Hi there, I'm newbie with a newbie question:

To deal with Bioinformatics data, such as sequence data, protein data,
or network biology data, which database system is good? Relation or OO
DB? MySQL is small and easy, however, is it adequate for the biological
data? Any ideas?

Thanks in advance,
CC

On Thu, 22 Jun 2006 23:41:21 -0700, CC wrote:
MySQL is used in many places in the bioinf world; that alone makes it a
candidate. For example, the Gene Ontology project's data are very
MySQL-specific.

Whether MySQL is a good choice for bioinf data handling is another
question. MySQL offers easy full-text indexing; so MySQL is not only
interesting because lots of people use it.

Some other candidates which would make sense considering:

- PostgreSQL offers user defined functions written in Perl (an
important language in the bioinf world). And there is even a
"BioPostgres" project: http://biopostgres.cs.ucla.edu/

- DB2 is the "king of recursion", in that it's currently the
RDBMS with most complete support for SQL:1999's recursive SQL
functions. Recursion is worth considering, because many
biological data are hierarchically structured.

- SQLite: Mostly targeted as a database built-in to an
application. But interesting because it's supposed to be
extremely fast for some kinds of database operations.

--
Greetings from Troels Arvin

CC wrote:
Acedb is widely used for bioinformatics:
http://www.acedb.org/


Unless you are using InnoDB storage for MySQL, you will be missing
referential integrity:
http://dev.mysql.com/doc/refman/5.0/...eign-keys.html

What's wrong with Postgres?

"CC" <chuangwoo (AT) gmail (DOT) com> wrote:




What sort of data do you have?



Paul...


--

plinehan __at__ yahoo __dot__ __com__

XP Pro, SP 2,

Oracle, 9.2.0.1.0 (Enterprise Ed.)
Interbase 6.0.1.0;

When asking database related questions, please give other posters
some clues, like operating system, version of db being used and DDL.
The exact text and/or number of error messages is useful (!= "it didn't work!").
Thanks.

Furthermore, as a courtesy to those who spend
time analysing and attempting to help, please
do not top post.

Trying to map the complex semantic network of a bioinformatics object
model to a relational database is one of the more challenging areas of
O/R mapping. You might want to take a look at somehting that allows you
to deal with the object model without having the imposed limits of an
O/R mapping layer.

Take a look at GemStone Facets (http://www.facetsodb.com). Facets
supplies a Java VM enhanced with a transparent OO persistence.

Bob

CC wrote:

Hi,

bob.walker (AT) gemstone (DOT) com wrote:
Also You can look at my experimental network OODB. It is developed for
modeling semantic neural network. Unfortunatelly it does not has an
english docs yet.

http://www.shuklin.com/ai/ht/en/cerebrum/

WBR,
Dmitry