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'with' field contents for IPI annotations

Evelyn Camon camon at ebi.ac.uk
Wed Mar 1 03:27:28 PST 2006


some questions still, sorry...

How will we know the difference between a group adding gene ids instead 
of protein Ids as the latter was not available and group adding a gene 
id for other reasons???

If Consortium member has difficultly getting Uniprot ids we should 
address these concerns and the appropriate contacts can be made.
I appreciate these thing can take time and solution is needed in the 
interim.

When a UniProt protein Id does become available and an internal protein 
id does not exist are gene ids later being updated to UniProt protein 
Ids???? or Internation Protein Index identifier???

many thanks

Evelyn

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
>>>>>>>
>>>>>>
>>>>>>
>>
> 
> 


-- 
Evelyn Camon
GOA Coordinator
Senior Scientific Curator
European Bioinformatics Institute
Tel:01223-494465
Fax:01223-494468
E-mail: camon at ebi.ac.uk
URL: http://www.ebi.ac.uk/goa




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