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'with' field contents for IPI annotations

Doug howe dhowe at cs.uoregon.edu
Wed Mar 1 09:55:49 PST 2006


The IPI evidence code doc states:

 "We recommend making an entry in the "with" column when using this 
evidence code; i.e., include an identifier for the "other" protein (or 
other macromolecule) involved in the interaction."

 From this statement, one could conclude that Gene record IDs are not 
allowed.

-Doug

Midori Harris wrote:
> Can someone point me to the offending bit of documentation? The Annotation 
> Guide does have this:
>
>   "Note that a gene ID may be used in the 'with' column for a IPI 
>    annotation, or for an ISS annotation based on amino acid sequence or 
>    protein structure similarity, if the database does not have identifiers
>    for individual gene products."
>
> ... so if there's anyting elsewhere that says otherwise, it needs fixing!  
>
> (The existing passage can also be reworded to explicitly allow 'for
> whatever reason, you can't tell which protein ID to use'.)
>
> thanks,
> m
>
> On Tue, 28 Feb 2006, Suzanna Lewis wrote:
>
>   
>> I'm with you on this Karen, but apparently it made it into the 
>> documentation somewhere.
>>
>> On Feb 28, 2006, at 5:01 PM, Karen Christie wrote:
>>
>>     
>>> I don't believe we've ever implemented a restriction that the ID in the
>>> with column had to be a protein ID for IPI with, because I would have
>>> objected strenously to the suggestion, especially early on when some 
>>> SGD
>>> genes didn't even have corresponding protein IDs.
>>>
>>> -Karen
>>>
>>>
>>> On Tue, 28 Feb 2006, Suzanna Lewis wrote:
>>>
>>>       
>>>> BTW, I'm not sure when and where that restriction on the with column
>>>> arose, it seems quite unnecessary.
>>>>
>>>> -S
>>>>
>>>> On Feb 28, 2006, at 3:43 PM, Doug howe wrote:
>>>>
>>>>         
>>>>> Perhaps this also relates to the relationship between the evidence
>>>>> code and the allowed type of object in the 'with' column.  Does it
>>>>> create a computational problem if IPI annotations have both protein
>>>>> and gene IDs in the 'with' column since one is sequence and one is DB
>>>>> identifier?  I suppose it isn't all that bad since no matter what you
>>>>> put there, it will have a dbxref associated with it...
>>>>>
>>>>> -Doug
>>>>>
>>>>> Kimberly Van Auken wrote:
>>>>>           
>>>>>> Hi Doug--
>>>>>>
>>>>>> We have come across this situation here at WormBase and have found
>>>>>> that even though we have
>>>>>> protein IDs corresponding to all confirmed (or even partially
>>>>>> confirmed) transcripts, it is often
>>>>>> difficult, if not impossible, to tell exactly which proteins authors
>>>>>> studied in interaction experiments,
>>>>>> be it two-hybrid assays, co-IPs, etc.
>>>>>>
>>>>>> In these cases, we feel that putting the gene ID in the WITH column
>>>>>> is the best compromise.
>>>>>> Doing so still allows users to identify the interacting entities, 
>>>>>> but
>>>>>> does not make any potentially
>>>>>> misleading statements about exactly which proteins were involved.
>>>>>>
>>>>>> I am also curious to know how other groups handle this. Best,
>>>>>> Kimberly
>>>>>>
>>>>>>
>>>>>>
>>>>>> Doug howe wrote:
>>>>>>
>>>>>>             
>>>>>>> We (curators working from primary literature) often find
>>>>>>> circumstances for IPI annotation where the authors do not provide
>>>>>>> specific information about exactly which protein they are working
>>>>>>> with...though we usually know which gene it came from.  So when
>>>>>>> making IPI annotations, where the exact sequence of the protein
>>>>>>> involved is questionable, is it better to put a representative
>>>>>>> protein ID in the "with" field, put the ID of the gene itself in 
>>>>>>> the
>>>>>>> with field (is this even valid?), or leave the "with" field empty?
>>>>>>>
>>>>>>> How often do other groups actually find that they know the exact
>>>>>>> protein sequence ID of the interacting proteins?
>>>>>>> -Doug
>>>>>>>
>>>>>>>               
>>>>>>             
>>     
>
>   



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