This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.
MySQL is a popular open source database management system (DBMS). It's generally considered to be the easiest of all relational database management systems to install (Unix or Windows). It's not always viewed as favorably by database experts as it lacks certain features that they may consider useful, but one cannot deny that MySQL has proved its utility in both the open source and commercial worlds. An excellent first database for those who have no prior experience with relational databases.
Scott Cain's thoughts on why you shouldn't use MySQL for Chado
Note: I plan on fleshing this out more, but I wanted to get my thoughts down while I'm thinking about it.
MySQL is a very good database for some things: it is very fast as a read only database, and so is quite good for driving data displays like GBrowse. My experience outlined below describes why I learned to distrust it for 'important' data.
Some things that make me wary:
- The ability to either have or not have transactional integrity (and look out if you accidentally forget to declare one of your tables as INNODB). See http://sql-info.de/en/mysql/transaction-innodb-table.html, http://sql-info.de/en/mysql/database-definition.html#2_3 and http://sql-info.de/en/mysql/database-definition.html#2_4
- Silent dropping or truncation of data (To me, this is a VERY BIG DEAL if you care about your data.) See http://sql-info.de/mysql/gotchas.html#1_13 for a simple example that is still broken on MySQL 5.0.45.
- See the story below about silently throwing away data when inserting it; while MySQL 5 doesn't appear to be affected by this, you might see why my perception of MySQL is perhaps a little shaded by these events.
- Poor support for triggers (for example, you can't have more than one trigger that has the same trigger action time and event and triggers do not get executed when the event is caused by a cascading foreign key action (and Chado makes considerable use of cascading deletes, so this could affect trigger results)).
- We already have several years of development of tools devoted to PostgreSQL. I don't have the time to devote to porting, especially since PostgreSQL is an excellent RDBMS.
How I learned to distrust MySQL
When I started working on GMOD in 2002, the first project I tackled was to write a port of the GBrowse / GFF adaptor to PostgreSQL. I did a perfect job the first time through (not really, but pretend it's true for the moment). When I went to load some test data, the load failed and PostgreSQL barfed with an unfriendly error message, even though the same data loaded without incident using the MySQL adaptor. After spending a few days looking for bugs in the PostgreSQL adaptor that I'd written, I started looking at the data. It turns out that the test data (the entire WormBase GFF at the time) had data in it that violated a unique constraint on the fdata table. That is the main data table, and the constraint was over (fref,fbin,fstart,fstop,ftypeid,gid). Basically, the WormBase GFF had a data bug in it, and PostgreSQL was doing the right thing: I was trying to load something that was inconsistent with what I told it to expect, and it threw an error and stopped the load (and rolled back to the previous state, since it has transactions like any good database server should).
The only question for me at that point was, why didn't MySQL do the same thing, or at least give a warning (which to me would still be unacceptable, but it would be something)? Because it was designed to silently throw away data that violated a unique constraint! So, how about that? MySQL just decided I didn't need the data that was in that line. I should mention that, although the WormBase GFF had lines that violated the unique constraint, the lines that violated it were not 100% identical: some data in the ninth column were unique, so that data just disappeared from GBrowse. Nice.