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Draft evidence code ontology

Karen Christie kchris at genome.Stanford.EDU
Fri Feb 27 12:14:04 PST 2004


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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