[Gmod-help] MySQL Chado Schema

[kevin greer]

Hi Dave,

I have been working with the Chado schema for a little while now and I 
have a couple of questions.  Basically, we are trying to decide if we 
should use Chado in PostgreSQL or try to port it to MySQL.

1. Do you know when version 1.0 is going to be released?
2. How stable is the schema, (i.e. how often is it changed)?  By schema 
I am referring to everything in the database (tables, views, SPs, triggers).
3. How are the sequences for multiple strains of the same organism 
denoted.  I assume that people are using dbxrefs (feature_dbxref), but I 
wanted to check if you know how most people are handling this?
4. I did a test port of some of the schema into MySQL and found a couple 
of things that MySQL couldn't handle, and which seem a little odd to 
me.  In particular there are a couple of tables that have fields that 
are type 'text' (for example uniquename) that is then used in a unique 
constraint.  I am not sure exactly how PostrgeSQL handles text fields 
but usually they are stored separately from the rest of the table so I 
would expect that having a unique constraint on this column might impact 
performance (and MySQL doesn't allow it).  Also, since it is a 
uniquename that humans will need to use, I am wondering why it needs to 
be such a large field.  Anyway, for MySQL it would be necessary change 
the datatype to something like varchar(255) so I just wanted to make 
sure that I wouldn't be shortening a field that needed to be that long 
for some reason.
5. Is there any plan to support MySQL in the future?  I am pretty sure 
that the answer is no, but I wanted to make sure.  Also, has there been 
much demand for supporting MySQL?

Thanks,
   Kevin

Dave Clements, GMOD Help Desk wrote:
> Hi Kevin,
>
> MySQL is not officially supported by GMOD for Chado.  Chado takes 
> advantage of many DBMS features, such as foreign keys and other 
> integrity constraints, that were not available in MySQL when Chado was 
> created.  We strongly encourage people to use PostgreSQL.
>
> If you use MySQL you will have to do some porting of both the schema 
> definition (the DDL), and of the the tools that use Chado.  You also 
> still may not be able to get the same level of data constraints in 
> MySQL as you can with Postgres.  I believe there are a few sites out 
> there that run Chado on MySQL, but I don't know who they are.
>
> I will:
> 1. Fix the website to more clearly state the above.
> 2. See if I can find out who, if anyone, runs Chado on MySQL.  I'll 
> add that list of users to the web site.  I'll also let you know what I 
> find out.
> 3. Post this email to the Gmod-schema mailing list.  That list 
> discusses all things Chado.  I recommend subscribing to it if you 
> haven't already done so.
>
> Thanks,
>
> Dave C.
> GMOD Help Desk
>
>
>
> On Jan 15, 2008 4:59 PM, kevin greer < kevin at agcol.arizona.edu 
> <mailto:kevin at agcol.arizona.edu>> wrote:
>
>     Hello,
>
>     Is there a MySQL version of the Chado schema available.  Do you
>     know of
>     any issues with deploying the Chado database in using MySQL?
>
>     Thanks,
>       Kevin
>
>
>

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