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Draft evidence code ontology

Harold Drabkin hjd at informatics.jax.org
Fri Feb 27 13:44:21 PST 2004


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

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.

Perhaps we need 

Inferered from Experiment
Then Direct Assay
Then Indirect Assay

??
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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