Re: [Gusdev-gusdev] DoTS:NAEntry and topology

[Fidel S. <fi...@vb...>]

Chris Stoeckert <sto...@pc...> writes:

     > Hi Fidel,

Hi Chris.  Thanks for your response.

     > What are you trying to get from LOCUS?
     > Here's an example for the kit gene (maybe you can send me a more
     > relevant one for you).
     > LOCUS NM_021099 5132 bp mRNA linear ROD 20-DEC-2003
     > Is it the "linear" info?

Yes, it is the "linear" (or "circular") info.

     > I agree that NAEntry table would be a good place for this and I would
     > recommend that the NAEntry table have a "topology" attribute added.
     > I'm guessing that this information was lost because it's not something
     > that we at CBIL use.

Understood.

     > My understanding is that nothing should should break by adding this
     > column but would like others to confirm (Steve? Angel?)

It sounds good.

Fidel


     > I also don't think that you would need to add set/get methods just
     > alter the existing one for NAEntry.
>
     > Chris
>
     > On Jan 6, 2004, at 11:35 AM, Fidel Salas wrote:
>
     > I need help in finding a quick solution to the following requirement.
>
     > I need topology information for any given GenBank DNA sequence or
     > entry.  This information is found in the LOCUS line of a GenBank
     > entry.  For reasons unclear to me, the GBParser plugin parses this and
     > then silently drops it.
>
     > Since I am about to create a new GUS database, I would like to add a
     > column to DoTS:NAEntry that will hold the topology information.  The
     > main question is: will I break anything if I add this column to the
     > tables sql script?
>
     > Also, what is the reason this information is dropped?
>
     > I am assuming getting GBParser to populate this new column would
     > involve just getting the objrelp generator to add set and get methods.
     > Is this all that would need to be done?
>
     > Thanks
>
     > Fidel
>
>
>
>
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