[GeneX-dev] [Fwd: Re: about GeneX DB schema.]

[Harry M. <man...@ho...>]

-------- Original Message --------
Subject: Re: about GeneX DB schema.
Date: Wed, 1 Mar 2000 13:53:29 +0100
From: Andrea Splendiani <an...@bt...>
To: Harry Mangalam <man...@ho...>
References: <010...@lo...> <010...@bt...> <3A9...@ho...>

Il mer, 21 feb 2001, hai scritto:
> Hi Andrea - nice to hear from you again.  I'm taking the liberty of posting my reply to the NCGR GeneX develeopment list.  If you want to have even wider response, you could also post it to: the
> Sourceforge list which has even more readers who might care to respond.
> 
> Andrea Splendiani wrote:
> If I follow you, this shouldn't matter very much - Affy data is fine for our schema and you are allowed to have null data in many of the fields that desccribe the technology
I've tried to use your schema but I've seen that there's no agreement from the
biologists on the meaning of the fields in tables!
I'm now trying to start from EBI schema, which has an higher view. But I still
want the DB to have a Genex compatible output (i.e.: GeneXML).
Planning to build one day my own import/export filetr to GeneXML, I have to
questions:
1) since I'm going to use fields probably different from yours, which is the
minimus set of infos that are required to build a valid GeneXML document ?
2) In the Experiment description, if I fallow EBI schema, I'll have data
structered in samples and teatment between them... say
sample-delay-sample-delay for a cinetics. Do you structure it in the same way
? If not, how can I map it between the two way ?

By the way, here there's a lot of confusion abaut DB design, so that my idea is
to develop something as quick as possible to have a prototype and to gain some
hint from its usage. Then I may change the DB-schema (but I have to choose data
now in a way that they'll be compatible to the new schema).

Another question: all your tools have a GeneXML interarface ? Even flat-file or
some other format ?
What have you used to develop the GeneXML parser ? And to develop the "dumper"
is there any tool or it is necessary to make it in a custom way ?

bye,
Andrea Splendiani