gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] date format bug in submit row plugin

[Sucheta T. <su...@vb...>]

Thanks!!

It works now.

Sucheta

> Sucheta Tripathy wrote:
>
>>Hi,
>>
>>Thanks. I can't provide sysdate here since I am uploading the release
>> date
>>of the database.
>>
>>
>>
> Sorry, I wasn't clear. I mean that you need to provide a date string in
> the same format as oracle's default format. The easiest way to find out
> the format is to envoke SYSDATE to view a sample date string. For example:
>
> SQL> select SYSDATE from DUAL;
>
> SYSDATE
> -------------------
> 2004-03-29 11:32:19
>
> States that I must put a fou digit year first, followed by month
> followed by month day. Even using the TO_DATE() function, oracle will
> not make the correct translation with your example:
>
> SQL> select to_date('15-DEC-03') from dual;
>
> TO_DATE('15-DEC-03'
> -------------------
> 0015-12-03 00:00:00
>
> But If I follow the convention of the default date format, to_date works:
>
> SQL> select to_date('2003-DEC-15') from dual;
>
> TO_DATE('2003-DEC-1
> -------------------
> 2003-12-15 00:00:00
>
> In order for your date format to work, you must supply the alternate
> format to the TO_DATE function:
>  SQL> select to_date('15-DEC-03', 'DD-MON-YY') from dual;
>
> TO_DATE('15-DEC-03'
> -------------------
> 2003-12-15 00:00:00
>
> Angel
>
>>Probably I have to look into the other options you suggested.
>>
>>Sucheta
>>
>>
>>
>>>This should be controlled by the oracle default date format. do "select
>>>sysdate from dual;" and you should get the default date format for
>>>inserting dates in your local oracle installation. Failing that, there
>>>is a TO_DATE() function in  oracle that we may be able to use in the
>>>object layer for any columsn that have DATE type, but this may not
>>>translate well to PostgreSQL.
>>>
>>>Angel
>>>
>>>
>>>Sucheta Tripathy wrote:
>>>
>>>
>>>
>>>>Hi,
>>>>
>>>>I just found that uploading data into sres.externaldatabaserelease has
>>>> a
>>>>problem.
>>>>
>>>>The attribute release_date does not get the date format correctly. For
>>>>example if I provide the date like 15-DEC-03 it shows date like
>>>>12/3/0015.
>>>>
>>>>Is there a fix available for this?
>>>>
>>>>Thanks
>>>>
>>>>Sucheta
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>GenToo technologies. Learn everything from fundamentals to system
>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>
>>
>>
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] date format bug in submit row plugin

[Angel P. <an...@pc...>]

Sucheta Tripathy wrote:

>Hi,
>
>Thanks. I can't provide sysdate here since I am uploading the release date
>of the database.
>
>  
>
Sorry, I wasn't clear. I mean that you need to provide a date string in 
the same format as oracle's default format. The easiest way to find out 
the format is to envoke SYSDATE to view a sample date string. For example:

SQL> select SYSDATE from DUAL;

SYSDATE
-------------------
2004-03-29 11:32:19

States that I must put a fou digit year first, followed by month 
followed by month day. Even using the TO_DATE() function, oracle will 
not make the correct translation with your example:

SQL> select to_date('15-DEC-03') from dual;

TO_DATE('15-DEC-03'
-------------------
0015-12-03 00:00:00

But If I follow the convention of the default date format, to_date works:

SQL> select to_date('2003-DEC-15') from dual;

TO_DATE('2003-DEC-1
-------------------
2003-12-15 00:00:00

In order for your date format to work, you must supply the alternate 
format to the TO_DATE function:
 SQL> select to_date('15-DEC-03', 'DD-MON-YY') from dual;

TO_DATE('15-DEC-03'
-------------------
2003-12-15 00:00:00

Angel

>Probably I have to look into the other options you suggested.
>
>Sucheta
>
>  
>
>>This should be controlled by the oracle default date format. do "select
>>sysdate from dual;" and you should get the default date format for
>>inserting dates in your local oracle installation. Failing that, there
>>is a TO_DATE() function in  oracle that we may be able to use in the
>>object layer for any columsn that have DATE type, but this may not
>>translate well to PostgreSQL.
>>
>>Angel
>>
>>
>>Sucheta Tripathy wrote:
>>
>>    
>>
>>>Hi,
>>>
>>>I just found that uploading data into sres.externaldatabaserelease has a
>>>problem.
>>>
>>>The attribute release_date does not get the date format correctly. For
>>>example if I provide the date like 15-DEC-03 it shows date like
>>>12/3/0015.
>>>
>>>Is there a fix available for this?
>>>
>>>Thanks
>>>
>>>Sucheta
>>>
>>>
>>>
>>>
>>>      
>>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>GenToo technologies. Learn everything from fundamentals to system
>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>  
>

Re: [Gusdev-gusdev] date format bug in submit row plugin

[Sucheta T. <su...@vb...>]

Hi,

Thanks. I can't provide sysdate here since I am uploading the release date
of the database.

Probably I have to look into the other options you suggested.

Sucheta

> This should be controlled by the oracle default date format. do "select
> sysdate from dual;" and you should get the default date format for
> inserting dates in your local oracle installation. Failing that, there
> is a TO_DATE() function in  oracle that we may be able to use in the
> object layer for any columsn that have DATE type, but this may not
> translate well to PostgreSQL.
>
> Angel
>
>
> Sucheta Tripathy wrote:
>
>>Hi,
>>
>>I just found that uploading data into sres.externaldatabaserelease has a
>>problem.
>>
>>The attribute release_date does not get the date format correctly. For
>>example if I provide the date like 15-DEC-03 it shows date like
>> 12/3/0015.
>>
>>Is there a fix available for this?
>>
>>Thanks
>>
>>Sucheta
>>
>>
>>
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] date format bug in submit row plugin

[Angel P. <an...@pc...>]

This should be controlled by the oracle default date format. do "select 
sysdate from dual;" and you should get the default date format for 
inserting dates in your local oracle installation. Failing that, there 
is a TO_DATE() function in  oracle that we may be able to use in the 
object layer for any columsn that have DATE type, but this may not 
translate well to PostgreSQL.

Angel


Sucheta Tripathy wrote:

>Hi,
>
>I just found that uploading data into sres.externaldatabaserelease has a
>problem.
>
>The attribute release_date does not get the date format correctly. For
>example if I provide the date like 15-DEC-03 it shows date like 12/3/0015.
>
>Is there a fix available for this?
>
>Thanks
>
>Sucheta
>
>
>  
>

[Gusdev-gusdev] date format bug in submit row plugin

[Sucheta T. <su...@vb...>]

Hi,

I just found that uploading data into sres.externaldatabaserelease has a
problem.

The attribute release_date does not get the date format correctly. For
example if I provide the date like 15-DEC-03 it shows date like 12/3/0015.

Is there a fix available for this?

Thanks

Sucheta


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] ga +update

[Sucheta T. <su...@vb...>]

I think (from my experience), just change the version in the source code
then ga +update will work. For example in case you are modifying submitrow
plugin then change line 76  $Revsion 1.4 to $Revision 1.5 . It will work.

Sucheta
> Hi,
>
> if I modifie a perl module, and I do not want to registe the module with
> another name with ga +create...
>
> The upate does not work:
> Error:   GUS::CLASS::secondtest61 with CVS revision 1.7 is already
> registered.  You don't need to do a +update.
>
> (You see already number 61 :-))
>
> Cheers,
> Thomas
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

[Gusdev-gusdev] ga +update

[Thomas O. <ot...@fi...>]

Hi,

if I modifie a perl module, and I do not want to registe the module with 
another name with ga +create...

The upate does not work:
Error:   GUS::CLASS::secondtest61 with CVS revision 1.7 is already 
registered.  You don't need to do a +update.

(You see already number 61 :-))

Cheers,
Thomas

Re: [Gusdev-gusdev] Perl-DBD-Oracle - info request

[Michael S. <msa...@pc...>]

Hi Alberto,

It should be fairly trivial to install DBD::Oracle from source (or, if  
you already have CPAN installed, then that approach is even easier).

First, the read me for DBD::Oracle:   
http://cpan.uwinnipeg.ca/htdocs/DBD-Oracle/README.html

Download DBD::Oracle:   
http://cpan.uwinnipeg.ca/cpan/authors/id/T/TI/TIMB/DBD-Oracle 
-1.15.tar.gz

Uncompress the archive, and then:

perl Makefile.PL
make test
make install

I frequently have make test fail-- usually it's not a big deal, because  
it does connection test with a database, and I don't provide the  
necessary information to allow those to happen.  In this case, you can  
just to a force install.

--Mike

On Mar 22, 2004, at 8:31 AM, Alberto Davila wrote:

> Hi,
>
> When trying to install GUS, I needed the following module:
>
> "Perl-DBD-Oracle"
>
> I found it in RPMSeek and RPMFind, but trying to install it I got the
> following errors:
>
> [root@genome download]# rpm -ivh perl-DBD-Oracle-1.03-1.i386.rpm
> warning: perl-DBD-Oracle-1.03-1.i386.rpm: V3 DSA signature: NOKEY, key
> ID bfbaf0e8
> error: Failed dependencies:
>         libclntsh.so.8.0 is needed by perl-DBD-Oracle-1.03-1
>         libskgxp8.so is needed by perl-DBD-Oracle-1.03-1
>
> Someone suggested me to use the CPAN2RPM tool, I did and got the errors
> listed below.
>
> I use:
>
> Fedora Core 1
> Kernel: kernel-2.4.22-1.2174.nptl
> Perl: This is perl, v5.8.3 built for i386-linux-thread-multi
>
> and have Oracle9i installed with all the environment variables
> configured.
>
> Would you have any tips to provide ?
>
>
> Thanks and best regards, Alberto
>
> **********
>
>
> [root@tryps script]# cpan2rpm --version 1.15
> http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBD-Oracle-1.15.tar.gz
>
> -- cpan2rpm - Ver: 2.026 --
> Signatures not set up
> Upgrade check
> CPAN+ not found - using old interface
>
> -- module:
> http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBD-Oracle 
> -1.15.tar.gz --
> Metadata retrieval
> Tarball extraction: [/usr/src/redhat/SOURCES/DBD-Oracle-1.15.tar.gz]
> Generating spec file
> SPEC: /usr/src/redhat/SPECS/DBD-Oracle.spec
> Generating package
> Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.50893
> + umask 022
> + cd /usr/src/redhat/BUILD
> + LANG=C
> + export LANG
> + unset DISPLAY
> + cd /usr/src/redhat/BUILD
> + rm -rf DBD-Oracle-1.15
> + /usr/bin/gzip -dc /usr/src/redhat/SOURCES/DBD-Oracle-1.15.tar.gz
> + tar -xf -
> + STATUS=0
> + '[' 0 -ne 0 ']'
> + cd DBD-Oracle-1.15
> ++ /usr/bin/id -u
> + '[' 0 = 0 ']'
> + /bin/chown -Rhf root .
> ++ /usr/bin/id -u
> + '[' 0 = 0 ']'
> + /bin/chgrp -Rhf root .
> + /bin/chmod -Rf a+rX,g-w,o-w .
> + chmod -R u+w /usr/src/redhat/BUILD/DBD-Oracle-1.15
> + exit 0
> Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.9207
> + umask 022
> + cd /usr/src/redhat/BUILD
> + cd DBD-Oracle-1.15
> + LANG=C
> + export LANG
> + unset DISPLAY
> + grep -rsl '^#!.*perl' .
> + grep -v '.bak$'
> + xargs --no-run-if-empty /usr/bin/perl -MExtUtils::MakeMaker -e
> 'MY->fixin(@ARGV)'
> + CFLAGS=-O2 -g -pipe -march=i386 -mcpu=i686
> ++ /usr/bin/perl -MExtUtils::MakeMaker -e ' print
> qq|PREFIX=/var/tmp/perl-DBD-Oracle-1.15-root/usr| if
> $ExtUtils::MakeMaker::VERSION =~ /5\.9[1-6]|6\.0[0-5]/ '
> + /usr/bin/perl Makefile.PL
> Using DBI 1.37 installed in
> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBI
>
>  Configuring DBD::Oracle ...
>
>>>>     Remember to actually *READ* the README file!
>         Especially if you have any problems.
>
>   The ORACLE_HOME environment variable must be set.
>   It must be set to hold the path to an Oracle installation directory
>   on this machine (or a machine with a compatible architecture).
>   See the README.clients file for more information.
>   ABORTED!
> error: Bad exit status from /var/tmp/rpm-tmp.9207 (%build)
>
>
> RPM build errors:
>     Bad exit status from /var/tmp/rpm-tmp.9207 (%build)
> RPM build failed [1] at /usr/bin/cpan2rpm line 1044.
> -- Done --
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Perl-DBD-Oracle - info request

[Thomas O. <ot...@fi...>]

Alberto -

I think you installed the perlmodul with the root user. The error message:

  The ORACLE_HOME environment variable must be set.
  It must be set to hold the path to an Oracle installation directory
  on this machine (or a machine with a compatible architecture).
  See the README.clients file for more information.
  ABORTED!

looks like, that you have also to set the $ORACLE_HOME variable for this 
user. This seem to be the reason for the abort.

Cheers,
Thomas

Alberto Davila wrote:

>Hi,
>
>When trying to install GUS, I needed the following module:
>
>"Perl-DBD-Oracle"
>
>I found it in RPMSeek and RPMFind, but trying to install it I got the
>following errors:
>
>[root@genome download]# rpm -ivh perl-DBD-Oracle-1.03-1.i386.rpm
>warning: perl-DBD-Oracle-1.03-1.i386.rpm: V3 DSA signature: NOKEY, key
>ID bfbaf0e8
>error: Failed dependencies:
>        libclntsh.so.8.0 is needed by perl-DBD-Oracle-1.03-1
>        libskgxp8.so is needed by perl-DBD-Oracle-1.03-1
>
>Someone suggested me to use the CPAN2RPM tool, I did and got the errors
>listed below.
>
>I use:
>
>Fedora Core 1
>Kernel: kernel-2.4.22-1.2174.nptl
>Perl: This is perl, v5.8.3 built for i386-linux-thread-multi
>
>and have Oracle9i installed with all the environment variables
>configured.
>
>Would you have any tips to provide ? 
>
>
>Thanks and best regards, Alberto
>
>**********
>
>
>[root@tryps script]# cpan2rpm --version 1.15
>http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBD-Oracle-1.15.tar.gz
> 
>-- cpan2rpm - Ver: 2.026 --
>Signatures not set up
>Upgrade check
>CPAN+ not found - using old interface
> 
>-- module:
>http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBD-Oracle-1.15.tar.gz --
>Metadata retrieval
>Tarball extraction: [/usr/src/redhat/SOURCES/DBD-Oracle-1.15.tar.gz]
>Generating spec file
>SPEC: /usr/src/redhat/SPECS/DBD-Oracle.spec
>Generating package
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.50893
>+ umask 022
>+ cd /usr/src/redhat/BUILD
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ cd /usr/src/redhat/BUILD
>+ rm -rf DBD-Oracle-1.15
>+ /usr/bin/gzip -dc /usr/src/redhat/SOURCES/DBD-Oracle-1.15.tar.gz
>+ tar -xf -
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ cd DBD-Oracle-1.15
>++ /usr/bin/id -u
>+ '[' 0 = 0 ']'
>+ /bin/chown -Rhf root .
>++ /usr/bin/id -u
>+ '[' 0 = 0 ']'
>+ /bin/chgrp -Rhf root .
>+ /bin/chmod -Rf a+rX,g-w,o-w .
>+ chmod -R u+w /usr/src/redhat/BUILD/DBD-Oracle-1.15
>+ exit 0
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.9207
>+ umask 022
>+ cd /usr/src/redhat/BUILD
>+ cd DBD-Oracle-1.15
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ grep -rsl '^#!.*perl' .
>+ grep -v '.bak$'
>+ xargs --no-run-if-empty /usr/bin/perl -MExtUtils::MakeMaker -e
>'MY->fixin(@ARGV)'
>+ CFLAGS=-O2 -g -pipe -march=i386 -mcpu=i686
>++ /usr/bin/perl -MExtUtils::MakeMaker -e ' print
>qq|PREFIX=/var/tmp/perl-DBD-Oracle-1.15-root/usr| if
>$ExtUtils::MakeMaker::VERSION =~ /5\.9[1-6]|6\.0[0-5]/ '
>+ /usr/bin/perl Makefile.PL
>Using DBI 1.37 installed in
>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBI
> 
> Configuring DBD::Oracle ...
> 
>  
>
>>>>    Remember to actually *READ* the README file!
>>>>        
>>>>
>        Especially if you have any problems.
> 
>  The ORACLE_HOME environment variable must be set.
>  It must be set to hold the path to an Oracle installation directory
>  on this machine (or a machine with a compatible architecture).
>  See the README.clients file for more information.
>  ABORTED!
>error: Bad exit status from /var/tmp/rpm-tmp.9207 (%build)
> 
> 
>RPM build errors:
>    Bad exit status from /var/tmp/rpm-tmp.9207 (%build)
>RPM build failed [1] at /usr/bin/cpan2rpm line 1044.
>-- Done --
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

[Gusdev-gusdev] Perl-DBD-Oracle - info request

[Alberto D. <da...@io...>]

Hi,

When trying to install GUS, I needed the following module:

"Perl-DBD-Oracle"

I found it in RPMSeek and RPMFind, but trying to install it I got the
following errors:

[root@genome download]# rpm -ivh perl-DBD-Oracle-1.03-1.i386.rpm
warning: perl-DBD-Oracle-1.03-1.i386.rpm: V3 DSA signature: NOKEY, key
ID bfbaf0e8
error: Failed dependencies:
        libclntsh.so.8.0 is needed by perl-DBD-Oracle-1.03-1
        libskgxp8.so is needed by perl-DBD-Oracle-1.03-1

Someone suggested me to use the CPAN2RPM tool, I did and got the errors
listed below.

I use:

Fedora Core 1
Kernel: kernel-2.4.22-1.2174.nptl
Perl: This is perl, v5.8.3 built for i386-linux-thread-multi

and have Oracle9i installed with all the environment variables
configured.

Would you have any tips to provide ? 


Thanks and best regards, Alberto

**********


[root@tryps script]# cpan2rpm --version 1.15
http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBD-Oracle-1.15.tar.gz
 
-- cpan2rpm - Ver: 2.026 --
Signatures not set up
Upgrade check
CPAN+ not found - using old interface
 
-- module:
http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBD-Oracle-1.15.tar.gz --
Metadata retrieval
Tarball extraction: [/usr/src/redhat/SOURCES/DBD-Oracle-1.15.tar.gz]
Generating spec file
SPEC: /usr/src/redhat/SPECS/DBD-Oracle.spec
Generating package
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.50893
+ umask 022
+ cd /usr/src/redhat/BUILD
+ LANG=C
+ export LANG
+ unset DISPLAY
+ cd /usr/src/redhat/BUILD
+ rm -rf DBD-Oracle-1.15
+ /usr/bin/gzip -dc /usr/src/redhat/SOURCES/DBD-Oracle-1.15.tar.gz
+ tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd DBD-Oracle-1.15
++ /usr/bin/id -u
+ '[' 0 = 0 ']'
+ /bin/chown -Rhf root .
++ /usr/bin/id -u
+ '[' 0 = 0 ']'
+ /bin/chgrp -Rhf root .
+ /bin/chmod -Rf a+rX,g-w,o-w .
+ chmod -R u+w /usr/src/redhat/BUILD/DBD-Oracle-1.15
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.9207
+ umask 022
+ cd /usr/src/redhat/BUILD
+ cd DBD-Oracle-1.15
+ LANG=C
+ export LANG
+ unset DISPLAY
+ grep -rsl '^#!.*perl' .
+ grep -v '.bak$'
+ xargs --no-run-if-empty /usr/bin/perl -MExtUtils::MakeMaker -e
'MY->fixin(@ARGV)'
+ CFLAGS=-O2 -g -pipe -march=i386 -mcpu=i686
++ /usr/bin/perl -MExtUtils::MakeMaker -e ' print
qq|PREFIX=/var/tmp/perl-DBD-Oracle-1.15-root/usr| if
$ExtUtils::MakeMaker::VERSION =~ /5\.9[1-6]|6\.0[0-5]/ '
+ /usr/bin/perl Makefile.PL
Using DBI 1.37 installed in
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBI
 
 Configuring DBD::Oracle ...
 
>>>     Remember to actually *READ* the README file!
        Especially if you have any problems.
 
  The ORACLE_HOME environment variable must be set.
  It must be set to hold the path to an Oracle installation directory
  on this machine (or a machine with a compatible architecture).
  See the README.clients file for more information.
  ABORTED!
error: Bad exit status from /var/tmp/rpm-tmp.9207 (%build)
 
 
RPM build errors:
    Bad exit status from /var/tmp/rpm-tmp.9207 (%build)
RPM build failed [1] at /usr/bin/cpan2rpm line 1044.
-- Done --

Re: [Gusdev-gusdev] ga memory alloc

[Steve F. <sfi...@pc...>]

thomas-

see below

Thomas Otto wrote:

> Hallo,
>
> I am programming the parser for the kegg tables... (the moment I 
> arrived at a beta stage, I will provide the stuff)
>
> 2 Questions:
> - When I am initialing a new object,  like "my $Reaction = 
> GUS::Model::CLASS::REACTION->new('NAME'...." does the variable 
> $Reaction holds all the values of the table? I have an explosion of my 
> memory need, I cannot feed!

no.  it only holds the data for one row.    but, if you are creating 
lots and lots of objects, the cache may be getting very big.   after you 
are done with your objects (like at the bottom of your loop), within the 
plugin, call $self->undefPointerCache() to empty the cache.   See 
GUS::Rad::Plugin::ProcessResultLoader

>
> - Does a method exist that does following:  "select PRIMERYKEY from 
> other_tables where OTHER_ROW='something' ?"

you can create an object of the Other type by saying Other->new(hash) 
where the hash has the values you want to select on.   You will get back 
the first object that matches those values.   Then you can get the 
object's primary key.

steve

>
> That's it
>
> - Thomas
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] ga memory alloc

[Thomas O. <ot...@fi...>]

Hallo,

I am programming the parser for the kegg tables... (the moment I arrived 
at a beta stage, I will provide the stuff)

2 Questions:
- When I am initialing a new object,  like "my $Reaction = 
GUS::Model::CLASS::REACTION->new('NAME'...." does the variable $Reaction 
holds all the values of the table? I have an explosion of my memory 
need, I cannot feed!

- Does a method exist that does following:  "select PRIMERYKEY from 
other_tables where OTHER_ROW='something' ?"

That's it

- Thomas

[Gusdev-gusdev] Re: Fwd: [Gmod-schema] chado, Bio::DB::GFF, biosql

[Jessica K. <jki...@ug...>]

Chris,

	We have installed Gbrowse, but we do not=20
have it sitting on top of GUS. Sorry.

	Jessie


At 10:26 AM -0500 3/15/04, Chris Stoeckert wrote:
>Hi Jessie,
>You folks have hooked up Gbrowse to GUS haven't=20
>you? Do you know how the response time is for=20
>retrieving sequence?
>Chris
>
>Begin forwarded message:
>
>>From: "Vsevolod (Simon) Ilyushchenko" <si...@cs...>
>>Date: March 15, 2004 10:19:04 AM EST
>>To: Lincoln Stein <ls...@cs...>
>>Cc: Hilmar Lapp <hl...@gn...>, Scott Cain=20
>><ca...@cs...>, p.l...@me..., gmod=20
>>schema <gmo...@li...>
>>Subject: Re: [Gmod-schema] chado, Bio::DB::GFF, biosql
>>
>>Hi all,
>>
>>Here you go. Chart attached, full data below.
>>
>>I ran the comparison on intervals from 10 kbp=20
>>to 300 kbp. GFF has essentially constant access=20
>>time, Biosql's time grows pretty much linearly,=20
>>Chado's time grows even faster. Chado starts=20
>>off being almost twice as fast as Biosql, but=20
>>they even out around 150 Kbp and after that=20
>>Biosql is somewhat faster.
>>
>>Details: for all three methods. I used the same=20
>>1 Mbp snippet of chromosome II of Arabidopsis.=20
>>I ran wget 11 times consequetively for each=20
>>combination of storage methods and ranges, then=20
>>took the median value for each run. The machine=20
>>is a single-CPU 1.8 Ghz Pentium 4 with 256 MB=20
>>of RAM running Fedora Core 1 and apache 1.3.27.=20
>>I used bioperl-1.4, Genome-Browser 1.58 (I have=20
>>been warned against using its latest CVS=20
>>version, as it does not coexist with Chado yet)=20
>>and the current CVS snapshots of bioperl-db and=20
>>gmod.
>>
>>Simon
>>
>>The data in all columns except the first is access time in seconds.
>>
>>Range,	GFF 	Chado 	Biosql 
>>kbp
>>
>>10	1.61	1.77	3.24
>>20	1.63	1.96	3.59
>>30	1.63	2.13	3.8
>>40	1.66	2.23	3.96
>>50	1.65	2.33	4.17
>>60	1.66	2.36	4.26
>>70	1.68	2.44	4.44
>>80	1.71	3.01	4.93
>>90	1.78	4.37	5.74
>>
>>100	1.81	4.71	6.16
>>110	1.86	5.26	6.67
>>120	1.9	5.64	7.01
>>130	1.73	6.73	7.52
>>140	1.75	7.68	8
>>150	1.76	8.43	8.55
>>160	1.78	10.7	9.63
>>170	1.78	11.43	10.24
>>180	1.81	11.66	10.72
>>190	1.81	12.33	11.22
>>200	1.82	13.21	11.7
>>210	1.82	14.03	12.04
>>220	1.83	14.84	12.55
>>230	1.84	15.51	12.9
>>240	1.86	15.76	13.32
>>250	1.87	16.13	13.54
>>260	1.88	16.58	13.8
>>270	1.89	17.23	14.28
>>280	1.9	17.71	14.72
>>290	1.91	18.13	14.96
>>300	1.92	18.5	15.36
>>
>>Lincoln Stein wrote:
>>>-----BEGIN PGP SIGNED MESSAGE-----
>>>Hash: SHA1
>>>An easy thing to do would be to take a large=20
>>>GenBank record, such as an arabidopsis=20
>>>chromosome, import it into the three databases=20
>>>and then run gbrowse off them.  We could do=20
>>>simple page load timings using LWP.
>>>Does anyone reading this have a burning desire to run this test?
>>>Lincoln
>>
>>--
>>
>>Simon (Vsevolod ILyushchenko)   si...@cs...
>>				http://www.simonf.com
>>
>>The unknown is honoured, the known is neglected -
>>                              until all is known.
>>
>>               The C=FA Chulaind myth
>
>
>Content-Type: image/gif;
>	x-unix-mode=3D0666;
>	name=3D"gbrowse.gif"
>Content-Disposition: inline;
>	filename=3Dgbrowse.gif
>
>Attachment converted: ApiComputer:gbrowse.gif (GIFf/prvw) (0012A92B)


-- 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
Jessica Kissinger                   
Center for Tropical & Emerging Global Diseases
& Department of Genetics
University of Georgia
422 Biological Sciences
Athens, GA 30602-2606		    

TEL: +1 (706) 542-6562/6563
=46AX: +1 (706) 542-3582
e-mail    jki...@ug...
http://www.ctegd.uga.edu/people_pages/kissinger.html
PGP-Key: http://www.arches.uga.edu/~jkissing/public_key.html
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Re: [Gusdev-gusdev] kegg

[Deborah F. P. <pi...@pc...>]

There is a set of tables in the current schema that were designed to 
accomodate interaction data of unspecified type. This includes 
dots.Interaction,dots.InteractionLnteractionLOE. dots.InteractionLOE, 
dots.InteractionType, dots.EffectorActionType, and maybe dots.rowset and 
sots.rowsetmember. Data from KEGG was migrated to these table from a set 
of Pathway tables that existed in a previous version of the GUS schema. It 
might be a good idea to look at these tables to see if they can accomodate 
the data you want to insert. 


                                                             Debbie

 On Fri, 12 Mar 2004, Angel Pizarro wrote:

> Thomas and Terry,
> I think that both OMIM and KEGG are good candidates for integration into 
> GUS. Here is my advise on how to proceed and get you guys running as 
> quick as possible:
> 
> 1) Create new schema spaces OMIM and KEGG. Enter this data into 
> Core.DatabaseInfo.
> 2) Make the tables as GUS compliant and enter the Core.TableInfo information
> 3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by:
> %> touch $PROJETC_HOME/GUS/Model/schema/VERSION
> 4) rebuild the objects by:
> 
> %> build GUS/Model install -append
> 
> This should create new objects for these schema spaces for use in plugins
> 
> Document your schema and send it to the gusdev list once you have the 
> bugs worked and and THEN we can look to see if existing GUS tables 
> already fill that role or if these are new tables that should be folded 
> into GUS propoer or if these new tables actually do a better job that 
> the current GUS tables that holds this data.
> I think this is a good model for further GUS development, and we can 
> release these types of development efforts as "contributed" modules of 
> code. The contributed modules can be upgraded to "official" after they 
> pass a review process and provide data migration scripts.
> 
> Any comments?
> Angel
> 
> Thomas Otto wrote:
> 
> > ftp://ftp.genome.ad.jp/pub/
> > ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
> > from the secound directory I download and parsed the tar files. This 
> > suppose to be the files, like the kegg-engine are using them.
> >
> > Thomas
> >
> > Terry Clark wrote:
> >
> >> Thomas,
> >> Could you send a pointer to the KEGG FTP URL you are
> >> accessing and the names (or type of) files that you are using? I 
> >> would appreciate this to see how
> >> others are using KEGG.
> >>
> >> OMIM is orthogonal; I just described it and the
> >> parts of KEGG I addressed to explain the material
> >> on my web site.
> >>
> >> Terry
> >>
> >>
> >> On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
> >>  
> >>
> >>> Terry,
> >>>
> >>> first, I parse the information from the files of the ftp-server. I 
> >>> do not use the xml stuff.
> >>>
> >>> True, there is a lot of stuff in kegg, but I want to represent it in 
> >>> GUS, so...
> >>>
> >>> ... I think a link to OMIM makes sense, also to Motif/prosite. For 
> >>> me it is important to have all the relations without redundend.
> >>>
> >>> Give me some time, I will see, which parts might help me,
> >>>
> >>> cheers,
> >>> Thomas
> >>>
> >>>
> >>> Terry Clark wrote:
> >>>
> >>>   
> >>>
> >>>> Thomas,
> >>>>
> >>>> A few months ago I worked out a preliminary set of tables
> >>>> for *some* KEGG pathway data. 
> >>>> (By the way, those reactions are not complete in some of
> >>>> the XML files.) I expect you know, there are two representations
> >>>> in the XML: one with proteins as nodes; the other with reaction
> >>>> products as nodes and proteins as edges. I focused on explicitly 
> >>>> representing the latter (the <reaction> tag part of the XML) but 
> >>>> have toyed with the idea to do a comprehensive KEGG representation 
> >>>> in GUS unless someone else does it first :-)
> >>>>
> >>>> I also have a plugin to load the tables. All I am discussing has
> >>>> been implemented as a site-specific/local extension to GUS.  I put 
> >>>> the database files (not the plugin - we can talk
> >>>> about that later if you are interested) on the web page
> >>>>
> >>>> http://flora.uchicago.edu/gus/keggschemadraft/
> >>>>
> >>>> One file you might check first at the URL is     ** kegg-tables.sql 
> >>>> ***
> >>>>
> >>>> I am not satisfied with some of the design, and there may be some 
> >>>> uninspired things there - caveat emptor.  I was waiting for KEGG to 
> >>>> fix some problems in the reaction tags,
> >>>> and put together this operational db prototype in the meantime.
> >>>> (For example, check the missing - as of three weeks ago still - 
> >>>> reaction tags in the XML for phenylalanine metabolism.)
> >>>>
> >>>> Anyway the files I point to above might be useful to start with 
> >>>> rather than from scratch.
> >>>>
> >>>> I also hacked together some table(s) for EnzymeCommission
> >>>> numbers; there might be something in GUS for that, but at
> >>>> the time what I did seemed faster for my needs than otherwise.
> >>>> The OMIM parts there are not related to KEGG but part of a project 
> >>>> I am working on.
> >>>>
> >>>> Terry
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
> >>>>
> >>>>
> >>>>     
> >>>>
> >>>>> I think I will all the relation in one table... sort of 
> >>>>> EnzymeRelations...
> >>>>>
> >>>>> Thomas
> >>>>> Thomas Otto wrote:
> >>>>>
> >>>>>  
> >>>>>
> >>>>>       
> >>>>>
> >>>>>> Okay, an example:
> >>>>>> To every enzyme are several reaction associated. i.e. Enzymea, 
> >>>>>> has reaction1, ..., reaction n.
> >>>>>> (1) I could be to save the name of the reaction in the table 
> >>>>>> EnzymeClassAttribute
> >>>>>> (2) would be, to save nothing of this in the 
> >>>>>> EnzymeClassAttribute, but in a table (to create) 
> >>>>>> EnzymeReactionRelation.
> >>>>>>
> >>>>>> This will mean a lot of new table, because just for the enzymes 
> >>>>>> there are pathways, reaction, compound, substrate, product...
> >>>>>>
> >>>>>> But indeed, I also prefer #2, who is less redundend.
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Thomas
> >>>>>>
> >>>>>> Angel Pizarro wrote:
> >>>>>>
> >>>>>>   
> >>>>>>         
> >>>>>>
> >>>>>>> In the absence of an example of data a definite schema, 
> >>>>>>> definitely #2 as the data model of choice. You can always 
> >>>>>>> implement materialized view to speed-up/ease  queries.
> >>>>>>>
> >>>>>>> Cheers
> >>>>>>> Angel
> >>>>>>>
> >>>>>>> Thomas Otto wrote:
> >>>>>>>
> >>>>>>>     
> >>>>>>>           
> >>>>>>>
> >>>>>>>> That's what I was thinking about. So I want to know, which 
> >>>>>>>> representation of datas you prefer. (1 or 2, it is more a 
> >>>>>>>> general question).
> >>>>>>>>
> >>>>>>>> Thomas
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Angel Pizarro wrote:
> >>>>>>>>
> >>>>>>>>       
> >>>>>>>>             
> >>>>>>>>
> >>>>>>>>> OK, I don't see where you are getting EnzymCompoundRelation & 
> >>>>>>>>> CompoundClassAttribute from. Our current version of GUS does 
> >>>>>>>>> not have these tables. The SRes.EnzymeClass table is also 
> >>>>>>>>> looking very wacky to me. Propose a nice structure for this 
> >>>>>>>>> and we can put it in the next release of GUS.
> >>>>>>>>>
> >>>>>>>>> Angel
> >>>>>>>>>
> >>>>>>>>> Thomas Otto wrote:
> >>>>>>>>>
> >>>>>>>>>         
> >>>>>>>>>               
> >>>>>>>>>
> >>>>>>>>>> Hello,
> >>>>>>>>>>
> >>>>>>>>>> I am uploading some kegg data in the GUS system...
> >>>>>>>>>>
> >>>>>>>>>> So I looked which tables are existing, and which we are 
> >>>>>>>>>> needing i.e. for compound, reactions. Now I am not sure how 
> >>>>>>>>>> is the convention to relate the data.
> >>>>>>>>>>
> >>>>>>>>>> Example:
> >>>>>>>>>> The Enzymes are related to the compounds.
> >>>>>>>>>> (1) In EzymeClassAttribute I write the names of the compound 
> >>>>>>>>>> related to each enzyme. In CompoundClassAttribute I write 
> >>>>>>>>>> also all EC-numbers, related to it.
> >>>>>>>>>> (2) Other possibilty would be to utilize a thrid table 
> >>>>>>>>>> EnzymeCompoundRelation, where I put the primkeys of the 
> >>>>>>>>>> relations.
> >>>>>>>>>>
> >>>>>>>>>> (1) would be faster, easier to query, but redundend.
> >>>>>>>>>> (2) Cleaner
> >>>>>>>>>>
> >>>>>>>>>> What are you thinking I should use?
> >>>>>>>>>>
> >>>>>>>>>> Thanks,
> >>>>>>>>>> Thomas
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> -------------------------------------------------------
> >>>>>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>>>>> Free Linux tutorial presented by Daniel Robbins, President 
> >>>>>>>>>> and CEO of
> >>>>>>>>>> GenToo technologies. Learn everything from fundamentals to 
> >>>>>>>>>> system
> >>>>>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> Gusdev-gusdev mailing list
> >>>>>>>>>> Gus...@li...
> >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>>>>           
> >>>>>>>>>>                 
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>         
> >>>>>>>>>               
> >>>>>>>>
> >>>>>>> -------------------------------------------------------
> >>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>> Free Linux tutorial presented by Daniel Robbins, President and 
> >>>>>>> CEO of
> >>>>>>> GenToo technologies. Learn everything from fundamentals to system
> >>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> Gusdev-gusdev mailing list
> >>>>>>> Gus...@li...
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>
> >>>>>>>     
> >>>>>>>           
> >>>>>>
> >>>>>> -------------------------------------------------------
> >>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>> Free Linux tutorial presented by Daniel Robbins, President and 
> >>>>>> CEO of
> >>>>>> GenToo technologies. Learn everything from fundamentals to system
> >>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Gusdev-gusdev mailing list
> >>>>>> Gus...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>
> >>>>>>   
> >>>>>>         
> >>>>>
> >>>>> -------------------------------------------------------
> >>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>>> GenToo technologies. Learn everything from fundamentals to system
> >>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>> _______________________________________________
> >>>>> Gusdev-gusdev mailing list
> >>>>> Gus...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>  
> >>>>>
> >>>>>       
> >>>>
> >>>>
> >>>>     
> >>>
> >>
> >>
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by: IBM Linux Tutorials
> >> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >> GenToo technologies. Learn everything from fundamentals to system
> >> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>  
> >>
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] kegg

[Steve F. <sfi...@pc...>]

Yes, i agree that we should have a preliminary review.   In this case 
Thomas has provided the create table statements.   UML would also be an 
option.

I think the development of the plugin should just be a proof of concept, 
not a final submission.

After final review, then, yes, sample data and a clean plugin would be 
great.

steve

Terry Clark wrote:

>Angel, 
>
>This sounds good. I am not working on the KEGG tables
>at the moment so will that and OMIM to Thomas, but
>   "I'll be back..." (spoken with thick Austrian accent).
>
>I would be tempted also to ask for
>
>   1. test data for the tables and a plugin to load them
>      if not to query them, (maybe that's the "data migration scripts")
>
>   2. an entity-relationship or UML like diagram
>      as part of the documentation you mention
>
>The one problem I see is that after someone goes through
>all the trouble of creating new stuff, the GUS core group
>tells them, hey, look over there... Maybe some preliminary
>review, but gusdev could be that. 
>
>Terry
>
>
>On Fri, Mar 12, 2004 at 11:20:44AM -0500, Angel Pizarro wrote:
>  
>
>>Thomas and Terry,
>>I think that both OMIM and KEGG are good candidates for integration into 
>>GUS. Here is my advise on how to proceed and get you guys running as 
>>quick as possible:
>>
>>1) Create new schema spaces OMIM and KEGG. Enter this data into 
>>Core.DatabaseInfo.
>>2) Make the tables as GUS compliant and enter the Core.TableInfo information
>>3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by:
>>%> touch $PROJETC_HOME/GUS/Model/schema/VERSION
>>4) rebuild the objects by:
>>
>>%> build GUS/Model install -append
>>
>>This should create new objects for these schema spaces for use in plugins
>>
>>Document your schema and send it to the gusdev list once you have the 
>>bugs worked and and THEN we can look to see if existing GUS tables 
>>already fill that role or if these are new tables that should be folded 
>>into GUS propoer or if these new tables actually do a better job that 
>>the current GUS tables that holds this data.
>>I think this is a good model for further GUS development, and we can 
>>release these types of development efforts as "contributed" modules of 
>>code. The contributed modules can be upgraded to "official" after they 
>>pass a review process and provide data migration scripts.
>>
>>Any comments?
>>Angel
>>
>>Thomas Otto wrote:
>>
>>    
>>
>>>ftp://ftp.genome.ad.jp/pub/
>>>ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
>>>      
>>>
>>>from the secound directory I download and parsed the tar files. This 
>>    
>>
>>>suppose to be the files, like the kegg-engine are using them.
>>>
>>>Thomas
>>>
>>>Terry Clark wrote:
>>>
>>>      
>>>
>>>>Thomas,
>>>>Could you send a pointer to the KEGG FTP URL you are
>>>>accessing and the names (or type of) files that you are using? I 
>>>>would appreciate this to see how
>>>>others are using KEGG.
>>>>
>>>>OMIM is orthogonal; I just described it and the
>>>>parts of KEGG I addressed to explain the material
>>>>on my web site.
>>>>
>>>>Terry
>>>>
>>>>
>>>>On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
>>>>
>>>>
>>>>        
>>>>
>>>>>Terry,
>>>>>
>>>>>first, I parse the information from the files of the ftp-server. I 
>>>>>do not use the xml stuff.
>>>>>
>>>>>True, there is a lot of stuff in kegg, but I want to represent it in 
>>>>>GUS, so...
>>>>>
>>>>>... I think a link to OMIM makes sense, also to Motif/prosite. For 
>>>>>me it is important to have all the relations without redundend.
>>>>>
>>>>>Give me some time, I will see, which parts might help me,
>>>>>
>>>>>cheers,
>>>>>Thomas
>>>>>
>>>>>
>>>>>Terry Clark wrote:
>>>>>
>>>>> 
>>>>>
>>>>>          
>>>>>
>>>>>>Thomas,
>>>>>>
>>>>>>A few months ago I worked out a preliminary set of tables
>>>>>>for *some* KEGG pathway data. 
>>>>>>(By the way, those reactions are not complete in some of
>>>>>>the XML files.) I expect you know, there are two representations
>>>>>>in the XML: one with proteins as nodes; the other with reaction
>>>>>>products as nodes and proteins as edges. I focused on explicitly 
>>>>>>representing the latter (the <reaction> tag part of the XML) but 
>>>>>>have toyed with the idea to do a comprehensive KEGG representation 
>>>>>>in GUS unless someone else does it first :-)
>>>>>>
>>>>>>I also have a plugin to load the tables. All I am discussing has
>>>>>>been implemented as a site-specific/local extension to GUS.  I put 
>>>>>>the database files (not the plugin - we can talk
>>>>>>about that later if you are interested) on the web page
>>>>>>
>>>>>>http://flora.uchicago.edu/gus/keggschemadraft/
>>>>>>
>>>>>>One file you might check first at the URL is     ** kegg-tables.sql 
>>>>>>***
>>>>>>
>>>>>>I am not satisfied with some of the design, and there may be some 
>>>>>>uninspired things there - caveat emptor.  I was waiting for KEGG to 
>>>>>>fix some problems in the reaction tags,
>>>>>>and put together this operational db prototype in the meantime.
>>>>>>(For example, check the missing - as of three weeks ago still - 
>>>>>>reaction tags in the XML for phenylalanine metabolism.)
>>>>>>
>>>>>>Anyway the files I point to above might be useful to start with 
>>>>>>rather than from scratch.
>>>>>>
>>>>>>I also hacked together some table(s) for EnzymeCommission
>>>>>>numbers; there might be something in GUS for that, but at
>>>>>>the time what I did seemed faster for my needs than otherwise.
>>>>>>The OMIM parts there are not related to KEGG but part of a project 
>>>>>>I am working on.
>>>>>>
>>>>>>Terry
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
>>>>>>
>>>>>>
>>>>>>   
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>I think I will all the relation in one table... sort of 
>>>>>>>EnzymeRelations...
>>>>>>>
>>>>>>>Thomas
>>>>>>>Thomas Otto wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>>>Okay, an example:
>>>>>>>>To every enzyme are several reaction associated. i.e. Enzymea, 
>>>>>>>>has reaction1, ..., reaction n.
>>>>>>>>(1) I could be to save the name of the reaction in the table 
>>>>>>>>EnzymeClassAttribute
>>>>>>>>(2) would be, to save nothing of this in the 
>>>>>>>>EnzymeClassAttribute, but in a table (to create) 
>>>>>>>>EnzymeReactionRelation.
>>>>>>>>
>>>>>>>>This will mean a lot of new table, because just for the enzymes 
>>>>>>>>there are pathways, reaction, compound, substrate, product...
>>>>>>>>
>>>>>>>>But indeed, I also prefer #2, who is less redundend.
>>>>>>>>
>>>>>>>>Thanks,
>>>>>>>>Thomas
>>>>>>>>
>>>>>>>>Angel Pizarro wrote:
>>>>>>>>
>>>>>>>> 
>>>>>>>>       
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>>>>In the absence of an example of data a definite schema, 
>>>>>>>>>definitely #2 as the data model of choice. You can always 
>>>>>>>>>implement materialized view to speed-up/ease  queries.
>>>>>>>>>
>>>>>>>>>Cheers
>>>>>>>>>Angel
>>>>>>>>>
>>>>>>>>>Thomas Otto wrote:
>>>>>>>>>
>>>>>>>>>   
>>>>>>>>>         
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>>>That's what I was thinking about. So I want to know, which 
>>>>>>>>>>representation of datas you prefer. (1 or 2, it is more a 
>>>>>>>>>>general question).
>>>>>>>>>>
>>>>>>>>>>Thomas
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Angel Pizarro wrote:
>>>>>>>>>>
>>>>>>>>>>     
>>>>>>>>>>           
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>>>
>>>>>>>>>>>OK, I don't see where you are getting EnzymCompoundRelation & 
>>>>>>>>>>>CompoundClassAttribute from. Our current version of GUS does 
>>>>>>>>>>>not have these tables. The SRes.EnzymeClass table is also 
>>>>>>>>>>>looking very wacky to me. Propose a nice structure for this 
>>>>>>>>>>>and we can put it in the next release of GUS.
>>>>>>>>>>>
>>>>>>>>>>>Angel
>>>>>>>>>>>
>>>>>>>>>>>Thomas Otto wrote:
>>>>>>>>>>>
>>>>>>>>>>>       
>>>>>>>>>>>             
>>>>>>>>>>>
>>>>>>>>>>>                      
>>>>>>>>>>>
>>>>>>>>>>>>Hello,
>>>>>>>>>>>>
>>>>>>>>>>>>I am uploading some kegg data in the GUS system...
>>>>>>>>>>>>
>>>>>>>>>>>>So I looked which tables are existing, and which we are 
>>>>>>>>>>>>needing i.e. for compound, reactions. Now I am not sure how 
>>>>>>>>>>>>is the convention to relate the data.
>>>>>>>>>>>>
>>>>>>>>>>>>Example:
>>>>>>>>>>>>The Enzymes are related to the compounds.
>>>>>>>>>>>>(1) In EzymeClassAttribute I write the names of the compound 
>>>>>>>>>>>>related to each enzyme. In CompoundClassAttribute I write 
>>>>>>>>>>>>also all EC-numbers, related to it.
>>>>>>>>>>>>(2) Other possibilty would be to utilize a thrid table 
>>>>>>>>>>>>EnzymeCompoundRelation, where I put the primkeys of the 
>>>>>>>>>>>>relations.
>>>>>>>>>>>>
>>>>>>>>>>>>(1) would be faster, easier to query, but redundend.
>>>>>>>>>>>>(2) Cleaner
>>>>>>>>>>>>
>>>>>>>>>>>>What are you thinking I should use?
>>>>>>>>>>>>
>>>>>>>>>>>>Thanks,
>>>>>>>>>>>>Thomas
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>-------------------------------------------------------
>>>>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President 
>>>>>>>>>>>>and CEO of
>>>>>>>>>>>>GenToo technologies. Learn everything from fundamentals to 
>>>>>>>>>>>>system
>>>>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>>>>>>
>>>>>>>>>>>>_______________________________________________
>>>>>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>>>>>Gus...@li...
>>>>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>>>>>         
>>>>>>>>>>>>               
>>>>>>>>>>>>                        
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>       
>>>>>>>>>>>             
>>>>>>>>>>>                      
>>>>>>>>>>>
>>>>>>>>>-------------------------------------------------------
>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and 
>>>>>>>>>CEO of
>>>>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>>>
>>>>>>>>>_______________________________________________
>>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>>Gus...@li...
>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>>
>>>>>>>>>   
>>>>>>>>>         
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>-------------------------------------------------------
>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and 
>>>>>>>>CEO of
>>>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>>
>>>>>>>>_______________________________________________
>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>Gus...@li...
>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>
>>>>>>>> 
>>>>>>>>       
>>>>>>>>                
>>>>>>>>
>>>>>>>-------------------------------------------------------
>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>>>>_______________________________________________
>>>>>>>Gusdev-gusdev mailing list
>>>>>>>Gus...@li...
>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>              
>>>>>>>
>>>>>>   
>>>>>>            
>>>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>GenToo technologies. Learn everything from fundamentals to system
>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>      
>>>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] kegg

[Thomas O. <ot...@fi...>]

Hi,

I think I give kegg a try... now I have an idea of the relations and 
first steps.

The moment I am done, I will provide a new namespace, ga - module for 
uploading and the link for the data.

Cheers,
Thomas

Terry Clark wrote:

>Angel, 
>
>This sounds good. I am not working on the KEGG tables
>at the moment so will that and OMIM to Thomas, but
>   "I'll be back..." (spoken with thick Austrian accent).
>
>I would be tempted also to ask for
>
>   1. test data for the tables and a plugin to load them
>      if not to query them, (maybe that's the "data migration scripts")
>
>   2. an entity-relationship or UML like diagram
>      as part of the documentation you mention
>
>The one problem I see is that after someone goes through
>all the trouble of creating new stuff, the GUS core group
>tells them, hey, look over there... Maybe some preliminary
>review, but gusdev could be that. 
>
>Terry
>
>
>On Fri, Mar 12, 2004 at 11:20:44AM -0500, Angel Pizarro wrote:
>  
>
>>Thomas and Terry,
>>I think that both OMIM and KEGG are good candidates for integration into 
>>GUS. Here is my advise on how to proceed and get you guys running as 
>>quick as possible:
>>
>>1) Create new schema spaces OMIM and KEGG. Enter this data into 
>>Core.DatabaseInfo.
>>2) Make the tables as GUS compliant and enter the Core.TableInfo information
>>3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by:
>>%> touch $PROJETC_HOME/GUS/Model/schema/VERSION
>>4) rebuild the objects by:
>>
>>%> build GUS/Model install -append
>>
>>This should create new objects for these schema spaces for use in plugins
>>
>>Document your schema and send it to the gusdev list once you have the 
>>bugs worked and and THEN we can look to see if existing GUS tables 
>>already fill that role or if these are new tables that should be folded 
>>into GUS propoer or if these new tables actually do a better job that 
>>the current GUS tables that holds this data.
>>I think this is a good model for further GUS development, and we can 
>>release these types of development efforts as "contributed" modules of 
>>code. The contributed modules can be upgraded to "official" after they 
>>pass a review process and provide data migration scripts.
>>
>>Any comments?
>>Angel
>>
>>Thomas Otto wrote:
>>
>>    
>>
>>>ftp://ftp.genome.ad.jp/pub/
>>>ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
>>>      
>>>
>>>from the secound directory I download and parsed the tar files. This 
>>    
>>
>>>suppose to be the files, like the kegg-engine are using them.
>>>
>>>Thomas
>>>
>>>Terry Clark wrote:
>>>
>>>      
>>>
>>>>Thomas,
>>>>Could you send a pointer to the KEGG FTP URL you are
>>>>accessing and the names (or type of) files that you are using? I 
>>>>would appreciate this to see how
>>>>others are using KEGG.
>>>>
>>>>OMIM is orthogonal; I just described it and the
>>>>parts of KEGG I addressed to explain the material
>>>>on my web site.
>>>>
>>>>Terry
>>>>
>>>>
>>>>On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
>>>>
>>>>
>>>>        
>>>>
>>>>>Terry,
>>>>>
>>>>>first, I parse the information from the files of the ftp-server. I 
>>>>>do not use the xml stuff.
>>>>>
>>>>>True, there is a lot of stuff in kegg, but I want to represent it in 
>>>>>GUS, so...
>>>>>
>>>>>... I think a link to OMIM makes sense, also to Motif/prosite. For 
>>>>>me it is important to have all the relations without redundend.
>>>>>
>>>>>Give me some time, I will see, which parts might help me,
>>>>>
>>>>>cheers,
>>>>>Thomas
>>>>>
>>>>>
>>>>>Terry Clark wrote:
>>>>>
>>>>> 
>>>>>
>>>>>          
>>>>>
>>>>>>Thomas,
>>>>>>
>>>>>>A few months ago I worked out a preliminary set of tables
>>>>>>for *some* KEGG pathway data. 
>>>>>>(By the way, those reactions are not complete in some of
>>>>>>the XML files.) I expect you know, there are two representations
>>>>>>in the XML: one with proteins as nodes; the other with reaction
>>>>>>products as nodes and proteins as edges. I focused on explicitly 
>>>>>>representing the latter (the <reaction> tag part of the XML) but 
>>>>>>have toyed with the idea to do a comprehensive KEGG representation 
>>>>>>in GUS unless someone else does it first :-)
>>>>>>
>>>>>>I also have a plugin to load the tables. All I am discussing has
>>>>>>been implemented as a site-specific/local extension to GUS.  I put 
>>>>>>the database files (not the plugin - we can talk
>>>>>>about that later if you are interested) on the web page
>>>>>>
>>>>>>http://flora.uchicago.edu/gus/keggschemadraft/
>>>>>>
>>>>>>One file you might check first at the URL is     ** kegg-tables.sql 
>>>>>>***
>>>>>>
>>>>>>I am not satisfied with some of the design, and there may be some 
>>>>>>uninspired things there - caveat emptor.  I was waiting for KEGG to 
>>>>>>fix some problems in the reaction tags,
>>>>>>and put together this operational db prototype in the meantime.
>>>>>>(For example, check the missing - as of three weeks ago still - 
>>>>>>reaction tags in the XML for phenylalanine metabolism.)
>>>>>>
>>>>>>Anyway the files I point to above might be useful to start with 
>>>>>>rather than from scratch.
>>>>>>
>>>>>>I also hacked together some table(s) for EnzymeCommission
>>>>>>numbers; there might be something in GUS for that, but at
>>>>>>the time what I did seemed faster for my needs than otherwise.
>>>>>>The OMIM parts there are not related to KEGG but part of a project 
>>>>>>I am working on.
>>>>>>
>>>>>>Terry
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
>>>>>>
>>>>>>
>>>>>>   
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>I think I will all the relation in one table... sort of 
>>>>>>>EnzymeRelations...
>>>>>>>
>>>>>>>Thomas
>>>>>>>Thomas Otto wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>>>Okay, an example:
>>>>>>>>To every enzyme are several reaction associated. i.e. Enzymea, 
>>>>>>>>has reaction1, ..., reaction n.
>>>>>>>>(1) I could be to save the name of the reaction in the table 
>>>>>>>>EnzymeClassAttribute
>>>>>>>>(2) would be, to save nothing of this in the 
>>>>>>>>EnzymeClassAttribute, but in a table (to create) 
>>>>>>>>EnzymeReactionRelation.
>>>>>>>>
>>>>>>>>This will mean a lot of new table, because just for the enzymes 
>>>>>>>>there are pathways, reaction, compound, substrate, product...
>>>>>>>>
>>>>>>>>But indeed, I also prefer #2, who is less redundend.
>>>>>>>>
>>>>>>>>Thanks,
>>>>>>>>Thomas
>>>>>>>>
>>>>>>>>Angel Pizarro wrote:
>>>>>>>>
>>>>>>>> 
>>>>>>>>       
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>>>>In the absence of an example of data a definite schema, 
>>>>>>>>>definitely #2 as the data model of choice. You can always 
>>>>>>>>>implement materialized view to speed-up/ease  queries.
>>>>>>>>>
>>>>>>>>>Cheers
>>>>>>>>>Angel
>>>>>>>>>
>>>>>>>>>Thomas Otto wrote:
>>>>>>>>>
>>>>>>>>>   
>>>>>>>>>         
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>>>That's what I was thinking about. So I want to know, which 
>>>>>>>>>>representation of datas you prefer. (1 or 2, it is more a 
>>>>>>>>>>general question).
>>>>>>>>>>
>>>>>>>>>>Thomas
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Angel Pizarro wrote:
>>>>>>>>>>
>>>>>>>>>>     
>>>>>>>>>>           
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>>>
>>>>>>>>>>>OK, I don't see where you are getting EnzymCompoundRelation & 
>>>>>>>>>>>CompoundClassAttribute from. Our current version of GUS does 
>>>>>>>>>>>not have these tables. The SRes.EnzymeClass table is also 
>>>>>>>>>>>looking very wacky to me. Propose a nice structure for this 
>>>>>>>>>>>and we can put it in the next release of GUS.
>>>>>>>>>>>
>>>>>>>>>>>Angel
>>>>>>>>>>>
>>>>>>>>>>>Thomas Otto wrote:
>>>>>>>>>>>
>>>>>>>>>>>       
>>>>>>>>>>>             
>>>>>>>>>>>
>>>>>>>>>>>                      
>>>>>>>>>>>
>>>>>>>>>>>>Hello,
>>>>>>>>>>>>
>>>>>>>>>>>>I am uploading some kegg data in the GUS system...
>>>>>>>>>>>>
>>>>>>>>>>>>So I looked which tables are existing, and which we are 
>>>>>>>>>>>>needing i.e. for compound, reactions. Now I am not sure how 
>>>>>>>>>>>>is the convention to relate the data.
>>>>>>>>>>>>
>>>>>>>>>>>>Example:
>>>>>>>>>>>>The Enzymes are related to the compounds.
>>>>>>>>>>>>(1) In EzymeClassAttribute I write the names of the compound 
>>>>>>>>>>>>related to each enzyme. In CompoundClassAttribute I write 
>>>>>>>>>>>>also all EC-numbers, related to it.
>>>>>>>>>>>>(2) Other possibilty would be to utilize a thrid table 
>>>>>>>>>>>>EnzymeCompoundRelation, where I put the primkeys of the 
>>>>>>>>>>>>relations.
>>>>>>>>>>>>
>>>>>>>>>>>>(1) would be faster, easier to query, but redundend.
>>>>>>>>>>>>(2) Cleaner
>>>>>>>>>>>>
>>>>>>>>>>>>What are you thinking I should use?
>>>>>>>>>>>>
>>>>>>>>>>>>Thanks,
>>>>>>>>>>>>Thomas
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>-------------------------------------------------------
>>>>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President 
>>>>>>>>>>>>and CEO of
>>>>>>>>>>>>GenToo technologies. Learn everything from fundamentals to 
>>>>>>>>>>>>system
>>>>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>>>>>>
>>>>>>>>>>>>_______________________________________________
>>>>>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>>>>>Gus...@li...
>>>>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>>>>>         
>>>>>>>>>>>>               
>>>>>>>>>>>>                        
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>       
>>>>>>>>>>>             
>>>>>>>>>>>                      
>>>>>>>>>>>
>>>>>>>>>-------------------------------------------------------
>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and 
>>>>>>>>>CEO of
>>>>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>>>
>>>>>>>>>_______________________________________________
>>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>>Gus...@li...
>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>>
>>>>>>>>>   
>>>>>>>>>         
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>-------------------------------------------------------
>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and 
>>>>>>>>CEO of
>>>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>>
>>>>>>>>_______________________________________________
>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>Gus...@li...
>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>
>>>>>>>> 
>>>>>>>>       
>>>>>>>>                
>>>>>>>>
>>>>>>>-------------------------------------------------------
>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>>>>_______________________________________________
>>>>>>>Gusdev-gusdev mailing list
>>>>>>>Gus...@li...
>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>              
>>>>>>>
>>>>>>   
>>>>>>            
>>>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>GenToo technologies. Learn everything from fundamentals to system
>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>      
>>>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

Re: [Gusdev-gusdev] kegg

[<tw...@cs...>]

Angel, 

This sounds good. I am not working on the KEGG tables
at the moment so will that and OMIM to Thomas, but
   "I'll be back..." (spoken with thick Austrian accent).

I would be tempted also to ask for

   1. test data for the tables and a plugin to load them
      if not to query them, (maybe that's the "data migration scripts")

   2. an entity-relationship or UML like diagram
      as part of the documentation you mention

The one problem I see is that after someone goes through
all the trouble of creating new stuff, the GUS core group
tells them, hey, look over there... Maybe some preliminary
review, but gusdev could be that. 

Terry


On Fri, Mar 12, 2004 at 11:20:44AM -0500, Angel Pizarro wrote:
> Thomas and Terry,
> I think that both OMIM and KEGG are good candidates for integration into 
> GUS. Here is my advise on how to proceed and get you guys running as 
> quick as possible:
> 
> 1) Create new schema spaces OMIM and KEGG. Enter this data into 
> Core.DatabaseInfo.
> 2) Make the tables as GUS compliant and enter the Core.TableInfo information
> 3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by:
> %> touch $PROJETC_HOME/GUS/Model/schema/VERSION
> 4) rebuild the objects by:
> 
> %> build GUS/Model install -append
> 
> This should create new objects for these schema spaces for use in plugins
> 
> Document your schema and send it to the gusdev list once you have the 
> bugs worked and and THEN we can look to see if existing GUS tables 
> already fill that role or if these are new tables that should be folded 
> into GUS propoer or if these new tables actually do a better job that 
> the current GUS tables that holds this data.
> I think this is a good model for further GUS development, and we can 
> release these types of development efforts as "contributed" modules of 
> code. The contributed modules can be upgraded to "official" after they 
> pass a review process and provide data migration scripts.
> 
> Any comments?
> Angel
> 
> Thomas Otto wrote:
> 
> >ftp://ftp.genome.ad.jp/pub/
> >ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
> >from the secound directory I download and parsed the tar files. This 
> >suppose to be the files, like the kegg-engine are using them.
> >
> >Thomas
> >
> >Terry Clark wrote:
> >
> >>Thomas,
> >>Could you send a pointer to the KEGG FTP URL you are
> >>accessing and the names (or type of) files that you are using? I 
> >>would appreciate this to see how
> >>others are using KEGG.
> >>
> >>OMIM is orthogonal; I just described it and the
> >>parts of KEGG I addressed to explain the material
> >>on my web site.
> >>
> >>Terry
> >>
> >>
> >>On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
> >> 
> >>
> >>>Terry,
> >>>
> >>>first, I parse the information from the files of the ftp-server. I 
> >>>do not use the xml stuff.
> >>>
> >>>True, there is a lot of stuff in kegg, but I want to represent it in 
> >>>GUS, so...
> >>>
> >>>... I think a link to OMIM makes sense, also to Motif/prosite. For 
> >>>me it is important to have all the relations without redundend.
> >>>
> >>>Give me some time, I will see, which parts might help me,
> >>>
> >>>cheers,
> >>>Thomas
> >>>
> >>>
> >>>Terry Clark wrote:
> >>>
> >>>  
> >>>
> >>>>Thomas,
> >>>>
> >>>>A few months ago I worked out a preliminary set of tables
> >>>>for *some* KEGG pathway data. 
> >>>>(By the way, those reactions are not complete in some of
> >>>>the XML files.) I expect you know, there are two representations
> >>>>in the XML: one with proteins as nodes; the other with reaction
> >>>>products as nodes and proteins as edges. I focused on explicitly 
> >>>>representing the latter (the <reaction> tag part of the XML) but 
> >>>>have toyed with the idea to do a comprehensive KEGG representation 
> >>>>in GUS unless someone else does it first :-)
> >>>>
> >>>>I also have a plugin to load the tables. All I am discussing has
> >>>>been implemented as a site-specific/local extension to GUS.  I put 
> >>>>the database files (not the plugin - we can talk
> >>>>about that later if you are interested) on the web page
> >>>>
> >>>>http://flora.uchicago.edu/gus/keggschemadraft/
> >>>>
> >>>>One file you might check first at the URL is     ** kegg-tables.sql 
> >>>>***
> >>>>
> >>>>I am not satisfied with some of the design, and there may be some 
> >>>>uninspired things there - caveat emptor.  I was waiting for KEGG to 
> >>>>fix some problems in the reaction tags,
> >>>>and put together this operational db prototype in the meantime.
> >>>>(For example, check the missing - as of three weeks ago still - 
> >>>>reaction tags in the XML for phenylalanine metabolism.)
> >>>>
> >>>>Anyway the files I point to above might be useful to start with 
> >>>>rather than from scratch.
> >>>>
> >>>>I also hacked together some table(s) for EnzymeCommission
> >>>>numbers; there might be something in GUS for that, but at
> >>>>the time what I did seemed faster for my needs than otherwise.
> >>>>The OMIM parts there are not related to KEGG but part of a project 
> >>>>I am working on.
> >>>>
> >>>>Terry
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
> >>>>
> >>>>
> >>>>    
> >>>>
> >>>>>I think I will all the relation in one table... sort of 
> >>>>>EnzymeRelations...
> >>>>>
> >>>>>Thomas
> >>>>>Thomas Otto wrote:
> >>>>>
> >>>>> 
> >>>>>
> >>>>>      
> >>>>>
> >>>>>>Okay, an example:
> >>>>>>To every enzyme are several reaction associated. i.e. Enzymea, 
> >>>>>>has reaction1, ..., reaction n.
> >>>>>>(1) I could be to save the name of the reaction in the table 
> >>>>>>EnzymeClassAttribute
> >>>>>>(2) would be, to save nothing of this in the 
> >>>>>>EnzymeClassAttribute, but in a table (to create) 
> >>>>>>EnzymeReactionRelation.
> >>>>>>
> >>>>>>This will mean a lot of new table, because just for the enzymes 
> >>>>>>there are pathways, reaction, compound, substrate, product...
> >>>>>>
> >>>>>>But indeed, I also prefer #2, who is less redundend.
> >>>>>>
> >>>>>>Thanks,
> >>>>>>Thomas
> >>>>>>
> >>>>>>Angel Pizarro wrote:
> >>>>>>
> >>>>>>  
> >>>>>>        
> >>>>>>
> >>>>>>>In the absence of an example of data a definite schema, 
> >>>>>>>definitely #2 as the data model of choice. You can always 
> >>>>>>>implement materialized view to speed-up/ease  queries.
> >>>>>>>
> >>>>>>>Cheers
> >>>>>>>Angel
> >>>>>>>
> >>>>>>>Thomas Otto wrote:
> >>>>>>>
> >>>>>>>    
> >>>>>>>          
> >>>>>>>
> >>>>>>>>That's what I was thinking about. So I want to know, which 
> >>>>>>>>representation of datas you prefer. (1 or 2, it is more a 
> >>>>>>>>general question).
> >>>>>>>>
> >>>>>>>>Thomas
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>Angel Pizarro wrote:
> >>>>>>>>
> >>>>>>>>      
> >>>>>>>>            
> >>>>>>>>
> >>>>>>>>>OK, I don't see where you are getting EnzymCompoundRelation & 
> >>>>>>>>>CompoundClassAttribute from. Our current version of GUS does 
> >>>>>>>>>not have these tables. The SRes.EnzymeClass table is also 
> >>>>>>>>>looking very wacky to me. Propose a nice structure for this 
> >>>>>>>>>and we can put it in the next release of GUS.
> >>>>>>>>>
> >>>>>>>>>Angel
> >>>>>>>>>
> >>>>>>>>>Thomas Otto wrote:
> >>>>>>>>>
> >>>>>>>>>        
> >>>>>>>>>              
> >>>>>>>>>
> >>>>>>>>>>Hello,
> >>>>>>>>>>
> >>>>>>>>>>I am uploading some kegg data in the GUS system...
> >>>>>>>>>>
> >>>>>>>>>>So I looked which tables are existing, and which we are 
> >>>>>>>>>>needing i.e. for compound, reactions. Now I am not sure how 
> >>>>>>>>>>is the convention to relate the data.
> >>>>>>>>>>
> >>>>>>>>>>Example:
> >>>>>>>>>>The Enzymes are related to the compounds.
> >>>>>>>>>>(1) In EzymeClassAttribute I write the names of the compound 
> >>>>>>>>>>related to each enzyme. In CompoundClassAttribute I write 
> >>>>>>>>>>also all EC-numbers, related to it.
> >>>>>>>>>>(2) Other possibilty would be to utilize a thrid table 
> >>>>>>>>>>EnzymeCompoundRelation, where I put the primkeys of the 
> >>>>>>>>>>relations.
> >>>>>>>>>>
> >>>>>>>>>>(1) would be faster, easier to query, but redundend.
> >>>>>>>>>>(2) Cleaner
> >>>>>>>>>>
> >>>>>>>>>>What are you thinking I should use?
> >>>>>>>>>>
> >>>>>>>>>>Thanks,
> >>>>>>>>>>Thomas
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>-------------------------------------------------------
> >>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President 
> >>>>>>>>>>and CEO of
> >>>>>>>>>>GenToo technologies. Learn everything from fundamentals to 
> >>>>>>>>>>system
> >>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
> >>>>>>>>>>
> >>>>>>>>>>_______________________________________________
> >>>>>>>>>>Gusdev-gusdev mailing list
> >>>>>>>>>>Gus...@li...
> >>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>>>>          
> >>>>>>>>>>                
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>        
> >>>>>>>>>              
> >>>>>>>>
> >>>>>>>-------------------------------------------------------
> >>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>>Free Linux tutorial presented by Daniel Robbins, President and 
> >>>>>>>CEO of
> >>>>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
> >>>>>>>
> >>>>>>>_______________________________________________
> >>>>>>>Gusdev-gusdev mailing list
> >>>>>>>Gus...@li...
> >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>
> >>>>>>>    
> >>>>>>>          
> >>>>>>
> >>>>>>-------------------------------------------------------
> >>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>Free Linux tutorial presented by Daniel Robbins, President and 
> >>>>>>CEO of
> >>>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
> >>>>>>
> >>>>>>_______________________________________________
> >>>>>>Gusdev-gusdev mailing list
> >>>>>>Gus...@li...
> >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>
> >>>>>>  
> >>>>>>        
> >>>>>
> >>>>>-------------------------------------------------------
> >>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>_______________________________________________
> >>>>>Gusdev-gusdev mailing list
> >>>>>Gus...@li...
> >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>> 
> >>>>>
> >>>>>      
> >>>>
> >>>>
> >>>>    
> >>>
> >>
> >>
> >>-------------------------------------------------------
> >>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>GenToo technologies. Learn everything from fundamentals to system
> >>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >> 
> >>
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: IBM Linux Tutorials
> >Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >GenToo technologies. Learn everything from fundamentals to system
> >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] kegg

[Angel P. <an...@pc...>]

Thomas and Terry,
I think that both OMIM and KEGG are good candidates for integration into 
GUS. Here is my advise on how to proceed and get you guys running as 
quick as possible:

1) Create new schema spaces OMIM and KEGG. Enter this data into 
Core.DatabaseInfo.
2) Make the tables as GUS compliant and enter the Core.TableInfo information
3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by:
%> touch $PROJETC_HOME/GUS/Model/schema/VERSION
4) rebuild the objects by:

%> build GUS/Model install -append

This should create new objects for these schema spaces for use in plugins

Document your schema and send it to the gusdev list once you have the 
bugs worked and and THEN we can look to see if existing GUS tables 
already fill that role or if these are new tables that should be folded 
into GUS propoer or if these new tables actually do a better job that 
the current GUS tables that holds this data.
I think this is a good model for further GUS development, and we can 
release these types of development efforts as "contributed" modules of 
code. The contributed modules can be upgraded to "official" after they 
pass a review process and provide data migration scripts.

Any comments?
Angel

Thomas Otto wrote:

> ftp://ftp.genome.ad.jp/pub/
> ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
> from the secound directory I download and parsed the tar files. This 
> suppose to be the files, like the kegg-engine are using them.
>
> Thomas
>
> Terry Clark wrote:
>
>> Thomas,
>> Could you send a pointer to the KEGG FTP URL you are
>> accessing and the names (or type of) files that you are using? I 
>> would appreciate this to see how
>> others are using KEGG.
>>
>> OMIM is orthogonal; I just described it and the
>> parts of KEGG I addressed to explain the material
>> on my web site.
>>
>> Terry
>>
>>
>> On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
>>  
>>
>>> Terry,
>>>
>>> first, I parse the information from the files of the ftp-server. I 
>>> do not use the xml stuff.
>>>
>>> True, there is a lot of stuff in kegg, but I want to represent it in 
>>> GUS, so...
>>>
>>> ... I think a link to OMIM makes sense, also to Motif/prosite. For 
>>> me it is important to have all the relations without redundend.
>>>
>>> Give me some time, I will see, which parts might help me,
>>>
>>> cheers,
>>> Thomas
>>>
>>>
>>> Terry Clark wrote:
>>>
>>>   
>>>
>>>> Thomas,
>>>>
>>>> A few months ago I worked out a preliminary set of tables
>>>> for *some* KEGG pathway data. 
>>>> (By the way, those reactions are not complete in some of
>>>> the XML files.) I expect you know, there are two representations
>>>> in the XML: one with proteins as nodes; the other with reaction
>>>> products as nodes and proteins as edges. I focused on explicitly 
>>>> representing the latter (the <reaction> tag part of the XML) but 
>>>> have toyed with the idea to do a comprehensive KEGG representation 
>>>> in GUS unless someone else does it first :-)
>>>>
>>>> I also have a plugin to load the tables. All I am discussing has
>>>> been implemented as a site-specific/local extension to GUS.  I put 
>>>> the database files (not the plugin - we can talk
>>>> about that later if you are interested) on the web page
>>>>
>>>> http://flora.uchicago.edu/gus/keggschemadraft/
>>>>
>>>> One file you might check first at the URL is     ** kegg-tables.sql 
>>>> ***
>>>>
>>>> I am not satisfied with some of the design, and there may be some 
>>>> uninspired things there - caveat emptor.  I was waiting for KEGG to 
>>>> fix some problems in the reaction tags,
>>>> and put together this operational db prototype in the meantime.
>>>> (For example, check the missing - as of three weeks ago still - 
>>>> reaction tags in the XML for phenylalanine metabolism.)
>>>>
>>>> Anyway the files I point to above might be useful to start with 
>>>> rather than from scratch.
>>>>
>>>> I also hacked together some table(s) for EnzymeCommission
>>>> numbers; there might be something in GUS for that, but at
>>>> the time what I did seemed faster for my needs than otherwise.
>>>> The OMIM parts there are not related to KEGG but part of a project 
>>>> I am working on.
>>>>
>>>> Terry
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
>>>>
>>>>
>>>>     
>>>>
>>>>> I think I will all the relation in one table... sort of 
>>>>> EnzymeRelations...
>>>>>
>>>>> Thomas
>>>>> Thomas Otto wrote:
>>>>>
>>>>>  
>>>>>
>>>>>       
>>>>>
>>>>>> Okay, an example:
>>>>>> To every enzyme are several reaction associated. i.e. Enzymea, 
>>>>>> has reaction1, ..., reaction n.
>>>>>> (1) I could be to save the name of the reaction in the table 
>>>>>> EnzymeClassAttribute
>>>>>> (2) would be, to save nothing of this in the 
>>>>>> EnzymeClassAttribute, but in a table (to create) 
>>>>>> EnzymeReactionRelation.
>>>>>>
>>>>>> This will mean a lot of new table, because just for the enzymes 
>>>>>> there are pathways, reaction, compound, substrate, product...
>>>>>>
>>>>>> But indeed, I also prefer #2, who is less redundend.
>>>>>>
>>>>>> Thanks,
>>>>>> Thomas
>>>>>>
>>>>>> Angel Pizarro wrote:
>>>>>>
>>>>>>   
>>>>>>         
>>>>>>
>>>>>>> In the absence of an example of data a definite schema, 
>>>>>>> definitely #2 as the data model of choice. You can always 
>>>>>>> implement materialized view to speed-up/ease  queries.
>>>>>>>
>>>>>>> Cheers
>>>>>>> Angel
>>>>>>>
>>>>>>> Thomas Otto wrote:
>>>>>>>
>>>>>>>     
>>>>>>>           
>>>>>>>
>>>>>>>> That's what I was thinking about. So I want to know, which 
>>>>>>>> representation of datas you prefer. (1 or 2, it is more a 
>>>>>>>> general question).
>>>>>>>>
>>>>>>>> Thomas
>>>>>>>>
>>>>>>>>
>>>>>>>> Angel Pizarro wrote:
>>>>>>>>
>>>>>>>>       
>>>>>>>>             
>>>>>>>>
>>>>>>>>> OK, I don't see where you are getting EnzymCompoundRelation & 
>>>>>>>>> CompoundClassAttribute from. Our current version of GUS does 
>>>>>>>>> not have these tables. The SRes.EnzymeClass table is also 
>>>>>>>>> looking very wacky to me. Propose a nice structure for this 
>>>>>>>>> and we can put it in the next release of GUS.
>>>>>>>>>
>>>>>>>>> Angel
>>>>>>>>>
>>>>>>>>> Thomas Otto wrote:
>>>>>>>>>
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>>
>>>>>>>>>> Hello,
>>>>>>>>>>
>>>>>>>>>> I am uploading some kegg data in the GUS system...
>>>>>>>>>>
>>>>>>>>>> So I looked which tables are existing, and which we are 
>>>>>>>>>> needing i.e. for compound, reactions. Now I am not sure how 
>>>>>>>>>> is the convention to relate the data.
>>>>>>>>>>
>>>>>>>>>> Example:
>>>>>>>>>> The Enzymes are related to the compounds.
>>>>>>>>>> (1) In EzymeClassAttribute I write the names of the compound 
>>>>>>>>>> related to each enzyme. In CompoundClassAttribute I write 
>>>>>>>>>> also all EC-numbers, related to it.
>>>>>>>>>> (2) Other possibilty would be to utilize a thrid table 
>>>>>>>>>> EnzymeCompoundRelation, where I put the primkeys of the 
>>>>>>>>>> relations.
>>>>>>>>>>
>>>>>>>>>> (1) would be faster, easier to query, but redundend.
>>>>>>>>>> (2) Cleaner
>>>>>>>>>>
>>>>>>>>>> What are you thinking I should use?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Thomas
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>>> Free Linux tutorial presented by Daniel Robbins, President 
>>>>>>>>>> and CEO of
>>>>>>>>>> GenToo technologies. Learn everything from fundamentals to 
>>>>>>>>>> system
>>>>>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gusdev-gusdev mailing list
>>>>>>>>>> Gus...@li...
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>>>           
>>>>>>>>>>                 
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>
>>>>>>> -------------------------------------------------------
>>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>> Free Linux tutorial presented by Daniel Robbins, President and 
>>>>>>> CEO of
>>>>>>> GenToo technologies. Learn everything from fundamentals to system
>>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Gusdev-gusdev mailing list
>>>>>>> Gus...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>
>>>>>>>     
>>>>>>>           
>>>>>>
>>>>>> -------------------------------------------------------
>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>> Free Linux tutorial presented by Daniel Robbins, President and 
>>>>>> CEO of
>>>>>> GenToo technologies. Learn everything from fundamentals to system
>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click 
>>>>>>
>>>>>> _______________________________________________
>>>>>> Gusdev-gusdev mailing list
>>>>>> Gus...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>>   
>>>>>>         
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>> GenToo technologies. Learn everything from fundamentals to system
>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>  
>>>>>
>>>>>       
>>>>
>>>>
>>>>     
>>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IBM Linux Tutorials
>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>> GenToo technologies. Learn everything from fundamentals to system
>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>  
>>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] kegg

[Thomas O. <ot...@fi...>]

ftp://ftp.genome.ad.jp/pub/
ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
from the secound directory I download and parsed the tar files. This 
suppose to be the files, like the kegg-engine are using them.

Thomas

Terry Clark wrote:

>Thomas,
>Could you send a pointer to the KEGG FTP URL you are
>accessing and the names (or type of) files that 
>you are using? I would appreciate this to see how
>others are using KEGG.
>
>OMIM is orthogonal; I just described it and the
>parts of KEGG I addressed to explain the material
>on my web site.
>
>Terry
>
>
>On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
>  
>
>>Terry,
>>
>>first, I parse the information from the files of the ftp-server. I do 
>>not use the xml stuff.
>>
>>True, there is a lot of stuff in kegg, but I want to represent it in 
>>GUS, so...
>>
>>... I think a link to OMIM makes sense, also to Motif/prosite. For me it 
>>is important to have all the relations without redundend.
>>
>>Give me some time, I will see, which parts might help me,
>>
>>cheers,
>>Thomas
>>
>>
>>Terry Clark wrote:
>>
>>    
>>
>>>Thomas,
>>>
>>>A few months ago I worked out a preliminary set of tables
>>>for *some* KEGG pathway data.  
>>>
>>>(By the way, those reactions are not complete in some of
>>>the XML files.) I expect you know, there are two representations
>>>in the XML: one with proteins as nodes; the other with reaction
>>>products as nodes and proteins as edges. 
>>>I focused on explicitly representing the latter 
>>>(the <reaction> tag part of the XML) but have toyed with 
>>>the idea to do a comprehensive KEGG representation in GUS unless 
>>>someone else does it first :-)
>>>
>>>I also have a plugin to load the tables. All I am discussing has
>>>been implemented as a site-specific/local extension to GUS.  
>>>I put the database files (not the plugin - we can talk
>>>about that later if you are interested) on the web page
>>>
>>>http://flora.uchicago.edu/gus/keggschemadraft/
>>>
>>>One file you might check first at the URL is   
>>>   ** kegg-tables.sql ***
>>>
>>>I am not satisfied with some of the design, and there may 
>>>be some uninspired things there - caveat emptor.  I was 
>>>waiting for KEGG to fix some problems in the reaction tags,
>>>and put together this operational db prototype in the meantime.
>>>(For example, check the missing - as of three weeks ago still - 
>>>reaction tags in the XML for phenylalanine metabolism.)
>>>
>>>Anyway the files I point to above might be useful to 
>>>start with rather than from scratch.
>>>
>>>I also hacked together some table(s) for EnzymeCommission
>>>numbers; there might be something in GUS for that, but at
>>>the time what I did seemed faster for my needs than otherwise.
>>>The OMIM parts there are not related to KEGG but part of 
>>>a project I am working on. 
>>>
>>>
>>>Terry
>>>
>>>
>>>
>>>
>>>
>>>On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
>>>
>>>
>>>      
>>>
>>>>I think I will all the relation in one table... sort of EnzymeRelations...
>>>>
>>>>Thomas
>>>>Thomas Otto wrote:
>>>>
>>>>  
>>>>
>>>>        
>>>>
>>>>>Okay, an example:
>>>>>To every enzyme are several reaction associated. i.e. Enzymea, has 
>>>>>reaction1, ..., reaction n.
>>>>>(1) I could be to save the name of the reaction in the table 
>>>>>EnzymeClassAttribute
>>>>>(2) would be, to save nothing of this in the EnzymeClassAttribute, but 
>>>>>in a table (to create) EnzymeReactionRelation.
>>>>>
>>>>>This will mean a lot of new table, because just for the enzymes there 
>>>>>are pathways, reaction, compound, substrate, product...
>>>>>
>>>>>But indeed, I also prefer #2, who is less redundend.
>>>>>
>>>>>Thanks,
>>>>>Thomas
>>>>>
>>>>>Angel Pizarro wrote:
>>>>>
>>>>>    
>>>>>
>>>>>          
>>>>>
>>>>>>In the absence of an example of data a definite schema, definitely #2 
>>>>>>as the data model of choice. You can always implement materialized 
>>>>>>view to speed-up/ease  queries.
>>>>>>
>>>>>>Cheers
>>>>>>Angel
>>>>>>
>>>>>>Thomas Otto wrote:
>>>>>>
>>>>>>      
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>That's what I was thinking about. So I want to know, which 
>>>>>>>representation of datas you prefer. (1 or 2, it is more a general 
>>>>>>>question).
>>>>>>>
>>>>>>>Thomas
>>>>>>>
>>>>>>>
>>>>>>>Angel Pizarro wrote:
>>>>>>>
>>>>>>>        
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>>>OK, I don't see where you are getting EnzymCompoundRelation & 
>>>>>>>>CompoundClassAttribute from. Our current version of GUS does not 
>>>>>>>>have these tables. The SRes.EnzymeClass table is also looking very 
>>>>>>>>wacky to me. Propose a nice structure for this and we can put it in 
>>>>>>>>the next release of GUS.
>>>>>>>>
>>>>>>>>Angel
>>>>>>>>
>>>>>>>>Thomas Otto wrote:
>>>>>>>>
>>>>>>>>          
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>>>>Hello,
>>>>>>>>>
>>>>>>>>>I am uploading some kegg data in the GUS system...
>>>>>>>>>
>>>>>>>>>So I looked which tables are existing, and which we are needing 
>>>>>>>>>i.e. for compound, reactions. Now I am not sure how is the 
>>>>>>>>>convention to relate the data.
>>>>>>>>>
>>>>>>>>>Example:
>>>>>>>>>The Enzymes are related to the compounds.
>>>>>>>>>(1) In EzymeClassAttribute I write the names of the compound 
>>>>>>>>>related to each enzyme. In CompoundClassAttribute I write also all 
>>>>>>>>>EC-numbers, related to it.
>>>>>>>>>(2) Other possibilty would be to utilize a thrid table 
>>>>>>>>>EnzymeCompoundRelation, where I put the primkeys of the relations.
>>>>>>>>>
>>>>>>>>>(1) would be faster, easier to query, but redundend.
>>>>>>>>>(2) Cleaner
>>>>>>>>>
>>>>>>>>>What are you thinking I should use?
>>>>>>>>>
>>>>>>>>>Thanks,
>>>>>>>>>Thomas
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>-------------------------------------------------------
>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>>>>>>_______________________________________________
>>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>>Gus...@li...
>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>>            
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>          
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>-------------------------------------------------------
>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>>>_______________________________________________
>>>>>>Gusdev-gusdev mailing list
>>>>>>Gus...@li...
>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>>      
>>>>>>
>>>>>>            
>>>>>>
>>>>>-------------------------------------------------------
>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>    
>>>>>
>>>>>          
>>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>  
>>>>
>>>>        
>>>>
>>>
>>>      
>>>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

Re: [Gusdev-gusdev] Relation between tables

[<tw...@cs...>]

Thomas,
Could you send a pointer to the KEGG FTP URL you are
accessing and the names (or type of) files that 
you are using? I would appreciate this to see how
others are using KEGG.

OMIM is orthogonal; I just described it and the
parts of KEGG I addressed to explain the material
on my web site.

Terry


On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
> Terry,
> 
> first, I parse the information from the files of the ftp-server. I do 
> not use the xml stuff.
> 
> True, there is a lot of stuff in kegg, but I want to represent it in 
> GUS, so...
> 
> ... I think a link to OMIM makes sense, also to Motif/prosite. For me it 
> is important to have all the relations without redundend.
> 
> Give me some time, I will see, which parts might help me,
> 
> cheers,
> Thomas
> 
> 
> Terry Clark wrote:
> 
> >Thomas,
> >
> >A few months ago I worked out a preliminary set of tables
> >for *some* KEGG pathway data.  
> >
> >(By the way, those reactions are not complete in some of
> >the XML files.) I expect you know, there are two representations
> >in the XML: one with proteins as nodes; the other with reaction
> >products as nodes and proteins as edges. 
> >I focused on explicitly representing the latter 
> >(the <reaction> tag part of the XML) but have toyed with 
> >the idea to do a comprehensive KEGG representation in GUS unless 
> >someone else does it first :-)
> >
> >I also have a plugin to load the tables. All I am discussing has
> >been implemented as a site-specific/local extension to GUS.  
> >I put the database files (not the plugin - we can talk
> >about that later if you are interested) on the web page
> >
> > http://flora.uchicago.edu/gus/keggschemadraft/
> >
> >One file you might check first at the URL is   
> >    ** kegg-tables.sql ***
> >
> >I am not satisfied with some of the design, and there may 
> >be some uninspired things there - caveat emptor.  I was 
> >waiting for KEGG to fix some problems in the reaction tags,
> >and put together this operational db prototype in the meantime.
> >(For example, check the missing - as of three weeks ago still - 
> >reaction tags in the XML for phenylalanine metabolism.)
> >
> >Anyway the files I point to above might be useful to 
> >start with rather than from scratch.
> >
> >I also hacked together some table(s) for EnzymeCommission
> >numbers; there might be something in GUS for that, but at
> >the time what I did seemed faster for my needs than otherwise.
> >The OMIM parts there are not related to KEGG but part of 
> >a project I am working on. 
> >
> >
> >Terry
> >
> >
> >
> >
> >
> >On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
> > 
> >
> >>I think I will all the relation in one table... sort of EnzymeRelations...
> >>
> >>Thomas
> >>Thomas Otto wrote:
> >>
> >>   
> >>
> >>>Okay, an example:
> >>>To every enzyme are several reaction associated. i.e. Enzymea, has 
> >>>reaction1, ..., reaction n.
> >>>(1) I could be to save the name of the reaction in the table 
> >>>EnzymeClassAttribute
> >>>(2) would be, to save nothing of this in the EnzymeClassAttribute, but 
> >>>in a table (to create) EnzymeReactionRelation.
> >>>
> >>>This will mean a lot of new table, because just for the enzymes there 
> >>>are pathways, reaction, compound, substrate, product...
> >>>
> >>>But indeed, I also prefer #2, who is less redundend.
> >>>
> >>>Thanks,
> >>>Thomas
> >>>
> >>>Angel Pizarro wrote:
> >>>
> >>>     
> >>>
> >>>>In the absence of an example of data a definite schema, definitely #2 
> >>>>as the data model of choice. You can always implement materialized 
> >>>>view to speed-up/ease  queries.
> >>>>
> >>>>Cheers
> >>>>Angel
> >>>>
> >>>>Thomas Otto wrote:
> >>>>
> >>>>       
> >>>>
> >>>>>That's what I was thinking about. So I want to know, which 
> >>>>>representation of datas you prefer. (1 or 2, it is more a general 
> >>>>>question).
> >>>>>
> >>>>>Thomas
> >>>>>
> >>>>>
> >>>>>Angel Pizarro wrote:
> >>>>>
> >>>>>         
> >>>>>
> >>>>>>OK, I don't see where you are getting EnzymCompoundRelation & 
> >>>>>>CompoundClassAttribute from. Our current version of GUS does not 
> >>>>>>have these tables. The SRes.EnzymeClass table is also looking very 
> >>>>>>wacky to me. Propose a nice structure for this and we can put it in 
> >>>>>>the next release of GUS.
> >>>>>>
> >>>>>>Angel
> >>>>>>
> >>>>>>Thomas Otto wrote:
> >>>>>>
> >>>>>>           
> >>>>>>
> >>>>>>>Hello,
> >>>>>>>
> >>>>>>>I am uploading some kegg data in the GUS system...
> >>>>>>>
> >>>>>>>So I looked which tables are existing, and which we are needing 
> >>>>>>>i.e. for compound, reactions. Now I am not sure how is the 
> >>>>>>>convention to relate the data.
> >>>>>>>
> >>>>>>>Example:
> >>>>>>>The Enzymes are related to the compounds.
> >>>>>>>(1) In EzymeClassAttribute I write the names of the compound 
> >>>>>>>related to each enzyme. In CompoundClassAttribute I write also all 
> >>>>>>>EC-numbers, related to it.
> >>>>>>>(2) Other possibilty would be to utilize a thrid table 
> >>>>>>>EnzymeCompoundRelation, where I put the primkeys of the relations.
> >>>>>>>
> >>>>>>>(1) would be faster, easier to query, but redundend.
> >>>>>>>(2) Cleaner
> >>>>>>>
> >>>>>>>What are you thinking I should use?
> >>>>>>>
> >>>>>>>Thanks,
> >>>>>>>Thomas
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>-------------------------------------------------------
> >>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>>>_______________________________________________
> >>>>>>>Gusdev-gusdev mailing list
> >>>>>>>Gus...@li...
> >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>             
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>           
> >>>>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>>       
> >>>>
> >>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>GenToo technologies. Learn everything from fundamentals to system
> >>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>_______________________________________________
> >>>Gusdev-gusdev mailing list
> >>>Gus...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>
> >>>     
> >>>
> >>
> >>
> >>-------------------------------------------------------
> >>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>GenToo technologies. Learn everything from fundamentals to system
> >>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>   
> >>
> >
> > 
> >
> 

Re: [Gusdev-gusdev] Relation between tables

[<tw...@cs...>]

> (By the way, those reactions are not complete in some of
> the XML files.) I expect you know, there are two representations

What reactions? How did that permutation happen?
Sorry for the typos. It is early still ...
but the gist is in the email.

Terry



On Fri, Mar 12, 2004 at 06:35:16AM -0600, Terry Clark wrote:
> Thomas,
> 
> A few months ago I worked out a preliminary set of tables
> for *some* KEGG pathway data.  
> 
> (By the way, those reactions are not complete in some of
> the XML files.) I expect you know, there are two representations
> in the XML: one with proteins as nodes; the other with reaction
> products as nodes and proteins as edges. 
> I focused on explicitly representing the latter 
> (the <reaction> tag part of the XML) but have toyed with 
> the idea to do a comprehensive KEGG representation in GUS unless 
> someone else does it first :-)
> 
> I also have a plugin to load the tables. All I am discussing has
> been implemented as a site-specific/local extension to GUS.  
> I put the database files (not the plugin - we can talk
> about that later if you are interested) on the web page
> 
>   http://flora.uchicago.edu/gus/keggschemadraft/
> 
> One file you might check first at the URL is   
>      ** kegg-tables.sql ***
> 
> I am not satisfied with some of the design, and there may 
> be some uninspired things there - caveat emptor.  I was 
> waiting for KEGG to fix some problems in the reaction tags,
> and put together this operational db prototype in the meantime.
> (For example, check the missing - as of three weeks ago still - 
> reaction tags in the XML for phenylalanine metabolism.)
> 
> Anyway the files I point to above might be useful to 
> start with rather than from scratch.
> 
> I also hacked together some table(s) for EnzymeCommission
> numbers; there might be something in GUS for that, but at
> the time what I did seemed faster for my needs than otherwise.
> The OMIM parts there are not related to KEGG but part of 
> a project I am working on. 
> 
> 
> Terry
> 
> 
> 
> 
> 
> On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
> > I think I will all the relation in one table... sort of EnzymeRelations...
> > 
> > Thomas
> > Thomas Otto wrote:
> > 
> > >Okay, an example:
> > >To every enzyme are several reaction associated. i.e. Enzymea, has 
> > >reaction1, ..., reaction n.
> > >(1) I could be to save the name of the reaction in the table 
> > >EnzymeClassAttribute
> > >(2) would be, to save nothing of this in the EnzymeClassAttribute, but 
> > >in a table (to create) EnzymeReactionRelation.
> > >
> > >This will mean a lot of new table, because just for the enzymes there 
> > >are pathways, reaction, compound, substrate, product...
> > >
> > >But indeed, I also prefer #2, who is less redundend.
> > >
> > >Thanks,
> > >Thomas
> > >
> > >Angel Pizarro wrote:
> > >
> > >>In the absence of an example of data a definite schema, definitely #2 
> > >>as the data model of choice. You can always implement materialized 
> > >>view to speed-up/ease  queries.
> > >>
> > >>Cheers
> > >>Angel
> > >>
> > >>Thomas Otto wrote:
> > >>
> > >>>That's what I was thinking about. So I want to know, which 
> > >>>representation of datas you prefer. (1 or 2, it is more a general 
> > >>>question).
> > >>>
> > >>>Thomas
> > >>>
> > >>>
> > >>>Angel Pizarro wrote:
> > >>>
> > >>>>OK, I don't see where you are getting EnzymCompoundRelation & 
> > >>>>CompoundClassAttribute from. Our current version of GUS does not 
> > >>>>have these tables. The SRes.EnzymeClass table is also looking very 
> > >>>>wacky to me. Propose a nice structure for this and we can put it in 
> > >>>>the next release of GUS.
> > >>>>
> > >>>>Angel
> > >>>>
> > >>>>Thomas Otto wrote:
> > >>>>
> > >>>>>Hello,
> > >>>>>
> > >>>>>I am uploading some kegg data in the GUS system...
> > >>>>>
> > >>>>>So I looked which tables are existing, and which we are needing 
> > >>>>>i.e. for compound, reactions. Now I am not sure how is the 
> > >>>>>convention to relate the data.
> > >>>>>
> > >>>>>Example:
> > >>>>>The Enzymes are related to the compounds.
> > >>>>>(1) In EzymeClassAttribute I write the names of the compound 
> > >>>>>related to each enzyme. In CompoundClassAttribute I write also all 
> > >>>>>EC-numbers, related to it.
> > >>>>>(2) Other possibilty would be to utilize a thrid table 
> > >>>>>EnzymeCompoundRelation, where I put the primkeys of the relations.
> > >>>>>
> > >>>>>(1) would be faster, easier to query, but redundend.
> > >>>>>(2) Cleaner
> > >>>>>
> > >>>>>What are you thinking I should use?
> > >>>>>
> > >>>>>Thanks,
> > >>>>>Thomas
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>-------------------------------------------------------
> > >>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> > >>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > >>>>>GenToo technologies. Learn everything from fundamentals to system
> > >>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > >>>>>_______________________________________________
> > >>>>>Gusdev-gusdev mailing list
> > >>>>>Gus...@li...
> > >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>
> > >>
> > >>
> > >>
> > >>-------------------------------------------------------
> > >>This SF.Net email is sponsored by: IBM Linux Tutorials
> > >>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > >>GenToo technologies. Learn everything from fundamentals to system
> > >>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > >>_______________________________________________
> > >>Gusdev-gusdev mailing list
> > >>Gus...@li...
> > >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >>
> > >
> > >
> > >
> > >
> > >-------------------------------------------------------
> > >This SF.Net email is sponsored by: IBM Linux Tutorials
> > >Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > >GenToo technologies. Learn everything from fundamentals to system
> > >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > >_______________________________________________
> > >Gusdev-gusdev mailing list
> > >Gus...@li...
> > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> > 
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Relation between tables

[<tw...@cs...>]

Thomas,

A few months ago I worked out a preliminary set of tables
for *some* KEGG pathway data.  

(By the way, those reactions are not complete in some of
the XML files.) I expect you know, there are two representations
in the XML: one with proteins as nodes; the other with reaction
products as nodes and proteins as edges. 
I focused on explicitly representing the latter 
(the <reaction> tag part of the XML) but have toyed with 
the idea to do a comprehensive KEGG representation in GUS unless 
someone else does it first :-)

I also have a plugin to load the tables. All I am discussing has
been implemented as a site-specific/local extension to GUS.  
I put the database files (not the plugin - we can talk
about that later if you are interested) on the web page

  http://flora.uchicago.edu/gus/keggschemadraft/

One file you might check first at the URL is   
     ** kegg-tables.sql ***

I am not satisfied with some of the design, and there may 
be some uninspired things there - caveat emptor.  I was 
waiting for KEGG to fix some problems in the reaction tags,
and put together this operational db prototype in the meantime.
(For example, check the missing - as of three weeks ago still - 
reaction tags in the XML for phenylalanine metabolism.)

Anyway the files I point to above might be useful to 
start with rather than from scratch.

I also hacked together some table(s) for EnzymeCommission
numbers; there might be something in GUS for that, but at
the time what I did seemed faster for my needs than otherwise.
The OMIM parts there are not related to KEGG but part of 
a project I am working on. 


Terry





On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
> I think I will all the relation in one table... sort of EnzymeRelations...
> 
> Thomas
> Thomas Otto wrote:
> 
> >Okay, an example:
> >To every enzyme are several reaction associated. i.e. Enzymea, has 
> >reaction1, ..., reaction n.
> >(1) I could be to save the name of the reaction in the table 
> >EnzymeClassAttribute
> >(2) would be, to save nothing of this in the EnzymeClassAttribute, but 
> >in a table (to create) EnzymeReactionRelation.
> >
> >This will mean a lot of new table, because just for the enzymes there 
> >are pathways, reaction, compound, substrate, product...
> >
> >But indeed, I also prefer #2, who is less redundend.
> >
> >Thanks,
> >Thomas
> >
> >Angel Pizarro wrote:
> >
> >>In the absence of an example of data a definite schema, definitely #2 
> >>as the data model of choice. You can always implement materialized 
> >>view to speed-up/ease  queries.
> >>
> >>Cheers
> >>Angel
> >>
> >>Thomas Otto wrote:
> >>
> >>>That's what I was thinking about. So I want to know, which 
> >>>representation of datas you prefer. (1 or 2, it is more a general 
> >>>question).
> >>>
> >>>Thomas
> >>>
> >>>
> >>>Angel Pizarro wrote:
> >>>
> >>>>OK, I don't see where you are getting EnzymCompoundRelation & 
> >>>>CompoundClassAttribute from. Our current version of GUS does not 
> >>>>have these tables. The SRes.EnzymeClass table is also looking very 
> >>>>wacky to me. Propose a nice structure for this and we can put it in 
> >>>>the next release of GUS.
> >>>>
> >>>>Angel
> >>>>
> >>>>Thomas Otto wrote:
> >>>>
> >>>>>Hello,
> >>>>>
> >>>>>I am uploading some kegg data in the GUS system...
> >>>>>
> >>>>>So I looked which tables are existing, and which we are needing 
> >>>>>i.e. for compound, reactions. Now I am not sure how is the 
> >>>>>convention to relate the data.
> >>>>>
> >>>>>Example:
> >>>>>The Enzymes are related to the compounds.
> >>>>>(1) In EzymeClassAttribute I write the names of the compound 
> >>>>>related to each enzyme. In CompoundClassAttribute I write also all 
> >>>>>EC-numbers, related to it.
> >>>>>(2) Other possibilty would be to utilize a thrid table 
> >>>>>EnzymeCompoundRelation, where I put the primkeys of the relations.
> >>>>>
> >>>>>(1) would be faster, easier to query, but redundend.
> >>>>>(2) Cleaner
> >>>>>
> >>>>>What are you thinking I should use?
> >>>>>
> >>>>>Thanks,
> >>>>>Thomas
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>-------------------------------------------------------
> >>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>_______________________________________________
> >>>>>Gusdev-gusdev mailing list
> >>>>>Gus...@li...
> >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>
> >>
> >>
> >>-------------------------------------------------------
> >>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>GenToo technologies. Learn everything from fundamentals to system
> >>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: IBM Linux Tutorials
> >Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >GenToo technologies. Learn everything from fundamentals to system
> >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Relation between tables

[Thomas O. <ot...@fi...>]

Okay, first an overview of the table and after that the sql code
Following table I need (* - to implement)
EnzymeClass
EnzymeClassAttribute
Pathway  - I do not know if the dots::pathway does what I want :-)
compound *
reaction *
Motif/Prosite
Disease *
Classment for Functions and Proteins *

Relations:
1. CompoundRelations * - will hold the relation to reaction, enzyme,
2. EnzymeRelations * - will hold the relation of the enzyms to reaction, 
Motif, Diesease
ECpathway - would be obsolete

The namespace should be sres.

Maybe I could put 1 and 2 together, but... anyhow, all data are related. 
(All information comes from kegg)

Here the tables:

the question of the two following table is, if it would be better to do 
a table compoundattribute...

CREATE TABLE SRes.compound  (
    compound_id          number(12)                                    
NOT NULL,
    ENTRY            VARCHAR2(90)                                      
NOT NULL,
    NAME            VARCHAR2(90)                                      
NOT NULL,
    FORMULA            VARCHAR2(90)                                      
NULL,
    DBLINKS            
VARCHAR2(120)                                      NULL,
    MODIFICATION_DATE                  
DATE                                          NOT NULL,
    USER_READ                          NUMBER(1) 
...
CREATE TABLE SRes.reaction  (
    reaction_id          number(5)                                    
NOT NULL,
    ENTRY            VARCHAR2(90)                                      
NOT NULL,
    NAME            VARCHAR2(90)                                      NULL,
    DEFINITION            
VARCHAR2(90)                                      NULL,
    EQUATION            
VARCHAR2(120)                                      NULL,
    COMMENTS            
VARCHAR2(120)                                      NULL,
    MODIFICATION_DATE                  
DATE                                          NOT NULL,
    USER_READ                          NUMBER(1)
...
 Motif and Disease not sure, I think I will put the Attributes like in 
the EnzymeClassattribute - table



EnzymeRelations and CompoundRelations will be the same.
CREATE TABLE SRes.EnzymeRelations  (
    Enzyme_Relations_id         
 number(12)                                    NOT NULL,
    enzyme_class_id              number(12)                NOT NULL,
    foreign_id            number(12)                     NOT NULL,
    TYPE                Varchar2(20)            NOT NULL,
    MODIFICATION_DATE                  
DATE                                          NOT NULL,
 

So that's my idea.
Thomas


Steve Fischer wrote:

> Thomas-
>
> when you have a first draft of your ideas, send us the table or 
> tables, including the attributes and data types.   that way we will be 
> able to give you the best advice.
>
> steve
>
> Thomas Otto wrote:
>
>> I think I will all the relation in one table... sort of 
>> EnzymeRelations...
>>
>> Thomas
>> Thomas Otto wrote:
>>
>>> Okay, an example:
>>> To every enzyme are several reaction associated. i.e. Enzymea, has 
>>> reaction1, ..., reaction n.
>>> (1) I could be to save the name of the reaction in the table 
>>> EnzymeClassAttribute
>>> (2) would be, to save nothing of this in the EnzymeClassAttribute, 
>>> but in a table (to create) EnzymeReactionRelation.
>>>
>>> This will mean a lot of new table, because just for the enzymes 
>>> there are pathways, reaction, compound, substrate, product...
>>>
>>> But indeed, I also prefer #2, who is less redundend.
>>>
>>> Thanks,
>>> Thomas
>>>
>>> Angel Pizarro wrote:
>>>
>>>> In the absence of an example of data a definite schema, definitely 
>>>> #2 as the data model of choice. You can always implement 
>>>> materialized view to speed-up/ease  queries.
>>>>
>>>> Cheers
>>>> Angel
>>>>
>>>> Thomas Otto wrote:
>>>>
>>>>> That's what I was thinking about. So I want to know, which 
>>>>> representation of datas you prefer. (1 or 2, it is more a general 
>>>>> question).
>>>>>
>>>>> Thomas
>>>>>
>>>>>
>>>>> Angel Pizarro wrote:
>>>>>
>>>>>> OK, I don't see where you are getting EnzymCompoundRelation & 
>>>>>> CompoundClassAttribute from. Our current version of GUS does not 
>>>>>> have these tables. The SRes.EnzymeClass table is also looking 
>>>>>> very wacky to me. Propose a nice structure for this and we can 
>>>>>> put it in the next release of GUS.
>>>>>>
>>>>>> Angel
>>>>>>
>>>>>> Thomas Otto wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I am uploading some kegg data in the GUS system...
>>>>>>>
>>>>>>> So I looked which tables are existing, and which we are needing 
>>>>>>> i.e. for compound, reactions. Now I am not sure how is the 
>>>>>>> convention to relate the data.
>>>>>>>
>>>>>>> Example:
>>>>>>> The Enzymes are related to the compounds.
>>>>>>> (1) In EzymeClassAttribute I write the names of the compound 
>>>>>>> related to each enzyme. In CompoundClassAttribute I write also 
>>>>>>> all EC-numbers, related to it.
>>>>>>> (2) Other possibilty would be to utilize a thrid table 
>>>>>>> EnzymeCompoundRelation, where I put the primkeys of the relations.
>>>>>>>
>>>>>>> (1) would be faster, easier to query, but redundend.
>>>>>>> (2) Cleaner
>>>>>>>
>>>>>>> What are you thinking I should use?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Thomas
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -------------------------------------------------------
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Re: [Gusdev-gusdev] Relation between tables

[Steve F. <sfi...@pc...>]

Thomas-

when you have a first draft of your ideas, send us the table or tables, 
including the attributes and data types.   that way we will be able to 
give you the best advice.

steve

Thomas Otto wrote:

> I think I will all the relation in one table... sort of 
> EnzymeRelations...
>
> Thomas
> Thomas Otto wrote:
>
>> Okay, an example:
>> To every enzyme are several reaction associated. i.e. Enzymea, has 
>> reaction1, ..., reaction n.
>> (1) I could be to save the name of the reaction in the table 
>> EnzymeClassAttribute
>> (2) would be, to save nothing of this in the EnzymeClassAttribute, 
>> but in a table (to create) EnzymeReactionRelation.
>>
>> This will mean a lot of new table, because just for the enzymes there 
>> are pathways, reaction, compound, substrate, product...
>>
>> But indeed, I also prefer #2, who is less redundend.
>>
>> Thanks,
>> Thomas
>>
>> Angel Pizarro wrote:
>>
>>> In the absence of an example of data a definite schema, definitely 
>>> #2 as the data model of choice. You can always implement 
>>> materialized view to speed-up/ease  queries.
>>>
>>> Cheers
>>> Angel
>>>
>>> Thomas Otto wrote:
>>>
>>>> That's what I was thinking about. So I want to know, which 
>>>> representation of datas you prefer. (1 or 2, it is more a general 
>>>> question).
>>>>
>>>> Thomas
>>>>
>>>>
>>>> Angel Pizarro wrote:
>>>>
>>>>> OK, I don't see where you are getting EnzymCompoundRelation & 
>>>>> CompoundClassAttribute from. Our current version of GUS does not 
>>>>> have these tables. The SRes.EnzymeClass table is also looking very 
>>>>> wacky to me. Propose a nice structure for this and we can put it 
>>>>> in the next release of GUS.
>>>>>
>>>>> Angel
>>>>>
>>>>> Thomas Otto wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am uploading some kegg data in the GUS system...
>>>>>>
>>>>>> So I looked which tables are existing, and which we are needing 
>>>>>> i.e. for compound, reactions. Now I am not sure how is the 
>>>>>> convention to relate the data.
>>>>>>
>>>>>> Example:
>>>>>> The Enzymes are related to the compounds.
>>>>>> (1) In EzymeClassAttribute I write the names of the compound 
>>>>>> related to each enzyme. In CompoundClassAttribute I write also 
>>>>>> all EC-numbers, related to it.
>>>>>> (2) Other possibilty would be to utilize a thrid table 
>>>>>> EnzymeCompoundRelation, where I put the primkeys of the relations.
>>>>>>
>>>>>> (1) would be faster, easier to query, but redundend.
>>>>>> (2) Cleaner
>>>>>>
>>>>>> What are you thinking I should use?
>>>>>>
>>>>>> Thanks,
>>>>>> Thomas
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------
>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>> Free Linux tutorial presented by Daniel Robbins, President and 
>>>>>> CEO of
>>>>>> GenToo technologies. Learn everything from fundamentals to system
>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>>> _______________________________________________
>>>>>> Gusdev-gusdev mailing list
>>>>>> Gus...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>> GenToo technologies. Learn everything from fundamentals to system
>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>> _______________________________________________
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>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>>
>>
>>
>> -------------------------------------------------------
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>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>> GenToo technologies. Learn everything from fundamentals to system
>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
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> GenToo technologies. Learn everything from fundamentals to system
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Re: [Gusdev-gusdev] Relation between tables

[Thomas O. <ot...@fi...>]

I think I will all the relation in one table... sort of EnzymeRelations...

Thomas
Thomas Otto wrote:

> Okay, an example:
> To every enzyme are several reaction associated. i.e. Enzymea, has 
> reaction1, ..., reaction n.
> (1) I could be to save the name of the reaction in the table 
> EnzymeClassAttribute
> (2) would be, to save nothing of this in the EnzymeClassAttribute, but 
> in a table (to create) EnzymeReactionRelation.
>
> This will mean a lot of new table, because just for the enzymes there 
> are pathways, reaction, compound, substrate, product...
>
> But indeed, I also prefer #2, who is less redundend.
>
> Thanks,
> Thomas
>
> Angel Pizarro wrote:
>
>> In the absence of an example of data a definite schema, definitely #2 
>> as the data model of choice. You can always implement materialized 
>> view to speed-up/ease  queries.
>>
>> Cheers
>> Angel
>>
>> Thomas Otto wrote:
>>
>>> That's what I was thinking about. So I want to know, which 
>>> representation of datas you prefer. (1 or 2, it is more a general 
>>> question).
>>>
>>> Thomas
>>>
>>>
>>> Angel Pizarro wrote:
>>>
>>>> OK, I don't see where you are getting EnzymCompoundRelation & 
>>>> CompoundClassAttribute from. Our current version of GUS does not 
>>>> have these tables. The SRes.EnzymeClass table is also looking very 
>>>> wacky to me. Propose a nice structure for this and we can put it in 
>>>> the next release of GUS.
>>>>
>>>> Angel
>>>>
>>>> Thomas Otto wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I am uploading some kegg data in the GUS system...
>>>>>
>>>>> So I looked which tables are existing, and which we are needing 
>>>>> i.e. for compound, reactions. Now I am not sure how is the 
>>>>> convention to relate the data.
>>>>>
>>>>> Example:
>>>>> The Enzymes are related to the compounds.
>>>>> (1) In EzymeClassAttribute I write the names of the compound 
>>>>> related to each enzyme. In CompoundClassAttribute I write also all 
>>>>> EC-numbers, related to it.
>>>>> (2) Other possibilty would be to utilize a thrid table 
>>>>> EnzymeCompoundRelation, where I put the primkeys of the relations.
>>>>>
>>>>> (1) would be faster, easier to query, but redundend.
>>>>> (2) Cleaner
>>>>>
>>>>> What are you thinking I should use?
>>>>>
>>>>> Thanks,
>>>>> Thomas
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>> GenToo technologies. Learn everything from fundamentals to system
>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IBM Linux Tutorials
>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>> GenToo technologies. Learn everything from fundamentals to system
>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
>
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> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
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>