[Gusdev-gusdev] Inconsistency among Sequence tables

[<ju...@cs...>]

I recently began working with the DoTS.ExternalAASequence table for
the first time, and I noticed several discrepancies with this
table and the DoTS.ExternalNASequence and DoTS.NASequence tables,
one of which I feel is serious.

                   name            taxon_id    description      external_database_release_id
                   varchar2(255)   number(12)  varchar2(2000)   number(10)

ExternalNASequence  yes            yes         yes              yes
NASequence          no             yes         yes              no
ExternalAASequence  yes            no          yes              yes
AASequence          no             no          yes              yes


Looking at the above chart, we see that both AASequence
and ExternalAASequence lack the taxon_id.  This surely must
be an oversight, I cannot imagine why such a thing
could be intentional.

A minor annoyance is that NASequence and AASequence lack a
"name varchar2(255)" column and therefore must have all text
regarding a sequence in the description column.  For query
and display purposes, it is very useful to be
able to refer to a sequence by a shorter handle.

And a final odd observation: why does AASequence have
a external_database_release_id column?  If an AA sequence belongs
to an external database, then it should be in the ExternalAASequence
table.

First, I wonder how the lack of a taxon_id column in the
ExternalAASequence/AASequence tables has existed for so long.
Have these tables not been used much by the GUS community?

Second, I wonder if the maintainers of GUS are interested
in addressing this issue and possibly resolving these
discrepancies in a future GUS release.

I am using Version 3.0 of the schema.


Thanks, Josef




Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

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