[BioSQL-l] questions

[Tamas Hegedus]

Hi all,

Hilmar Lapp wrote:
> I'll write this up. I need it anyway for the paper.

=> I am also preparing a paper, reading and thinking more.
=> I see higher activity on the list.
==>> So I think this is a good time to ask a few questions.
Please note, I am wet biologist, but I like the programming. In the last 
2-3 years I was playing a little bit with RDBMS that does not mean I 
know everything about them: the steepness of my learning curve is pretty 
low (e.g. after a year I start to find the BioSQL schema very 
interesting :-)). But I would like to understand more things.

-----------------------------
DOCUMENTATION; WHYs; packing
-----------------------------
However, I know that BioSQL is under development, but it is not a 
'theoretical' projects, intend to be used by users.
More users, more feedback, more development, happier programmer.
But at this moment very difficult to recognize its advantages:
=> Why is BioSQL (RDBMS) better than other solution (e.g. flat files); 
why should I use it for my project?
=> What to download, from where to download? (In my opinion CVS is 
definitely for programmers not for biologist.)
=> What programs can I use to access the data? Only scripting? No! I can 
  use it e.g. with GBrowse, exactly what I need...
=> Is there any convinient way to query the database? I do not really 
want to learn SQL. How to perform and link queries/returned entries to 
'conventional' analysis tools (like pattern search)?
----
For developers: if you work on BioSQL constantly (from the beginning), 
you will know what column is for what (like 'Rank'), what are the role 
in a specific relation; but you can find  out these things, if you 
populate the database, and dig into it: so much energy needed that the 
developer find out an easier way to solve his problem.
----
I know that it is a huge work to create (and keep uptodate) a website. 
Personally I really do not like (hate) creating web-pages. But I think a 
web-site for BioSQL would greatly accelerate the BioSQL project.

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SCHEMA; RDBMSs
-----------------------------
I may rise the next question, since I do not see the deepness of BioSQL, 
I know only PgSQL and MySQL.

Why do you have different schema for different database servers (PgSQL, 
hsqldb, Oracle)? I guess why for MySQL...
Would not be possible to manage only one schema? It could free 
energies/time for other things.

E.g. generating the schema through an intelligent script (pseudo code):
db = create_biosql_conn( 'postgresql', db, user, pwd)
biodatabase_table = generate_table( name='Biodatabase', 
col_def=[('biodatabase_id', 'int', 'PK'), ( 'name', 'varchar( 128)'),..])
db.create_table( biodatabase_table);

I do not know how to formulate this: having an intermediate layer before 
the database drivers to translate a standard SQL/table creation for the 
appropriate RDBMS. Table creation is a simple example, e.g. implementing 
of sequences is not so simple (especially if you count with MySQL).
(The ODBC may be intend to do this? I do not know; but I do not think so 
after half an hour reading.)

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PYTHON
------------------------------
I prefer python over perl (e.g. because of this I had extra struggles to 
install BioSQL with SwissProt).

If I would know the object-mapping I think I could write a python script 
to load the the SwissProt into the BioSQL (it should be easy and 
straightforward).

============================================

Best regards,
Tamas

-- 
Tamas Hegedus, Research Fellow | phone: (1) 480-301-6041
Mayo Clinic Scottsdale         | fax:   (1) 480-301-7017
13000 E. Shea Blvd             | mailto:hegedus at mayo.edu
Scottsdale, AZ, 85259          | http://hegedus.brumart.org