Re: [Gusdev-gusdev] improving GUS install/evolution

[Terry C. <tc...@it...>]

One component of schema evolution is getting data 
into the schema; another side is moving new data 
into existing schema. 

Folks at UChicago and I have worked out an XML
based strategy for incorporating data into GUS. 
The idea is around a GUS XML that contains key constraints
as attributes, which is interpretted by a byacc
parser and processor (together these are a plugin).
The data-to-schema routing happens by way of the XML
and grammar.

There is a paper to appear in Applied Bioinformatics
(probably the next issue) about our GUX XML processed
by XMLGUS. We find this a useful tool in our production 
work. 

Now writing plugins is unnecessary for us apart 
from occasional special cases, which XMLGUS has hooks for.
We now use XML and context free grammars to define the
mapping from data to schema, in most of our cases. 
There is one case my colleague found it easier to write
a plugin from scratch    - I have yet to study this to
see what caused this.

The GUS install needs a way to incorporate local tables.
A GUS table need not be part of the canonical set of 
tables; some can be site specific. We add local tables now, 
but the process is very ad hoc. 

Presently, we are working now on automating the production
of the XMLGUS framework, and the table problem. It would
be useful to see what people are thinking about and
where the needs are.

Maybe such ideas could be discussed at a GUS meeting?

cheers,

Terry





On  0, Sucheta Tripathy <su...@vb...> wrote:
> Steve,
> 
> We at VBI welcome the idea of releasing a version with install data.
> 
> This has been the main cause of concern for GUS users who had to spend
> lots of time finding the pre-requisite data .
> 
> We can certainly contribute to the initial dataset.
> 
> In addition we would be more interested to initiate a discussion on
> functional annotation.
> 
> cheers
> 
> Sucheta
> 
> > folks-
> >
> > some people here at cbil and also at uga have begun thinking about how
> > to improve the GUS install, and how to manage schema evolution.
> >
> > the two pieces of the gus install are:
> >    (1) the database schema and initial data
> >    (2) the software
> >
> > mike at cbil has made progress on (1), and it seems like alan, ed and
> > haiming at uga have ideas about this.
> >
> > mike is promising to write to the group to give a report on his efforts.
> >
> > so, maybe that will be a good way to get the discussion rolling....
> >
> > if folks have ideas or energy to tackle (2) that would be great.
> >
> > steve
> >
> >
> >
> >
> >
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> 
> -- 
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
> 
> 
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