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Draft evidence code ontology

Karen Christie kchris at genome.Stanford.EDU
Fri Feb 27 15:18:02 PST 2004


Hi,

comments inserted below


On Fri, 27 Feb 2004, Harold Drabkin wrote:

> Forgot to add something:
> I wouldn't call it a strong assay, but it is an assay none-the-less.

I'm not objecting to calling it an assay. I agree with you there that it
is an assay, just not a direct one. Thus my actual argument was that the
IPI code (which is the one that includes 2-hybrid experiments) should NOT
map up into the IDA code in the way that Michael had proposed.

> I don't think the ontology (if we go this route; remember it was voted down
> a few go meetings ago) has to imply whether it's better than other type of
> assay. It's just a type of assay.

I also completely agree with you there. I don't think GO evidence codes
should attempt to denote quality, and they certainly don't do this right
now.

> Perhaps we need 
> 
> Inferered from Experiment
> Then Direct Assay
> Then Indirect Assay

The direct/indirect split might be tricky. Certainly for IPI, some of the
specific assays listed are direct, while others, e.g. 2-hybrid, are not.

-Karen

> ??
> On 2/27/04 3:14 PM, "Karen Christie" <kchris at genome.stanford.edu> wrote:
> 
> > Well, personally, I don't think I'd always want IPI to map up into
> > IDA, with respect to GO evidence codes.
> > 
> > For example, I don't think I'd consider 2-hybrid evidence to be IDA. While
> > it is true that you know what plasmids you put into the cell, you do not
> > know exactly what is binding. The presumption is generally that the target
> > portion (let's call it T) of the activator construct is binding to the
> > bait portion (let's call it B) of the DNA-binding construct, but this is
> > indirect. You have not actually done a direct assay of the proteins T and
> > B to determine that they interact directly with each other.
> > 
> > -Karen
> > 
> > 
> > IDA inferred from direct assay
> > Enzyme assays 
> > In vitro reconstitution (e.g. transcription)
> > Immunofluorescence (for cellular component)
> > Cell fractionation (for cellular component)
> > Physical interaction/binding assay (sometimes appropriate for cellular
> > component or molecular function)
> > 
> > 
> > IPI inferred from physical interaction
> > 2-hybrid interactions
> > Co-purification 
> > Co-immunoprecipitation
> > Ion/protein binding experiments
> > 
> > 
> > On Fri, 27 Feb 2004, Harold Drabkin wrote:
> > 
> >> Why wouldn't an experiment that fell under an IPI be a type of IDA?
> >> 
> >> On 2/27/04 11:23 AM, "Midori Harris" <midori at ebi.ac.uk> wrote:
> >> 
> >>> 
> >>>>   %IDA
> >>>>    %IPI etc
> >>> 
> >>> This still does not work for the specialized case of GO annotation.
> >>> 
> >>> m
> >>> 
> >>> 
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> >> 
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> > 
> > 
> > 
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> 



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