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Hi Dave,<br>
<br>
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. <br>
<br>
1. Do you know when version 1.0 is going to be released?<br>
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).<br>
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?<br>
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.<br>
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?<br>
<br>
Thanks,<br>
Kevin<br>
<br>
Dave Clements, GMOD Help Desk wrote:
<blockquote
cite="mid:71ee57c70801161157u7a9aed9w53bee6d36aca21db@mail.gmail.com"
type="cite">
<div class="gmail_quote">Hi Kevin,<br>
<br>
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.
<br>
<br>
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.
<br>
<br>
I will:<br>
1. Fix the website to more clearly state the above.<br>
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.
<br>
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.<br>
<br>
Thanks,
<br>
<br>
Dave C.<br>
<font color="#888888">GMOD Help Desk</font>
<div>
<div class="Wj3C7c"><br>
<br>
<br>
<div class="gmail_quote">On Jan 15, 2008 4:59 PM, kevin greer <<a
moz-do-not-send="true" href="mailto:kevin@agcol.arizona.edu"
target="_blank">
kevin@agcol.arizona.edu</a>> wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hello,<br>
<br>
Is there a MySQL version of the Chado schema available. Do you know of<br>
any issues with deploying the Chado database in using MySQL?<br>
<br>
Thanks,<br>
<font color="#888888"> Kevin<br>
</font></blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
</blockquote>
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