[Annotation] [Go] Evidence code for gfp and phoA fusions?

[Valerie Wood]

Judith Blake wrote:
>
>
> you say
> "It's again one of those cases where the curator combines two 
> different pieces of information to make an annotation. We should think 
> of better ways to deal with this."
>
> isn't this classicly 'IC'  ?

Most IC historically are from a single GO term

i.e cytoplasmic ribosome ->translation
RNA polymerase II transcription factor activity-nucleus

Using 2 pieces of information was added later.

It isn't necessarily clear in the evidence code docs  that you can use 
multiple pipe separated GO IDs in the from field.

Val

>
> Judy
>> In these cases I have done
>>
>> i)    integral to membrane ISS TMM:whatever_its_called
>> ii)    plasma membrane IDA
>> iii)    integral to plasma membrane IC from GO:0016021|GO:0005886 
>> (you can put pipe separated GO ids in the "from" column, this was 
>> added purely for this type of annotation.
>>
>> Its a bit clunky but at least you can pull the different annotation 
>> sources apart..
>>
>> Val
>>
>>
>> Pascale Gaudet wrote:
>>> But, can you really see 'intrinsic to the membrane' by GFP?
>>> I think you can only see that it's membrane, and you know it's 
>>> intrinsic because there are TM domains (which would be ISM).
>>> c
>>>
>>> Pascale
>>>
>>> David Hill wrote:
>>>> Hi Jim,
>>>>
>>>> I would use IDA. As long as the purpose of the experiment is to 
>>>> show the normal localization of the protein and the authors show no 
>>>> reason to believe that the tags mislocalize the protein, then the 
>>>> authors are looking at the normal distribution. Although these 
>>>> experiments are subject to mislocalization due to the tags, like 
>>>> all experiments are subject to artifact, I think we need to go with 
>>>> the authors conclusions.
>>>> I have annotated GFP fusions in mammalian cells using IDA.
>>>>
>>>> David
>>>>
>>>> Jim Hu wrote:
>>>>> We have a lot of annotations that would be made to intrinsic to 
>>>>> membrane based on expression of GFP and PhoA fusion proteins.  
>>>>> What evidence code would people use?
>>>>>
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Associate Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------ 
>>>>>
>>>>>
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>>
>>
>
>
>


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Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
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