Re: [GMOD-devel] RE: [Gmod-schema] cvs changes: companalysis module, sequence module

[Gudmundur A. T. <mu...@cs...>]

I agree, fnbeg/fnend doesn't make much sense to me either. If 5' is the 
meaning, then at least 5 should be in the name, and putting 'primer'  in 
the namelike Hilmar suggested is not too bad either.

           Mummi, CSHL


On Thursday, October 31, 2002, at 06:03 AM, Suzanna Lewis wrote:

> I find fnbeg and fnend completely uninterpretable. fn could
> stand for anything and would inevitably be confused and
> misused. Use either of the more intuitive names.
> My preference is for pos5 and pos3 because position is
> more neutral than end which may be construed as always
> being a terminal end rather than just a location.
>
> On Wednesday, October 30, 2002, at 06:45 PM, Scott Cain wrote:
>
>> I am sending this to the gmod-devel list to get the opinion of the
>> larger audience.
>>
>> I am inclined to agree with Colin about nomenclature, though I do agree
>> with you about bioperl's normal/incorrect use of boundaries.  Before
>> bioperl came along I did it the way you propose; it caused much
>> confusion when I changed my schema to correspond to the bioperl way.
>> Assuming we use Chris' proposed boundary coordinates, I think using
>> check constraints is a good idea.
>>
>> Other opinions?
>>
>> Scott
>>
>> On Wed, 2002-10-30 at 20:54, Colin Wiel wrote:
>>> I preferred your suggestion of pos5 and pos3, as well as my suggestion
>>> of end5 and end3.  I don't think a new chado user will figure out that
>>> fnbeg stands for "feature natural begin" as easily as they would  figure
>>> out that pos5 (or end5) is the "position of the 5' end".
>>>
>>> Colin
>>>
>>>> -----Original Message-----
>>>> From: gmo...@li... [mailto:gmod-schema-
>>>> ad...@li...] On Behalf Of Chris Mungall
>>>> Sent: Wednesday, October 30, 2002 4:46 PM
>>>> To: gmo...@li...
>>>> Subject: [Gmod-schema] cvs changes: companalysis module, sequence
>>> module
>>>>
>>>>
>>>> I have reworked the tables in the computational analysis module; they
>>> are
>>>> now a little less generic than before. there is some docs included in
>>> the
>>>> .sql - more needed though...
>>>>
>>>> the multiple alignment part (eg for clustal results) is still fluid
>>>>
>>>> I have also settled on
>>>>
>>>> fnbeg
>>>> fnend
>>>>
>>>> for specifying coordinates - feature natural begin, feature natural
>>> end
>>>>
>>>> ie this is the "real" begin and end
>>>>
>>>> we should also possibly include a check constraint to make this
>>> explicit
>>>> eg
>>>>
>>>> fstrand is null OR (fnend - fnbeg) * fstrand >= 0
>>>>
>>>>
>>>> this is opposed to the normal (erroneous in my opinion) use of
>>> start/begin
>>>> end/stop, as used in bioperl, where
>>>>
>>>> start <= end
>>>>
>>>> ie they actually mean (low, high)
>>>>
>>>> how do we feel about check constraints?
>>>>
>>>>
>>>>
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>> --  
>> ----------------------------------------------------------------------- 
>> -
>> Scott Cain, Ph. D.                                          ca...@cs...
>> GMOD Coordinator (http://www.gmod.org/)                      216-392-3087
>> Cold Spring Harbor Laboratory
>>
>>
>>
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