Help:Editing: Difference between revisions
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Before using this page, you may find it useful to consult [[Proteopedia:Getting_Started|Help:Getting Started in Proteopedia]], the [[Proteopedia:Video Guide|Video Guides]], and the main [[Help]] Page. | |||
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==<big>Help with Wikitext Syntax</big>== | ==<big>Help with Wikitext Syntax</big>== | ||
Please visit the <big>[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Cheatsheet] and [http://en.wikipedia.org/wiki/Help:Wiki_markup A Reference On Wikitext Syntax]</big>, both in Wikipedia, as they have a much more complete help reference dealing with wikitext, and Proteopedia uses the same wiki software. | Please visit the <big>[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Cheatsheet] and [http://en.wikipedia.org/wiki/Help:Wiki_markup A Reference On Wikitext Syntax]</big>, both in Wikipedia, as they have a much more complete help reference dealing with wikitext, and Proteopedia uses the same wiki software. | ||
==Use Sandboxes for practice editing== | ==Use Sandboxes for practice editing== | ||
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Please see [[Proteopedia:How to Make a Page]] for guidance as to how to make an excellent Proteopedia page. | Please see [[Proteopedia:How to Make a Page]] for guidance as to how to make an excellent Proteopedia page. | ||
== If you clicked on 'edit this page' but you cannot edit the page == | == Problems while editing == | ||
=== If you clicked on 'edit this page' but you cannot edit the page === | |||
* Make sure you are logged in. If you do not have a login account, go to the [[Special:Userlogin | Login / User Account]] page, and click '''request one'''. | * Make sure you are logged in. If you do not have a login account, go to the [[Special:Userlogin | Login / User Account]] page, and click '''request one'''. | ||
* If you are logged in (you see your name at the top of the page), and there is still no ''edit'' tab, please see [[Help:Protected_Pages]] for how to copy protected text into a new page that you can edit. | * If you are logged in (you see your name at the top of the page), and there is still no ''edit'' tab, please see [[Help:Protected_Pages]] for how to copy protected text into a new page that you can edit. | ||
=== If you get '''XML Error: Mismatched tags at line 1''' === | |||
Don't worry! You can fix this and recover your work. The instructions are at [[Help:Errors]]. | |||
=== If you get '''We could not process your edit due to a loss of session data''' === | |||
The full message says | |||
:<span style="color:red;">'''Sorry! We could not process your edit due to a loss of session data. Please try again. If it still doesn't work, try logging out and logging back in.'''</span> | |||
just under the 'Preview' heading. | |||
This is an infrequent error. See instructions at [[Help:Errors]]. | |||
==<big>To create or edit Proteopedia Scenes</big>== | ==<big>To create or edit Proteopedia Scenes</big>== | ||
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==Citing Literature References== | ==Citing Literature References== | ||
Each citation that is to appear as a numbered footnote at the bottom of an article should be '''enclosed between <ref> and </ref>'''. Only a number in brackets will be displayed in the text where you placed the reference. Clicking this bracketed number will jump to that reference at the bottom of the page, and block highlight it. Similarly, clicking the small upwards-pointing arrow that displays with the reference at the bottom of the page will jump to the place where it is cited, and block highlight the bracketed number. | Each citation that is to appear as a numbered footnote at the bottom of an article should be '''enclosed between <ref> and </ref>'''. Only a number in brackets will be displayed in the text where you placed the reference, like this<ref>This is just some text to illustrate that you can put any text in a reference/footnote.</ref>. Clicking this bracketed number will jump to that reference at the bottom of the page, and block highlight it. Similarly, clicking the small upwards-pointing arrow that displays with the reference at the bottom of the page will jump to the place where it is cited, and block highlight the bracketed number. | ||
While you can place any text between the <ref> and </ref> tags, there is a time-saving shortcut for publications indexed in PubMed (details below). | |||
To produce the list of numbered references at the bottom of the page, insert '''<references />''' (note the slash!). Typically this is placed after a title such as <nowiki>==References==</nowiki>. | To produce the list of numbered references at the bottom of the page, insert '''<references />''' (note the slash!). Typically this is placed after a title such as <nowiki>==References==</nowiki>. | ||
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<blockquote> | <blockquote> | ||
David and Jane Richardson introduced Kinemages in 1992 <ref>PMID:1304880</ref>. The following year, Roger Sayle released [[RasMol]] <ref name="rasmol">PMID:7482707</ref>. For web-based molecular visualization, [[Chime]] was very popular after its release in 1996, but in recent years, the [[Jmol]] java applet has become the best solution <ref name="jmol">Angel Herráez. Biomolecules in the computer: Jmol to the rescue. | David and Jane Richardson introduced Kinemages in 1992 <ref>PMID:1304880</ref>. The following year, Roger Sayle released [[RasMol]] <ref name="rasmol">PMID:7482707</ref>. For web-based molecular visualization, [[Chime]] was very popular after its release in 1996, but in recent years, the [[Jmol]] java applet has become the best solution <ref name="jmol">Angel Herráez. Biomolecules in the computer: Jmol to the rescue. | ||
[http://www3.interscience.wiley.com/journal/113449000/abstract Biochem. Mol. Biol. Ed. 34:255-261] (2006). [http://dx.doi.org/10.1002/bmb.2006.494034042644 DOI: 10.1002/bmb.2006.494034042644]</ref>. | [http://www3.interscience.wiley.com/journal/113449000/abstract Biochem. Mol. Biol. Ed. 34:255-261] (2006). [http://dx.doi.org/10.1002/bmb.2006.494034042644 DOI: 10.1002/bmb.2006.494034042644]</ref>. Angel Herráez has been a major leader in educational molecular visualization<ref name="jmol" />. Bob Hanson has been the primary developer of Jmol since 2006, and has [http://wiki.jmol.org/index.php/Literature recently implemented JSmol], a version that operates without [[Java]]. | ||
<ref>PMID: | </blockquote> | ||
Here is the wikitext for the previous paragraph with the <b><ref> tags in boldface</b>. Notice how a reference can be named (see <font color="red">red</font> below), and then cited again by name to avoid duplicating it in the reference list. (You could also see the wikitext by clicking the '''edit this page''' tab at the top of this article, but then be sure to click '''Cancel''' if you do not intend to change it.) | |||
<blockquote> | |||
David and Jane Richardson introduced Kinemages in 1992 <b><ref>PMID:1304880</ref></b>. The following year, Roger Sayle released <nowiki>[[RasMol]]</nowiki> <b><ref name="rasmol">PMID:7482707</ref></b>. For web-based molecular visualization, <nowiki>[[Chime]] was very popular after its release in 1996, but in recent years, [[Jmol]]</nowiki> has become the best solution <b><ref <font color="red">name="jmol"</font>>Angel Herráez. Biomolecules in the computer: Jmol to the rescue. <nowiki>[http://www3.interscience.wiley.com/journal/113449000/abstract Biochem. Mol. Biol. Ed. 34:255-261]</nowiki> (2006). <nowiki>[http://dx.doi.org/10.1002/bmb.2006.494034042644 DOI: 10.1002/bmb.2006.494034042644]</nowiki></ref></b>. Angel Herráez has been a major leader in educational molecular visualization<b><ref <font color="red">name="jmol"</font> /></b>. Bob Hanson has been the primary developer of Jmol since 2006, and has <nowiki>[http://wiki.jmol.org/index.php/Literature recently implemented JSmol], a version that operates without [[Java]]</nowiki>. | |||
</blockquote> | </blockquote> | ||
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===Citing by PubMed ID Number=== | ===Citing by PubMed ID Number=== | ||
When citing a publication indexed at PubMed | When citing a publication indexed at [http://pubmed.gov PubMed.Gov], type "PMID:" followed by the PubMedID number of the publication, and then enclose it between <ref> and </ref>. For example, type '''<nowiki><ref>PMID: 18673581</ref></nowiki>''' in the wikitext box and save the page. If you type the PubMedID in this manner, the properly formatted reference will created automatically at the bottom of the page (or wherever you place the necessary wikitext <nowiki>"<references/>"</nowiki>). The example reference: <ref>PMID: 18673581</ref>. | ||
====PubMed citations without footnote numbers==== | |||
It is also possible to list reference information from Pubmed without having them get assigned a bracketed number at the point of citation. This is done by adding them to the group '''xtra'''. For example this may be helpful when listing additional references indexed at Pubmed that don't contain items specifically cited in the text of the page. | |||
An example is "<nowiki><ref group="xtra">PMID:15068885</ref></nowiki>". If you type the PubMedID in this manner, the properly formatted reference will be created automatically wherever you place the necessary wikitext <nowiki>"<references group="xtra"/></nowiki>"". If you have a number of them to cite like this, putting all the additional references on one line eliminates excessive gaps in the page created when the items are hidden on the article page.<br> | |||
For example, the source,<br> | |||
<nowiki>Additional Literature and Resources</nowiki><br> | |||
<nowiki><ref group="xtra">PMID:15068885</ref><ref group="xtra">PMID:14749769</ref><ref group="xtra">PMID:1304880</ref></nowiki><br> | |||
<nowiki><references group="xtra"/></nowiki> | |||
will appear on the article page, as below:<br> | |||
<br> | |||
Additional Literature and Resources <ref group="xtra">PMID:15068885</ref><ref group="xtra">PMID:14749769</ref><ref group="xtra">PMID:1304880</ref> | |||
<references group="xtra"/> | |||
===Use DOI for citations not in PubMed=== | ===Use DOI for citations not in PubMed=== | ||
Nearly all recent publications have a DOI (Digital Object Identifier). Some journals, monographs, and other publications are not indexed in PubMed. For most of these references, it's enough to enter "DOI:" followed by the DOI identifier, and then enclose it between <ref> and </ref>. For example, type '''<nowiki><ref>DOI: 10.1002/bmb.2005.494033022442</ref></nowiki>''' in the wikitext box and save the page. | |||
When citing a reference for which the DOI is not enough for automatically retrieving the full reference, you will need to type (or copy and paste) the entire reference text along with the DOI. You can hyperlink the DOI to go to the cited document. Suppose that the reference is | |||
::Martz, E. Book review of Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M.. Biochem. Mol. Biol. Educ. 33:144-5 (2006). DOI: 10.1002/bmb.2005.494033022442 | |||
Then enter it in the wikitext like this (markup is '''bold'''; note two single quotes used for italics) | |||
::'''<nowiki><ref></nowiki>'''<nowiki>Martz, E. Book review of ''Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M. Biochem. Mol. Biol. Educ.'' 33:144-5 (2006). </nowiki>'''<nowiki>[http://dx.doi.org/10.1002/bmb.2005.494033022442</nowiki>'''<nowiki> DOI: 10.1002/bmb.2005.494033022442</nowiki>'''<nowiki>]</ref></nowiki>''' | |||
The resulting citation: <ref>Martz, E. Book review of <i>Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M.</i>. <i>Biochem. Mol. Biol. Educ.</i> 33:144-5 (2006). [http://dx.doi.org/10.1002/bmb.2005.494033022442 DOI: 10.1002/bmb.2005.494033022442]</ref>. | |||
===Not in PubMed, no DOI=== | ===Not in PubMed, no DOI=== | ||
For references not indexed at Pubmed, and lacking a DOI, you will need to put the information as you want it to appear in the reference list between the <ref> and </ref> tags. | For references not indexed at Pubmed, and lacking a DOI, you will need to put the information as you want it to appear in the reference list between the <ref> and </ref> tags. You may include hyperlinks (see hyperlinked DOI example above). You can also use <ref> and </ref> tags for footnotes that are not citations of publications (see '''References''' section below). | ||
===Repeat citations=== | ===Repeat citations=== | ||
If you want to cite the '''same publication again later''' in your text, you need to give a name to the first instance, for example <ref name="rasmol">...</ref>. Then, you can re-cite the same reference with this: <ref name="rasmol" />. (Note the trailing slash.) Here is how this will actually appear | If you want to cite the '''same publication again later''' in your text, you need to give a name to the first instance, for example <ref name="rasmol">...</ref>. Then, you can re-cite the same reference with this: <ref name="rasmol" />. (Note the trailing slash.) Here is how this will actually appear using two references already used in the first example of the '''Citing Literature References''' section | ||
<blockquote> | <blockquote> | ||
Although Sayle released RasMol in 1993, his publication did not appear until 1995<ref name="rasmol" />. Although Herráez wrote the cited paper on Jmol<ref name="jmol"/>, he appropriately credits Miguel Howard and Robert Hanson for most of Jmol's development for macromolecular displays. | Although Sayle released RasMol in 1993, his publication did not appear until 1995<ref name="rasmol" />. Although Herráez wrote the cited paper on Jmol<ref name="jmol"/>, he appropriately credits Miguel Howard and Robert Hanson for most of Jmol's development for macromolecular displays. | ||
</blockquote> | </blockquote> | ||
See the '''References''' section below and note how the each individual reference is listed only once with the separate instances linked. | |||
==Footnotes== | ==Footnotes== | ||
'''Footnotes:''' Literature references cited with the above method will appear as footnotes, for example at the bottom of this page. Footnotes are also a good place to put any technical or digressive notes to avoid having them intrude in the main text. You can put any footnote text between <ref> and </ref> tags. | '''Footnotes:''' Literature references cited with the above method will appear as footnotes, for example at the bottom of this page. Footnotes are also a good place to put any technical or digressive notes to avoid having them intrude in the main text. You can put any footnote text between <ref> and </ref> tags, for example <ref>This is an example of digressive text placed in a footnote.</ref>. | ||
The only thing you need to type into the wikitext at the bottom of your page, in order to display the footnotes and references there, are these two lines: | The only thing you need to type into the wikitext at the bottom of your page, in order to display the footnotes and references there, are these two lines: | ||
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The title of the References section can be any appropriate title, such as ''Literature Cited'', ''Footnotes'', ''Notes and References'', etc. | The title of the References section can be any appropriate title, such as ''Literature Cited'', ''Footnotes'', ''Notes and References'', etc. | ||
==Policies in Proteopedia== | ==Policies in Proteopedia== | ||
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==Tutorials== | ==Tutorials== | ||
Here is a list of tutorials that may help you | Here is a list of tutorials that may help you familiarize yourself with editing pages in Proteopedia | ||
*[[Proteopedia:Video_Guide]] | *[[Proteopedia:Video_Guide]] | ||
*[[User:Tom_Gluick/glutamine_synthetase]] | *[[User:Tom_Gluick/glutamine_synthetase]] | ||
*[[Help:Contents]] has a list of all tutorials and help within Proteopedia. | |||
==References== | ==References== | ||
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==See Also== | ==See Also== | ||
* [[Proteopedia:How to Make a Page|How to Make a Page]] | * [[Proteopedia:How to Make a Page|How to Make a Page]] | ||
* [[Help:Language Translation]] and [[Help:Text Directionality]] | |||
