Help:Reference Tutorial

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Introduction

Dr Mark Hill
Dr Mark Hill

This current page is not a list of references, but a resource to help students and contributors format their page citations. An extension has been installed in this site that allows automatic reference formatting even if only the PubMed ID number is known. In the examples below the PubMed ID number appears as XXXX, replace this with the number appearing after PMID on the PubMed Mediline database.

Note that extremely new PubMed entries or those appearing as links from Bookshelf may not work with the automatic formatting and may need to be manually formatted as a ref. This appears to be something to do with how references are initially added/linked within the PubMed database and for new entries generally resolved in a few weeks.

There is a separate page describing how references appear on this website. (More? References)


Mark Hill (talk) 10:58, 15 February 2018 (AEDT) Implemented new extension PubmedParser will eventually replace original extension Pubmed. Allows easier reference formatting changes (now APA) and local cache settings.

Wiki Code

  • In-text citation (superscript number):
{{#pmid:17304021|PMID17304021}}
  • In-text multiple citation (superscript same number):
<ref name="PMID17304021" />
  • Reference list:
{{#pmid:17304021}}


Editing Links: Editing Basics | Images | Tables | Referencing | Journal Searches | Copyright | Font Colours | Virtual Slide Permalink | My Preferences | One Page Wiki Card | Printing | Movies | Language Translation | Student Movies | Using OpenOffice | Internet Browsers | Moodle | Navigation/Contribution | Term Link | Short URLs | 2018 Test Student


Reference Links: Embryology Textbooks | Journals | Journal Searches | Reference Tutorial | Copyright | For Students | UNSW Online Textbooks | iBooks | Journals | RSS Feeds | Online | Societies | Online Databases | Historic - Textbooks | Pubmed Most Recent | Category:References

How to show the formatted PubMed Reference

If you do want the reference to appear as the full PubMed formatted reference at a specific location on a page simply use the tags:

{{#pmid:17304021}}

For example:

Hill MA. (2007). Early human development. Clin Obstet Gynecol , 50, 2-9. PMID: 17304021 DOI.


If you want the reference to appear as a PMID external link, simply use the text PMID XXXX. (note there should be a space but no colon between the text and the number).

For Example: PMID 17304021

How to Insert Any Reference

You are not restricted to using this automatic formatting, as any text enclosed by the tags:

<ref>your text here</ref>

Will insert a superscript number in the text where it is inserted and appear exactly as formatted in your reference list.


How to Insert PubMed References

This online site has an extension that allows automatic reference formatting if the PubMed ID number is known. Shown below is the code required to make the reference display correctly on your page. In addition, if the reference is cited more than once on a page there is specific code required to get the right citation list generated. At the bottom of this section is an example of how the code displays references.

Simply copy and paste the text shown in the examples below replacing XXXXX with the only the PubMed number (no text).

Single Instance on Page

Where the cited text, image or other referenced material appears place the following code:

{{#pmid:XXXXX1|PMIDXXXXX}}

Then make a section towards the bottom of the page called "References" and place the following text below the heading

<references/>


Shown below is an example of how a single citation will appear on the page and how the the reference list formats this citation. Note the reference list formatting is globally determined on this site and can be altered if required.

The human embryo development has been recently reviewed.[1]

References

  1. Hill MA. (2007). Early human development. Clin Obstet Gynecol , 50, 2-9. PMID: 17304021 DOI.

Multiple Instances on Page

If the material is cited multiple times upon a page, then it can appear as a single entry in you list if it is "named" in the first instance that it appears. Where the first cited text, image or other referenced material appears place the following code:

{{#pmid:XXXXX|PMIDXXXXX}}

Note the ref name must include the text PMID as a number alone is not allowed.

Future places where the above reference is cited place the following code:

<ref name="PMIDXXXXX"/>

Shown below is an example of how a multiple citations will appear on the page and how the the reference list formats this citation. Note that a single page can have multiple reference lists, but I prefer a single list, which will only contain references above the list.

The human embryo development has been recently reviewed.[1] Now we can use the same citation later on the page using just the reference name code.[1] Also see that no matter how many times we use this citation the numbering remains the same.[1]

Note that if you reorganise page content, ensure that the first instance of the reference has the ref name tag <ref name="PMIDXXXXX">.


References

  1. 1.0 1.1 1.2 Hill MA. (2007). Early human development. Clin Obstet Gynecol , 50, 2-9. PMID: 17304021 DOI.




Now all you have to do is Search the PubMed database.

Known Referencing Error

  • Occasionally some very recent references (July-August 2012) may not yet be linkable.
  • When you try to save one of these references a blank page will load with the following error message:
"Fault: Could not open file tmp\pubmedcache/d4/ for writing, at Persistant::save"
  • Do not panic, you have not lost all your work. The reference is simply not available to be loaded on the Wiki. You will not be able to continue editing the page until you have fixed the reference causing this error.
  • Use the browser back button to return to the project page.
  • Edit the reference entry to just the reference PMID number <ref>PMID 12345</ref> (without the colon)
  • You will be able to enter the complete reference manually later.


Medline Database

MEDLINE is a literature database of life sciences and biomedical information containing review and research articles. See also Project Referencing to generate references within your project, a reference list on your page and formatting the pubmed reference link.

  • Pubmed MEDLINE is the National Library of Medicine (NLM) USA premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences." (NCBI)
    • MH - I would prefer reference links to be added pointing to this database.
  • UNSW also has the MEDLINE database available through the Library using Sirius.
    • While it is essentially the same reference database, some papers will have different access rights based upon the university's subscriptions.

Searching with nearly any term will result in a large number of results that can be made more specific by either:

  1. Using "Preview/Index" option to carry out an additional search and then combining with your first result. (#1 AND #2) or
  2. Using "Limits" option to set limits on your search results. (review, years, english, etc)

Other Reference Databases

  • The referencing extension will only work with the PubMed Id number.
  • You can search for reference databases on Biomed Central or Public Library of Science or Journal home pages.
  • You will have to then find the PubMed Id number by Google searching with the paper title.
    • Multiple results will be found the PubMed Id number is shown by the link www.ncbi.nlm.nih.gov/pubmed/PubMed Id.


OMIM Database

  • OMIM - "OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype."

Note OMIM web entry addresses have recently been shifted from PubMed to omim.org

Referencing Templates

Note these are protected draft templates, not for general (student) usage.

PubMed Parser

Used to format references as they appear on the page (APA style). Note that historic references do not use this template or format.

Template variables

Admin only - 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.

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+).


{{{allauthorsi}}}. ({{{year}}}). {{{title}}}.  {{{journala}}} , {{{volume}}}, {{{pages}}}. PMID: [1] 

Code:

{{Pubmed}}

References footer

This footer is a "container" that has the NCBI disclaimer copyright template, and a link to this current Help page. This template can be updated if required to contain additional reference information.

Code:

{{References footer}}

Produces the following text and links:

NCBI - Policies and Guidelines | PubMed | Help:Reference Tutorial

NCBI disclaimer copyright

NCBI Website and Data Usage Policies and Disclaimers - the template below can be used at the bottom of pages containing a list of references and complies with the NCBI policy of displaying an acknowledgement linked to the NCBI page and a link to the Pubmed state page.

"Information that is created by or for the US government on this site is within the public domain. Public domain information on the National Library of Medicine (NLM) Web pages may be freely distributed and copied. However, it is requested that in any subsequent use of this work, NLM be given appropriate acknowledgment."


Code:

{{NCBI disclaimer copyright}}

Produces the following text and links:

NCBI - Policies and Guidelines | PubMed


External Links

External Links Notice - The dynamic nature of the internet may mean that some of these listed links may no longer function. If the link no longer works search the web with the link text or name. Links to any external commercial sites are provided for information purposes only and should never be considered an endorsement. UNSW Embryology is provided as an educational resource with no clinical information or commercial affiliation.


  • Extension:Pubmed - "The extension can fetch literature data from scientific articles stored in PubMed (www.pubmed.org), 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 WorldCat.org 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."
  • Son of Citation Machine - This online citation tool was originally created by David Warlick of The Landmark Project on October 29, 2000 and is part of the Landmarks for Schools Web site for teachers.
  • Extension: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."


Glossary Links

Glossary: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | Numbers | Symbols | Term Link

Cite this page: Hill, M.A. (2018, December 17) Embryology Reference Tutorial. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Help:Reference_Tutorial

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© Dr Mark Hill 2018, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G