': Error bars in experimental biology. ''J. Cell Biol.'' 2007;177:7-11. PMID: [https://www.ncbi.nlm.nih.gov/pubmed/17420288 17420288]. [https://dx.doi.org/10.1083/jcb.200611141 DOI]. | |||
|} | |||
Note: This template requires the [[Help:Extension:ParserFunctions|ParserFunctions]] extension (which provides <code><nowiki>{{#if:test|then|else}}</nowiki><code>) to link the DOI only if it is contained in the Pubmed data. | |||
===Adding <nowiki><ref></ref></nowiki> tags automatically=== | |||
You may add an additional parameter to the #PMID call to make the PubmedParser automatically insert <code><nowiki><ref></ref></nowiki></code> tags. The [[Extension:Cite|Cite]] extension will use these tags to build your bibliography. To reuse the reference, simply insert <code><nowiki><ref name="yourparameter" /></nowiki></code>. | |||
Example: | |||
<nowiki>{{#pmid:19782018|Alon2009}}</nowiki> | |||
This will produce the following output: | |||
{| class="wikitable" style="width:100%;" | |||
| <nowiki><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></nowiki> | |||
|} | |||
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 [[Extension:Cite|Cite]] extension, which contains whatever output your template "pubmed" produces from this. | |||
To cite this same paper again, simply type <code><nowiki><ref name="Alon2009" /></nowiki></code> | |||
==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". | |||
{| class="wikitable" | |||
|+ 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 | |||
| <nowiki>''et al.''</nowiki> | |||
|- | |||
| pubmedparser-initialseparator | |||
| Separator between last name and initials (e.g., ",") | |||
| [empty] | |||
|- | |||
| pubmedparser-initialperiod | |||
| Abbreviation symbol for the initials (e.g., "." or ". "). | |||
| [empty] | |||
|} | |||
==Installation== | |||
{{TNT|ExtensionInstall | |||
|download-link=[https://github.com/bovender/PubmedParser/releases Download] | |||
|db-update=Yes | |||
|registration=required | |||
}} | |||
{{TNT|Note|Older versions of the extension required the PHP parameter <code>allow_url_fopen</code> 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 == | |||
; 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: | |||
<nowiki>{{#pmid:123456|reload}}</nowiki> | |||
or | |||
<nowiki>{{#pmid:123456|Miller2011|reload}}</nowiki> | |||
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. |
Latest revision as of 11:51, 7 February 2018
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. 2024 Embryology Pubmed. Retrieved May 4, 2024, from https://embryology.med.unsw.edu.au/embryology/index.php/Template_talk:Pubmed
APA format
Cite this page: Hill, M.A. (2024, May 4) 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
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.