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

[Suzanna Lewis]

Yes, that would be the more conservative thing to do, but practically  
speaking my sense is that a) the splitting of orthology groups is  
rare and b) something is much, much better than nothing.

In other words this may be a practical compromise (since one is  
easier and it's a relatively safe assumption)

On Sep 19, 2007, at 10:16 PM, Karen Christie wrote:

> Also, I have a question.
>
> If the goal is to be able to use the contents of this column to be  
> able to identify when the annotations changed for the supporting  
> evidence and those changes need to be propagated back to the gene  
> being annotated, then is just picking one out of an orthology group  
> enough? If the orthology group got split into two portions, it  
> seems that the chance of picking up that there was a change in the  
> supporting evidence would be better if everything relevant was  
> present in that column.
>
> -Karen
>
>
> On Tue, 18 Sep 2007, Suzanna Lewis wrote:
>
>> Actually there are (hoped for) operational reasons for requiring a  
>> sequence accession in the 'with' column (and if there is >1 then a  
>> representative one is just fine, because from there we could get  
>> to the other orthologs).
>>
>> The hope is that doing this should, in theory, make it possible to  
>> build in triggers such that if the annotation of the sequence in  
>> the 'with' column changes, then this could ripple back to all the  
>> annotations that were dependent/derived from this original.
>>
>> I would very much hate to see us give up on this. The GO is one of  
>> the few group that is even trying to indicate provenance and  
>> traceability. It is difficult, but very important.
>>
>> -S
>>
>> On Sep 12, 2007, at 8:44 AM, Susan Tweedie wrote:
>>
>>> At the risk of returning us to square one on this... I'd like to  
>>> take a
>>> step back and revisit why we decided it was vital to have  
>>> something in
>>> the with column for ISS. I thought this stemmed from an attempt at
>>> enforcing quality annotations - we wanted to identify the similar
>>> 'thing' for which there is experimental evidence and to use ISS only
>>> where this was available. We then shifted ground a bit to  
>>> acknowledge
>>> that there are cases where there is a strong case for ISS  
>>> annotation but
>>> no single sequence can be identified for this column. So what do we
>>> actually achieve by filling-in the slot for these cases? It seems  
>>> to me
>>> this is more to do with us saying 'yup I'm being stringent about  
>>> my use
>>> of ISS so I've stuck something in this column to prove it' than  
>>> actually
>>> helping users. The 'how they did it' in the the paper just like  
>>> it is
>>> for other evidence codes. I'm not sure we 'gain' enough here to  
>>> justify
>>> mixing methods and objects in the 'with' column and I am  
>>> struggling to
>>> see the justification for making ISS a special case in this  
>>> respect. If
>>> we show a method for ISS, do we set a precedent and run the risk of
>>> users wanting to know whether it was RNAi or knock-out for IMP etc?
>>> I guess I'd just like to know we haven't just made this column  
>>> mandatory
>>> as a means of policing curators. I strongly agree that we should  
>>> fill in
>>> a sequence where possible and do our best (within reason) to be sure
>>> there is an experiment there somewhere but, if we are going to  
>>> accept
>>> that there are cases where we can't identify a suitable sequence,  
>>> can't
>>> we just trust curator judgement i.e. leave the column blank and let
>>> people read the paper to see details of how it was done?
>>> If we stick with the plan to keep 'with' mandatory for ISS then  
>>> Karen's
>>> system is very nice. But what do we do for cases like Michelle's  
>>> example
>>> where a whole variety of similarity based methods are used. I  
>>> find this
>>> crops up time after time and I wouldn't want to have to list all  
>>> methods
>>> in this column and it doesn't seem very satisfactory to pick
>>> representative examples?
>>> Susan
>>> On Tue, 2007-09-11 at 19:03 +0000, Valerie Wood wrote:
>>>> That OK,
>>>> I just think its rather a trawl to have to create something to  
>>>> go in the 'with' field when the PMID of the published algorithm  
>>>> is sufficient.
>>>> My other reasoning was that these aren't purely based on  
>>>> 'sequence similarity', they always include some 'other   
>>>> additional step' (although I agree they are 'sequence based')
>>>> and thirdly, this could become hazy, if we got functional  
>>>> prediction methods which combined sequence data with some  
>>>> experimental date (like cellular localization), for example,  
>>>> would be be RCA (I presume). It therefore seemed  that if the  
>>>> distinction was that ISS needed to have some 'object' which  
>>>> represented a sequence in the 'with' column (rather than  
>>>> allowing the with column to contain other types of things,  
>>>> referring to algorithms), it would be quite a nice distinction.   
>>>> If you can't locate this object  then the method probably  
>>>> includes something else in addition to 'sequence similarity'.
>>>> However, these were just for consideration, I really have no  
>>>> strong preference either way..... although I prefer easy :)
>>>> Val
>>>> "Gwinn-Giglio, Michelle" <MLGwinn at jcvi.org> wrote:
>>>>> Ben,
>>>>> Yes, sorry to not be clear - I was disagreeing with Val's  
>>>>> suggestion to use RCA for things like TMHMM and tRNAscan.  At  
>>>>> least I think that was Val's suggestion and that is what I  
>>>>> diasagree with.
>>>>> Sorry to disagree with you Val.  :)
>>>>> Michelle
>>>>> -----Original Message-----
>>>>> From: Benjamin Hitz [mailto:hitz at genome.stanford.edu]
>>>>> Sent: Tue 9/11/2007 1:05 PM
>>>>> To: Gwinn-Giglio, Michelle
>>>>> Cc: GO mailing list
>>>>> Subject: Re: [go] Putting method/program names into the with  
>>>>> field for ISS
>>>>> On Sep 11, 2007, at 7:55 AM, Gwinn-Giglio, Michelle wrote:
>>>>>> Hi,
>>>>>> I disagree.  I think taking this approach would significantly  
>>>>>> muddy
>>>>>> the waters in terms of distinguishing between ISS and RCA.
>>>>>> Anything that is based only on sequence analysis, be it simple
>>>>>> Blast or vastly more complicated modeling methods, should be ISS
>>>>>> because at their heart they are all comparing sequences of known
>>>>>> function to ones with unknown function.  Whether they do simple
>>>>>> alignments to make that comparison or more complicated models, it
>>>>>> is still a sequence based analysis.
>>>>> I did not suggest otherwise.
>>>>> Ben
>>>>> --
>>>>> Ben Hitz
>>>>> Senior Scientific Programmer ** Saccharomyces Genome Database  
>>>>> ** GO
>>>>> Consortium
>>>>> Stanford University ** hitz at genome.stanford.edu
>>
>