Template:Antibody/doc: Difference between revisions

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attempt to fix template - removed nonfunctional create antibody button
 
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<noinclude>{{Documentation subpage}}
{{timw|Antibody}}
</noinclude>
<!---->
<!---->
== Purpose ==
== Purpose ==
This template should be added to the main page of all antibodies documented on this wiki (and only the main page).  It will add a useful infobox using the information supplied (see below) and will automatically add the antibody to [[:Category:All antibodies]], plus the appropriate [[:Category:Antibodies by status|status]] and [[:Category:Antibodies by implementation type|implementation type]] categories.
This template should be added to the main page of all antibodies documented on this wiki (and only the main page).  It will add a useful infobox using the information supplied (see below) and will automatically add the antibody to <nowiki>[[Category:All antibodies]]</nowiki>.


== Usage ==  
== Usage ==  
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|- valign="top"
|- valign="top"
| align="left" |
| align="left" |
<span id="CutAndPaste">Cut and paste:</span>
<span id="CutAndPaste">Cutting and pasting the text below will create an infobox (see right):</span>
<pre>{{Antibody|templatemode =
<pre>{{Antibody
|name          =  
|name          =
|status        =
|antibodytype  =
|type1        =
|uniprotid    =
|type2        =
|xreactive    =
|username      =
|nonxreactive  =
|author        =
|against      =
|description  =
|provider-name =
|image        =
|provider-url  =
|imagesize    =
|westernblot  =
|update        =
|ip            =
|westernblot  = yes
|icc          =
|immunoprecipitation =
|ihc-cryo      =
|immunocytochemistry =
|ihc-paraffin  =
|immunohistochemistry =
}}</pre>
}}</pre>


For help with parameter values, see [[#Content parameters|below]].
For help with parameter values, see [[#Content parameters|below]].


| align="right"|{{Antibody|templatemode=nocats
| align="right"|{{Antibody
|name          = {{{name}}}
|name          = {{{name}}}
|status        = {{{status}}}
|antibodytype  = {{{antibodytype}}}
|type1        = {{{type1}}}
|uniprotid    = {{{uniprotid}}}
|type2        = {{{type2}}}
|xreactive    = {{{xreactive}}}
|username      = SomeUser
|nonxreactive  = {{{nonxreactive}}}
|author        = SomeAuthor
|against       = {{{against}}}
|image        = Placeholder.png
|provider-name = {{{provider-name}}}
|version       = {{{version}}}
|provider-url  = {{{provider-url}}}
|update        = {{{update}}}
|example      = {{{example}}}
|westernblot  = {{{westernblot}}}
|westernblot  = {{{westernblot}}}
|immunoprecipitation = {{{immunoprecipitation}}}
|ip            = {{{ip}}}
|immunocytochemistry = {{{immunocytochemistry}}}
|icc          = {{{icc}}}  
|immunohistochemistry = {{{immunohistochemistry}}}
|ihc-cryo      = {{{ihc-cryo}}}
|ihc-paraffin  = {{{ihc-paraffin}}}
}}
}}
|}
|}
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== Content parameters ==
== Content parameters ==
This section describes parameters that govern infobox content. For help with '''templatemode''' and other control parameters, please see  ''[[#Control parameters|Control parameters]]''.
This section describes parameters that govern infobox content.
 
<!-- BEFORE YOU EDIT THIS:
<!-- BEFORE YOU EDIT THIS:
     span ids on each parameter are used by the code in Template:Antibody.
     span ids on each parameter are used by the code in Template:Antibody.
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|
|
{|border="1"
{|border="1"
|+ '''Content parameters'''
|<span id="name">'''name'''</span> || '''Name''' of the antibody e.g. gamma Tubulin 1 Abcam 12345
|-
|<span id="antibodytype">'''antibodytype'''</span> || '''Type of antibody''' e.g. mouse monoclonal, lama polyclonal, etc.
|-
|<span id="uniprotid">'''uniprotid'''</span> || '''UNIPROT Database id''' of the antibody e.g. P23258
|-
|-
|<span id="name">'''name'''</span> || '''name of the antibody'''
| <span id="xreactive">'''xreactive'''</span>|| '''Cross-reactive against''': antibody works against proteins of these species; e.g. human and mouse
|-
|-
|<span id="status">'''status'''</span> || '''current release status'''
| <span id="nonxreactive">'''nonxreactive'''</span>|| '''Not Cross-reactive with''': antibody does not recognise proteins of these species; e.g. rat
One of:  
* ''[[:Category:Unstable antibodies|unstable]]'' (broken - documentation of this antibody is not complete)
* ''[[:Category:In-Progress antibodies|In-Progress]]'' (early stages of development, may change drastically.)
* ''[[:Category:Stable antibodies|stable]]'' (stable version)
* ''[[:Category:Antibodies with unknown status|unknown]]'' (default)
If the status is anything other than the above, it will be ignored and the default value of 'Unknown' will be displayed in the template instead.  In cases where the value is omitted, it will be categorised as [[:category:antibodies with unknown status|unknown]].  In cases where the value is invalid, it will be placed in a [[:category:antibodies with invalid status|special category]] so that the error can be caught and fixed.
|-
|-
| '''type1'''<br/>''type2''<br/>''type3''<br/>''type4''<br/>''type5''<br/>''type6''<br/> || <span id="type">'''implementation type'''</span><!-- id here so at top of documentation -->
| <span id="against">'''against'''</span>||'''Raised Against''':  type of molecule the antibody was raised against; e.g. peptide or full-length protein
 
|-
The  implementation strategy(s) employed in building this antibody. This parameter is used to create categories that help programmers find examples of various MediaWiki specific implementation strategies or patterns.  Although the values of this parameter sometimes coincide with the use case or purpose of an antibody, that is not reason for this parameter.  If the values you have chosen for this parameter do not adequately identify the [[w:Requirements|purpose]] or possible [[w:Use case|use case]]s, we recommend you add additional [[Help:Categories|category links]] as needed.
| <span id="provider-name">'''provider-name'''</span>||'''Commercial Provider''' or source for this antibody based upon experience.
 
Any other value for 'type' is invalid, and will cause the antibody to be placed in [[:Category:Antibodies with invalid or missing type]].
 
Note: Many antibodies have more than one type, if this applies to yours,replace <code><nowiki>|type=</nowiki></code> with <code><nowiki>|type1=|type2=|type3=...</nowiki></code>.  You may define up to six types for an antibody.
|-
|-
| <span id="username">'''username'''</span> || The author's username on OpenWetWare.org (if they have one). May be omitted, but if present it will be used to link to the author's user & user_talk page.
| <span id="provider-url">'''provider-url'''</span>||'''Commercial Provider URL''': web page related to this antibody.
|-
|-
| <span id="author">author</span>|| The antibody author's name, if different from their OpenWetWare.org username. Free text. If omitted then the 'username' field will be used (if present).
| <span id="westernblot">'''westernblot'''</span>|| '''Suitable for Western Blotting''': Is the antibody suitable for Western Blotting? Possible values: failed, worked, uncertain, untested
|-
|-
| <span id="description">'''description'''</span>|| '''short description'''
| <span id="ip">'''ip'''</span>|| '''Immunoprecipitation:''' as above; does the antibody work in this experiment? Possible values: failed, worked, uncertain, untested
|-
|-
| <span id="image">image</span>|| screenshot or logo of antibody
| <span id="icc">'''icc'''</span>|| '''Immunocytochemistry:''' As above; please add the evidence to the main page. Possible values: failed, worked, uncertain, untested
|-
|-
| <span id="imagesize">imagesize</span>|| ''facultative'', size of the image (default size is 220px)
| <span id="ihc-cryo">'''ihc-cryo'''</span>|| '''Immuno-histo-cryo-chemistry:''' Possible values: failed, worked, uncertain, untested
|-
|-
| <span id="update">update</span>|| date of the last update
| <span id="ihc-paraffin">'''ihc-paraffin'''</span>|| '''Immuno-histo-paraffin-chemistry''': Possible values: failed, worked, uncertain, untested
|}
|}


== Control parameters ==
{| border="1"
|+ '''Control parameters'''
|-
| '''templatemode''' || '''Controls auto-categorization of host page.'''


Normally left blank.  Alternate values are:
== Using the infobox ==
* ''nocats'' - suppresses categorization. Use this value if you are adding this template to [[Help:Subpage|subpages]] of an antibody or to how-to documentation of antibodies. For example, the usage image above sets <code>templatemode=nocats</code> because this isn't an actual antibody page and we don't want to add this page to any categories on account of it.
 
 
If this is left blank, this template will add the host page to [[:Category:All antibodies]] and to one or more additional categories, depending on the values assigned to the [[#Content parameters|Content parameters]].
|}


== Using the infobox ==
=== Existing antibody pages ===
=== Existing antibody pages ===
If you want to add the infobox to an existing page, copy and paste the code at the [[#CutAndPaste|top of this page]].
If you want to add the infobox to an existing page, copy and paste the code at the [[#CutAndPaste|top of this page]].
=== Create a new antibody article ===
If you want to create a new antibody page, enter the name below and click the button. A new page will be created with the infobox template already in place.
{{Antibody/CreateAntibodyInputBox}}


== Enhancing this template ==
== Enhancing this template ==
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=== Fixing documentation ===
=== Fixing documentation ===
If you would like to fix documentation, please be aware that documentation and code is split into two files:
If you would like to fix documentation, please be aware that documentation and code is split into two files:
* '''[[Template:Antibody/Doc]]''' - stores all documentation.
* '''[[Template:Antibody/doc]]''' - stores all documentation.
* '''[[Template:Antibody]]''' - stores only the code for the template and a small amount of non-included material (category links, transcluded documentation link).
* '''[[Template:Antibody]]''' - stores only the code for the template and a small amount of non-included material (category links, transcluded documentation link).


 
In addition, [[Template:Antibody/Sample]] stores the boiler plate that is preloaded into newly created pages and contains some basic documentation on how to fill in the template parameters.  It needs to be kept in sync with [[Template:Antibody/doc]].
In addition, [[Template:Antibody/Sample]] stores the boiler plate that is preloaded into newly created pages and contains some basic documentation on how to fill in the template parameters.  It needs to be kept in sync with [[Template:Antibody/Doc]].
 
=== The Create antibody button ===
To improve the create antibody button behavior:
* '''[[Template:Antibody/Sample]]:''' The boilerplate antibody that is preloaded into newly-created pages.
* '''[[Template:Antibody/CreateAntibodyInputBox]]:''' An input box that can be inserted wherever you want users to easily create antibodies.  For documentation on the <code><nowiki><inputbox></nowiki></code> tag, please see [[Antibody:InputBox]].
* '''[[Antibody:MyAntibody]]:''' - Defines a placeholder, in case a user accidentally hits the create button without changing the antibody name.


=== Infobox parameters ===
=== Infobox parameters ===
In general:
In general:
* To make this template easy to use, each label in the infobox is linked to documentation on the template parameter(s) it displays.  If you add a parameter, please be sure to also add it to the [[Template:Antibody/Doc#Content parameters|content parameter documentation]] and link its label to that documentation.
* To make this template easy to use, each label in the infobox is linked to documentation on the template parameter(s) it displays.  If you add a parameter, please be sure to also add it to the [[Template:Antibody/doc#Content parameters|content parameter documentation]] and link its label to that documentation.
 
 
To change/correct/add to the implementation type parameters:
* Check the [[Template_talk:Antibody|talk page]] - there have been some extensive discussions about this field.
* '''[[Template:Antibody/TypeSwitch]]:''' Stores the possible values for the type field.  Multiple values are implemented by calling this template with [[Template:Foreach]].
* '''[[Template:Antibody/TypeSwitchNoCats]]:''' Used instead of [[Template:Antibody/TypeSwitch]] when this template is used in <code>templatemode=nocats</code>.  Templates used with [[Template:Foreach]] can only take one parameter so we need to wrap the call to [[Template:Antibody/TypeSwitch]] with another template that sets the mode.
* '''[[Template:Antibody/Doc]]:''' Documentation for this template needs to be kept in sync with any changes to the implementation type taxonomy.


== Test case ==
== Test case ==
See if the following pages are still ok, after edited this template.
See if the following pages are still ok, after edited this template.
* [[Antibody:X]]
* [[Antibody:X]]
* [[User:Ans/{{FULLPAGENAME}}#{{FULLPAGENAME}}]]

Latest revision as of 10:49, 8 June 2010

Purpose

This template should be added to the main page of all antibodies documented on this wiki (and only the main page). It will add a useful infobox using the information supplied (see below) and will automatically add the antibody to [[Category:All antibodies]].

Usage

Cutting and pasting the text below will create an infobox (see right):

{{Antibody
|name          =
|antibodytype  =
|uniprotid     =
|xreactive     =
|nonxreactive  =
|against       =
|provider-name =
|provider-url  =
|westernblot   =
|ip            =
|icc           =
|ihc-cryo      =
|ihc-paraffin  =
}}

For help with parameter values, see below.

                       
List of OpenWetWare Antibodies
anti {{{name}}}
Antibody Type  {{{antibodytype}}}
Target UniProt ID  {{{uniprotid}}}
Cross-Reactive w  {{{xreactive}}}
Not Cross-Reactive w  {{{nonxreactive}}}
Raised Against  {{{against}}}
Provider  [{{{provider-url}}} {{{provider-name}}}]
Suitability for..
Western Blot  {{{westernblot}}}
Immunoprecipitation  {{{ip}}}
Staining fixed cells   {{{icc}}}
Staining cryo-sections  {{{ihc-cryo}}}
Staining paraffin sections  {{{ihc-paraffin}}}
Help


Content parameters

This section describes parameters that govern infobox content.

name Name of the antibody e.g. gamma Tubulin 1 Abcam 12345
antibodytype Type of antibody e.g. mouse monoclonal, lama polyclonal, etc.
uniprotid UNIPROT Database id of the antibody e.g. P23258
xreactive Cross-reactive against: antibody works against proteins of these species; e.g. human and mouse
nonxreactive Not Cross-reactive with: antibody does not recognise proteins of these species; e.g. rat
against Raised Against: type of molecule the antibody was raised against; e.g. peptide or full-length protein
provider-name Commercial Provider or source for this antibody based upon experience.
provider-url Commercial Provider URL: web page related to this antibody.
westernblot Suitable for Western Blotting: Is the antibody suitable for Western Blotting? Possible values: failed, worked, uncertain, untested
ip Immunoprecipitation: as above; does the antibody work in this experiment? Possible values: failed, worked, uncertain, untested
icc Immunocytochemistry: As above; please add the evidence to the main page. Possible values: failed, worked, uncertain, untested
ihc-cryo Immuno-histo-cryo-chemistry: Possible values: failed, worked, uncertain, untested
ihc-paraffin Immuno-histo-paraffin-chemistry: Possible values: failed, worked, uncertain, untested


Using the infobox

Existing antibody pages

If you want to add the infobox to an existing page, copy and paste the code at the top of this page.

Enhancing this template

If you would like to improve on this template, thanks! This is a complicated template so here is some help along the way:

Fixing documentation

If you would like to fix documentation, please be aware that documentation and code is split into two files:

  • Template:Antibody/doc - stores all documentation.
  • Template:Antibody - stores only the code for the template and a small amount of non-included material (category links, transcluded documentation link).

In addition, Template:Antibody/Sample stores the boiler plate that is preloaded into newly created pages and contains some basic documentation on how to fill in the template parameters. It needs to be kept in sync with Template:Antibody/doc.

Infobox parameters

In general:

  • To make this template easy to use, each label in the infobox is linked to documentation on the template parameter(s) it displays. If you add a parameter, please be sure to also add it to the content parameter documentation and link its label to that documentation.

Test case

See if the following pages are still ok, after edited this template.