Antibody:X: Difference between revisions

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===Header===
===Header===
I would favour ''anti Tubulin'' instead of the current ''Name: Tubulin''. It's a frequent short hand for antibody against tubulin. The Greek letter looks strange in this font.
I would favour ''anti Tubulin'' instead of the current ''Name: Tubulin''. It's a frequent short hand for antibody against tubulin.  
*[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done
 
The Greek letter looks strange in this font.
*[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)We need a better one then. Both should look at alternatives


===Uniprot links===
===Uniprot links===
Is it possible to generate a link from the UniProt ID similar to PMID 1234567? Something like '''Uniprot P23258'''. As far as I understand UniProt currently has the following URL structure: <nowiki>http://www.uniprot.org/uniprot/P23258</nowiki>
Is it possible to generate a link from the UniProt ID similar to PMID 1234567? Something like '''Uniprot P23258'''. As far as I understand UniProt currently has the following URL structure: <nowiki>http://www.uniprot.org/uniprot/P23258</nowiki>
*[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done. Added uniprotid field


===Additional field===
===Additional field===
I'm wondering whether antibody provider should be an infobox field. Nowadays, most antibody are purchased from companies instead of generated in the lab. In other words, most antibodies will have 1+ commercial provider that could be linked to here or in the main page.
I'm wondering whether antibody provider should be an infobox field. Nowadays, most antibody are purchased from companies instead of generated in the lab. In other words, most antibodies will have 1+ commercial provider that could be linked to here or in the main page.
*[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done. Added provider and link to example
**Should we make this always generate link to oww page?
**Do not want people putting url's here.
**make oww provider page instead. Link can go there.


===Putting parameters in order===
===Putting parameters in order===
Line 35: Line 44:
# '''Cross-reactive (with)'''
# '''Cross-reactive (with)'''
# '''Not cross-reactive (with)'''
# '''Not cross-reactive (with)'''
*[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done. Check and revise full list for me as needed.


Regarding experiment paraffin is generally the most challenging technique for an antibody, so it should come last after cryo.
Regarding experiment paraffin is generally the most challenging technique for an antibody, so it should come last after cryo.
*[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Will change


===Subdividing infobox parameters===
===Subdividing infobox parameters===
Logically, the bottom 5 are separate from the top half - experiments vs. antibody properties. It would be great if this were highlighted graphically, e.g. by drawing an additional box around the top and bottom halves. The bottom half could have the heading: "Suitability for.." or sth similar.
Logically, the bottom 5 are separate from the top half - experiments vs. antibody properties. It would be great if this were highlighted graphically, e.g. by drawing an additional box around the top and bottom halves. The bottom half could have the heading: "Suitability for.." or sth similar.
*[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)still working on this. box will appear soon. Templates are not easy with nested tables but not impossible


===Antibody type===
===Antibody type===
Line 48: Line 60:
:* raised in species: mouse, rat, guinea pig, rabbit, goat, chicken,..
:* raised in species: mouse, rat, guinea pig, rabbit, goat, chicken,..
**Need input: you tell me. Will do as you want. - ''let's go for one field since currently all non-mouse Ab are polyclonal''
**Need input: you tell me. Will do as you want. - ''let's go for one field since currently all non-mouse Ab are polyclonal''
***[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done


== Past changes ==
== Past changes ==
Line 55: Line 68:
* raised against: full-length protein, peptide
* raised against: full-length protein, peptide
** OK
** OK
***[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done


* cross-reactive against: mouse, rat, human,.. (this will always be the species it was raised against, here human and may be more species)
* cross-reactive against: mouse, rat, human,.. (this will always be the species it was raised against, here human and may be more species)
** OK
** OK
***[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done


* not cross-reactive against: as above
* not cross-reactive against: as above
** OK - ''made this italic to offset it from the species where this antibody can be used''
** OK - ''made this italic to offset it from the species where this antibody can be used''
***[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done


==For documentation==
==For documentation==
Line 72: Line 88:
** (I replaced the more cryptic names immunohistochemistry.. with more descriptive and more easily understood names)
** (I replaced the more cryptic names immunohistochemistry.. with more descriptive and more easily understood names)
** OK
** OK
***[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done


Usability evaluation:
Usability evaluation:
Line 79: Line 96:
* <font color=grey>untested</font>
* <font color=grey>untested</font>
** OK Coloring is automatic if one of the 4 tags above used. Otherwise it will be black. - ''Great, I like that.''
** OK Coloring is automatic if one of the 4 tags above used. Otherwise it will be black. - ''Great, I like that.''
***[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 09:55, 22 June 2009 (EDT)Done


==Description in main page==
==Description in main page==

Revision as of 06:55, 22 June 2009

                   
List of OpenWetWare Antibodies
anti γ Tubulin 1
Target UniProt ID  P23258
Cross-Reactive w  human
Not Cross-Reactive w  mouse, rat
Raised Against  peptide
Suitability for..
Western Blot  worked
Immunoprecipitation  untested
Staining fixed cells   uncertain
Staining cryo-sections  worked
Staining paraffin sections  failed
Help

Suggested changes to infobox template

Header

I would favour anti Tubulin instead of the current Name: Tubulin. It's a frequent short hand for antibody against tubulin.

The Greek letter looks strange in this font.

Uniprot links

Is it possible to generate a link from the UniProt ID similar to PMID 1234567? Something like Uniprot P23258. As far as I understand UniProt currently has the following URL structure: http://www.uniprot.org/uniprot/P23258

Additional field

I'm wondering whether antibody provider should be an infobox field. Nowadays, most antibody are purchased from companies instead of generated in the lab. In other words, most antibodies will have 1+ commercial provider that could be linked to here or in the main page.

  • Bill Flanagan (OpenWetWare.org at MIT) 09:55, 22 June 2009 (EDT)Done. Added provider and link to example
    • Should we make this always generate link to oww page?
    • Do not want people putting url's here.
    • make oww provider page instead. Link can go there.

Putting parameters in order

Suggested re-ordering of parameters:

  1. Target - most important info; should come top
  2. Antibody type
  3. Cross-reactive (with)
  4. Not cross-reactive (with)

Regarding experiment paraffin is generally the most challenging technique for an antibody, so it should come last after cryo.

Subdividing infobox parameters

Logically, the bottom 5 are separate from the top half - experiments vs. antibody properties. It would be great if this were highlighted graphically, e.g. by drawing an additional box around the top and bottom halves. The bottom half could have the heading: "Suitability for.." or sth similar.

Antibody type

  • we can either use description to contain source organisms and antibody type (e.g. mouse monoclonal IgG); antibody type would be more descriptive than description
OR
  • split it into 2 fields:
  • clonality: monoclonal or polyclonal (currently only antibodies raised in mice can be monoclonal, although that might change as technology advances)
  • raised in species: mouse, rat, guinea pig, rabbit, goat, chicken,..

Past changes

Parameters

  • target: e.g. standard protein name, possibly link to UniProt or NCBI protein
    • OK - put in an example target protein; abbreviation in target field, full name in box header
  • raised against: full-length protein, peptide
  • cross-reactive against: mouse, rat, human,.. (this will always be the species it was raised against, here human and may be more species)

For documentation

Usability for experiments

Types of experiments:

  • Protein blot (Western)
  • Immunoprecipitation (IP)
  • Staining fixed cells (ICC)
  • Staining paraffin sections (IHC-paraffin)
  • Staining cryo-sections (IHC-cryo)

Usability evaluation:

  • worked
  • uncertain
  • failed
  • untested


Description in main page

  • antibody created by..

Experimental evidence for infobox claims

Images

Description, conclusions..

Providers

  • company A with link & possible price
  • company B with link

Related Antibodies

List all related antibodies here.

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