[BiO BB] Database schema

Jun Ding junding at yahoo.com
Tue Feb 25 16:44:22 EST 2003


Here's the other annotation database schema that
implemented in MySQL. 
For how to set up it a database in MySQL:
1. In your computer, under
[Where_MySQL_installed]\data folder, create a
subfolder as your database name, like "Ensembl".
2. Copy all the text files your downloaded(which is
database tables) into this folder.
3. Go to [Where_MySQL_installed]\bin folder, type
"mysql", like:
shell>mysql -u root
4. A MySQL prompt will pop up, type "use
your_database_name" in this prompt, like:
C:\mysql\bin>mysql -u root
Welcome to the MySQL monitor.  Commands end with ; or
\g.
Your MySQL connection id is 1 to server version:
3.23.53-max-nt
Type 'help;' or '\h' for help. Type '\c' to clear the
buffer.
mysql>use Ensembl
Database changed
mysql>
4. Type "GRANT ALL PRIVILEGES ON *.* TO
monty at localhost IDENTIFIED BY 'some_pass' WITH GRANT
OPTION;" in mysql>. This will create a user monty with
password some_pass in your database and have the full
privileges on your database. Like:
mysql> GRANT ALL PRIVILEGES ON *.* TO
Takeshi at localhost
 IDENTIFIED BY 'Sasayama' WITH GRANT OPTION;
5. mysql>quit
   Bye
6. shell>mysql -D your_database_name -u user_name
Like:
C:\mysql\bin>mysql -D Ensembl -u Takeshi
Password: Sasayama
Welcome to the MySQL monitor.  Commands end with ; or
\g.
Your MySQL connection id is 3 to server version:
3.23.53-max-nt
Type 'help;' or '\h' for help. Type '\c' to clear the
buffer.
mysql>
7. Then your Ensembl database is set up in your MySQL.
use:
   SHOW DATABASES [LIKE wild]
or SHOW [OPEN] TABLES [FROM db_name] [LIKE wild]
or SHOW [FULL] COLUMNS FROM tbl_name [FROM db_name]
[LIKE wild]
commands in mysql> to view database structure and use
SELECT command to view data.


--- Takeshi Sasayama <sasa at muh.biglobe.ne.jp> wrote:
> Hi Daniel and Haifeng,
> 
> Thanks for your reply.
> Hopefully I would like to see kind of an overview
> which compares schemas of
> major genome databases. I mean general databases
> which have for example ID,
> Name, Description, various Features and Sequence,
> rather than specific
> databases. I could download mysql schema from
> Ensembl site but there is
> little explanation. There may be little common
> structure among those major
> databases, but I would like know outlines, without
> looking for documents in
> every site.
> 
> Thanks
> 
> Takeshi Sasayama
> 
> 
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