[go] Putting method/program names into the with field for ISS

[Benjamin Hitz]

All -

Just ignore me, somehow Michelle's message was marked 'unread' after  
the GO meeting...

Ben

On Sep 28, 2007, at 2:32 PM, Ben Hitz wrote:

>>
>
> I guess, first point. - I don't think there is any need to separate  
> "sequence" from "structure" since sequence is merely a proxy for  
> the chemical structure, so I will use sequence to mean both.  If  
> anyone has a contrary opinion, I would like to hear it.    I just  
> want to make this disclaimer so we can use "sequence" to mean both.
>
>> I think it is important to be able to distinguish methods that are  
>> based on just sequence analysis from everything else and that ISS  
>> should be the code to describe this.
>
> I don't necessarily disagree - but I don't take this as a given  
> either.  WHY is this important?   And why SOLEY sequence analysis  
> and not partially sequence analysis?
>
> Here are some things I think might be important:
> o That the association is based on some computational theory, not  
> an experiment (so it would not fall under the proposed EXP hierarchy.
> o That in cases where an association is transferred from a specific  
> gene product or family of gene products, that that the  
> "transferree" is mentioned.
> o whether or not the association has been reviewed by a curator
> o whether or not the method has been reviewed by a curator (sub  
> case if the above is not true)
> o whether or not this is a (computational) prediction based on  
> combining several sources of data (aka "Baysian Blah Blah Blah")
>
>> I think we need at least 2 categories:
>> -one for all things sequence based (ISS or whatever new name might  
>> be created)
>> -one for combinatorial analyses that bring together different  
>> types of information to reach a conclusion (ICA/RCA)
>
> You are not accounting for some other non-sequence, non- 
> combinatorial analysis.  For example - there are many algorithms  
> that infer biological process from pattern of physical interactions  
> - while this seems to me be your 2nd class (Non-sequence), it's  
> only based on 1 source of data.
>>
>> If people feel there should be a code for alignments and only  
>> alignments then we will need to split the sequence-based category  
>> into 2 which would then give us 3 total:
>> -orthology based evidence
>> -all other sequence based evidence
>> -combinatorial analyses that bring together different types of  
>> information to reach a conclusion (ICA/RCA)
>>
>> I favor the first option (2 categories, not 3) as I think it is  
>> cleaner and easier for people to understand.  If we feel the need  
>> to change the name of ISS to reflect this more encompassing  
>> definition, then OK, but that brings another whole can of worms  
>> with it (what about legacy data, will the community have a cow, etc.)
>
> There is a practical issue you are overlooking.  It is very  
> important that we capture WITH Information for certain types of  
> homology- or similarity- based methods of inference.   So important  
> that your association will be tossed back by MIke if you don't  
> provide this information.
> I would say this is necessary for:
> 1) all pairwise sequence alignment methods
> 2) all "curated ortholog" methods (sub set of 1, above)
> 3) all protein-family assignment based methods (Pfam, SMART, ProDom)
>
> So, for the above, WITH information is mandatory.  For other  
> methods it isn't.  It is much, much easier from a practical  
> standpoint to mandate WITH evidence code X, rather than mandate  
> WITH for some complicated subset of evidence code X.
>
> Should we take this to the evidence-code mailing list?
> Ben
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
> Consortium
> Stanford University ** hitz at genome.stanford.edu
>
>

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu