Antibody:X: Difference between revisions

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*[[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
*[[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
**[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 17:23, 22 June 2009 (EDT)Use the buttons at the bottom of the editor bar to use the characters here rather than the html equivalents starting with an ampersand and ending with a semicolon
**[[User:Bill Flanagan|Bill Flanagan (OpenWetWare.org at MIT)]] 17:23, 22 June 2009 (EDT)Use the buttons at the bottom of the editor bar to use the characters here rather than the html equivalents starting with an ampersand and ending with a semicolon
***No difference. (both types shown above)


===Uniprot links===
===Uniprot links===

Revision as of 14:33, 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.

(ΑαΒβΓγΔδΕεΖζΗηΘθΙιΚκΛλΜμΝνΞξΟοΠπΡρΣσςΤτΥυΦφΧχΨψΩω )

(ΑΒΓΔΕΖΗΘΙΚΛΜΝΞΟΠΡΣΤΥΦΧΨΩαβγδεζηθικλμνξοπρςστυφχψωϑϒϖ)


  • Bill Flanagan (OpenWetWare.org at MIT) 09:55, 22 June 2009 (EDT)We need a better one then. Both should look at alternatives
    • Bill Flanagan (OpenWetWare.org at MIT) 17:23, 22 June 2009 (EDT)Use the buttons at the bottom of the editor bar to use the characters here rather than the html equivalents starting with an ampersand and ending with a semicolon
      • No difference. (both types shown above)

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

  • Bill Flanagan (OpenWetWare.org at MIT) 09:55, 22 June 2009 (EDT)Done. Added uniprotid field
      • 15:13, 22 June 2009 (EDT)I've clearly mislabeled this. We should find a way to make display conditional on setting the target as a protein.
      • I'm not currently testing for a valid link but it may be useful: don't include it if it will throw an error. Good idea for a simple extension to only allow a link if it works. Later.

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.
      • Bill Flanagan (OpenWetWare.org at MIT) 15:13, 22 June 2009 (EDT)This is how it now is implemented. Put in the name of the provider. The info is formatted as an OWW link. Points to Provider:Antibody/Provider-Name where Provider-Name is the provider entered

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,..
    • Need input: you tell me. Will do as you want. - let's go for one field since currently all non-mouse Ab are polyclonal
    • Bill Flanagan (OpenWetWare.org at MIT) 15:21, 22 June 2009 (EDT)Do you still want to add clonaity (monoclonal or polyclonal)?
      • we can set the valid names to a pair but add others over time.
      • adding more values may require editing the template. will see if there's a way to use a list.
    • Bill Flanagan (OpenWetWare.org at MIT) 15:21, 22 June 2009 (EDT)Do you still want to add "raised in"?

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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