Chado: Oracle implemetaion

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Chado: Oracle implemetaion

Rachana Jain
Hello,
 
I am getting started with implementing chado schema (sequence, cv, organism modules) on oracle. I would appreciate if someone could let me know:
 
1) Oracle implementation of chado. I could do this by converting postgresql DDL to Oracle but I wanted to keep this my last option.
 
2) How to install SO on chado instance on Oracle.
 
Any help is much appreciated.
Regards
-Rachana
 


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Re: Chado: Oracle implemetaion

Joshua Orvis
Rachana -

Oracle has been used for Chado by a few groups, and a notable user I think of first is Eric Just.  I'll give him the opportunity to respond here, but I have the DDLs for representing several of the Chado modules in Oracle from his group that we also used for a short while.

Joshua



On Mon, Sep 27, 2010 at 5:41 PM, Rachana Jain <[hidden email]> wrote:
Hello,
 
I am getting started with implementing chado schema (sequence, cv, organism modules) on oracle. I would appreciate if someone could let me know:
 
1) Oracle implementation of chado. I could do this by converting postgresql DDL to Oracle but I wanted to keep this my last option.
 
2) How to install SO on chado instance on Oracle.
 
Any help is much appreciated.
Regards
-Rachana
 


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Re: Chado: Oracle implemetaion

Daniel Quest
Hey all,

I also went through the same process of converting the Postgres DDLs to Oracle for the Oak Ridge System this last summer.  We did make some minor modifications to some of the modules to get it to work better for us, but I am also happy to share what I have if people are interested.

-Daniel

On Mon, Sep 27, 2010 at 7:52 PM, Joshua Orvis <[hidden email]> wrote:
Rachana -

Oracle has been used for Chado by a few groups, and a notable user I think of first is Eric Just.  I'll give him the opportunity to respond here, but I have the DDLs for representing several of the Chado modules in Oracle from his group that we also used for a short while.

Joshua



On Mon, Sep 27, 2010 at 5:41 PM, Rachana Jain <[hidden email]> wrote:
Hello,
 
I am getting started with implementing chado schema (sequence, cv, organism modules) on oracle. I would appreciate if someone could let me know:
 
1) Oracle implementation of chado. I could do this by converting postgresql DDL to Oracle but I wanted to keep this my last option.
 
2) How to install SO on chado instance on Oracle.
 
Any help is much appreciated.
Regards
-Rachana
 


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Re: Chado: Oracle implemetaion

Joshua Orvis
In reply to this post by Joshua Orvis
Rachana -

There were no obvious major reasons to not use Oracle.  In terms of the GMOD community at large, the primary or "official" database engine seems to be PostgreSQL, so you'll perhaps get more community support using that.  Especially if you want to use other GMOD tools, things tend to be written first for that and can then be ported by others for other database engines.  MySQL is probably a popular runner-up in terms of community support.

For us at IGS, it was a mixture of this as well as a few other factors that moved us away from Oracle.  Oracle is recognized as being massively scalable, but PostgreSQL and MySQL have also made a lot of inroads there and have that "just works" usability that Oracle lacks.  Developers don't have to worry about maintaining tons of environmental settings, local client availability, etc. with other vendors that you do with Oracle.  Also, the others are free and Oracle requires an expensive license.  This may be skipped by those at a University or somewhere with a site license, but if you are at such an institution and write your software to expect Oracle you limit that software's use to other groups who also already have a license.

For us there weren't many technical reasons to move away from Oracle other than the environmental and client issues.  It was more the community compatibility and open nature of PostgreSQL and MySQL that made us switch.


Joshua

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

Hi Joshua,

Thanks for your email. May I ask why did you use oracle only for a short while? Were there any specific issues you remember in using oracle with chado?

Thanks
-Rachana

On Mon, Sep 27, 2010 at 6:52 PM, Joshua Orvis <[hidden email]> wrote:
Rachana -

Oracle has been used for Chado by a few groups, and a notable user I think of first is Eric Just.  I'll give him the opportunity to respond here, but I have the DDLs for representing several of the Chado modules in Oracle from his group that we also used for a short while.

Joshua



On Mon, Sep 27, 2010 at 5:41 PM, Rachana Jain <[hidden email]> wrote:
Hello,
 
I am getting started with implementing chado schema (sequence, cv, organism modules) on oracle. I would appreciate if someone could let me know:
 
1) Oracle implementation of chado. I could do this by converting postgresql DDL to Oracle but I wanted to keep this my last option.
 
2) How to install SO on chado instance on Oracle.
 
Any help is much appreciated.
Regards
-Rachana
 


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Re: Chado: Oracle implemetaion

Eric Just
In reply to this post by Joshua Orvis
Hi Rachana,

We at dictyBase have been using Chado in Oracle for about 5 years.  To generate the Oracle DDL, we used SQL Translator on the original PostgreSQL DDL.   There are a couple of GMOD scripts that load ontologies, so loading SO should not be a problem.  We chose Oracle because we had a site license and had other portions of our code accessing a legacy Oracle schema that we wanted to run in parallel with Chado. 

If possible, I recommend using Postgres because, like Josh said, the community and support are better.   That said,  if you choose Oracle, we are glad to share any of our code and lessons learned.

I am a little rusty in the details as I've moved to another project, but Siddhartha Basu who currently works at dictyBase on our Oracle Chado instance can provide more current thoughts/opinions on that.

Good luck with whatever you use.  Chado and the associated tools are great.

Eric

On Sep 27, 2010, at 6:52 PM, Joshua Orvis <[hidden email]> wrote:

Rachana -

Oracle has been used for Chado by a few groups, and a notable user I think of first is Eric Just.  I'll give him the opportunity to respond here, but I have the DDLs for representing several of the Chado modules in Oracle from his group that we also used for a short while.

Joshua



On Mon, Sep 27, 2010 at 5:41 PM, Rachana Jain <[hidden email]> wrote:
Hello,
 
I am getting started with implementing chado schema (sequence, cv, organism modules) on oracle. I would appreciate if someone could let me know:
 
1) Oracle implementation of chado. I could do this by converting postgresql DDL to Oracle but I wanted to keep this my last option.
 
2) How to install SO on chado instance on Oracle.
 
Any help is much appreciated.
Regards
-Rachana
 


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Re: Chado: Oracle implemetaion

Siddhartha Basu

Following up on eric,  use of SQL-Translator is strongly recommened.
Over the years,  perl's cross-rdbms tool support got excellent and so it
now almost covers almost most of the corners for doing the conversion. I
have used it with combination of
Bio-Chado-Schema(http://search.cpan.org/dist/Bio-Chado-Schema/) to
autogenerate a current version of cross database chado schema on the fly
for automated unit testing.
So,  to get started, i would suggest to get a working version of core database schema(table
defintions,  constraints,  indexes,  datatypes,  forign keys). Then try
to layer the views and database specific functions separtely if needed.
Here are few oracle specific issues that you might encounter( a lot of which
were being fine tuned by Eric) ....

* synonym table is not portable and cannot be used directly. It is a reserved keyword for
  oracle. The SQL-Translator based conversion will create '_synonym' for
  you. Along the same line the *comment* column in organism table will be '_comment' in
  oracle.
* You are going to encounter quite a handful of CLOB field(featureprop.value for example) in oracle for
  chado. Read the oracle guideline for searching/indexing CLOB field to tune your
  SQL query. At least,  you have to use the LIKE operator in the WHERE
  clause for those field or use Oracle text for added search
  functionallity.
* By default, oracle search with LIKE operator is case sensitive. For
  insensitive search follow the guideline here ...
  http://www.dba-oracle.com/t_oracle10g_release_2_case_insensitive_searches.htm
        At dictyBase,  we employ the 'query transformation' technique (using
  UPPER in left hand side expression) along with an extra function based index
  (to avoid a complete table scan,  for example in feature.name).

Hope this helps,  would be happy to share any code or ideas.

thanks,
-siddhartha


On Tue, 28 Sep 2010, Eric Just wrote:

>    Hi Rachana,
>    We at dictyBase have been using Chado in Oracle for about 5 years.  To
>    generate the Oracle DDL, we used SQL Translator on the original PostgreSQL
>    DDL.   There are a couple of GMOD scripts that load ontologies, so loading
>    SO should not be a problem.  We chose Oracle because we had a site license
>    and had other portions of our code accessing a legacy Oracle schema that
>    we wanted to run in parallel with Chado.
>    If possible, I recommend using Postgres because, like Josh said, the
>    community and support are better.   That said,  if you choose Oracle, we
>    are glad to share any of our code and lessons learned.
>    I am a little rusty in the details as I've moved to another project, but
>    Siddhartha Basu who currently works at dictyBase on our Oracle Chado
>    instance can provide more current thoughts/opinions on that.
>    Good luck with whatever you use.  Chado and the associated tools are
>    great.
>    Eric
>    On Sep 27, 2010, at 6:52 PM, Joshua Orvis <[hidden email]> wrote:
>
>      Rachana -
>
>      Oracle has been used for Chado by a few groups, and a notable user I
>      think of first is Eric Just.  I'll give him the opportunity to respond
>      here, but I have the DDLs for representing several of the Chado modules
>      in Oracle from his group that we also used for a short while.
>
>      Joshua
>
>      On Mon, Sep 27, 2010 at 5:41 PM, Rachana Jain <[hidden email]>
>      wrote:
>
>        Hello,                                                                
>                                                                              
>        I am getting started with implementing chado schema (sequence, cv,    
>        organism modules) on oracle. I would appreciate if someone could let  
>        me know:                                                              
>                                                                              
>        1) Oracle implementation of chado. I could do this by converting      
>        postgresql DDL to Oracle but I wanted to keep this my last option.    
>                                                                              
>        2) How to install SO on chado instance on Oracle.                      
>                                                                              
>        Any help is much appreciated.                                          
>        Regards                                                                
>        -Rachana                                                              
>        [hidden email]                                                    
>                                                                              
>
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>        and start using them to simplify application deployment and
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Re: Chado: Oracle implemetaion

Rachana Jain
In reply to this post by Rachana Jain
Hi Siddhartha and Eric,

Thanks a lot for your detailed replies. We have to stick with oracle due to organization policies. Neverthless, I now have a decently working version of the chado schema (sequence and cv modules). I used SwissSQL to convert the DDL to oracle DDL to generate a quick prototype version of the modules we needed.

I am now trying to input the sequence ontology data in the cv module. Could you please direct me to the scripts I could use for that?

I appreciate your help.
-Rachana

--- On Wed, 9/29/10, Siddhartha Basu <[hidden email]> wrote:

From: Siddhartha Basu <[hidden email]>
Subject: [Gmod-schema] Re: Chado: Oracle implemetaion
To: [hidden email]
Date: Wednesday, September 29, 2010, 7:49 AM


Following up on eric,  use of SQL-Translator is strongly recommened.
Over the years,  perl's cross-rdbms tool support got excellent and so it
now almost covers almost most of the corners for doing the conversion. I
have used it with combination of
Bio-Chado-Schema(http://search.cpan.org/dist/Bio-Chado-Schema/) to
autogenerate a current version of cross database chado schema on the fly
for automated unit testing.
So,  to get started, i would suggest to get a working version of core database schema(table
defintions,  constraints,  indexes,  datatypes,  forign keys). Then try
to layer the views and database specific functions separtely if needed.
Here are few oracle specific issues that you might encounter( a lot of which
were being fine tuned by Eric) ....

* synonym table is not portable and cannot be used directly. It is a reserved keyword for
  oracle. The SQL-Translator based conversion will create '_synonym' for
  you. Along the same line the *comment* column in organism table will be '_comment' in
  oracle.
* You are going to encounter quite a handful of CLOB field(featureprop.value for example) in oracle for
  chado. Read the oracle guideline for searching/indexing CLOB field to tune your
  SQL query. At least,  you have to use the LIKE operator in the WHERE
  clause for those field or use Oracle text for added search
  functionallity.
* By default, oracle search with LIKE operator is case sensitive. For
  insensitive search follow the guideline here ...
  http://www.dba-oracle.com/t_oracle10g_release_2_case_insensitive_searches.htm
    At dictyBase,  we employ the 'query transformation' technique (using
  UPPER in left hand side expression) along with an extra function based index
  (to avoid a complete table scan,  for example in feature.name).

Hope this helps,  would be happy to share any code or ideas.

thanks,
-siddhartha


On Tue, 28 Sep 2010, Eric Just wrote:

>    Hi Rachana,
>    We at dictyBase have been using Chado in Oracle for about 5 years.  To
>    generate the Oracle DDL, we used SQL Translator on the original PostgreSQL
>    DDL.   There are a couple of GMOD scripts that load ontologies, so loading
>    SO should not be a problem.  We chose Oracle because we had a site license
>    and had other portions of our code accessing a legacy Oracle schema that
>    we wanted to run in parallel with Chado.
>    If possible, I recommend using Postgres because, like Josh said, the
>    community and support are better.   That said,  if you choose Oracle, we
>    are glad to share any of our code and lessons learned.
>    I am a little rusty in the details as I've moved to another project, but
>    Siddhartha Basu who currently works at dictyBase on our Oracle Chado
>    instance can provide more current thoughts/opinions on that.
>    Good luck with whatever you use.  Chado and the associated tools are
>    great.
>    Eric
>    On Sep 27, 2010, at 6:52 PM, Joshua Orvis <[hidden email]> wrote:
>
>      Rachana -
>
>      Oracle has been used for Chado by a few groups, and a notable user I
>      think of first is Eric Just.  I'll give him the opportunity to respond
>      here, but I have the DDLs for representing several of the Chado modules
>      in Oracle from his group that we also used for a short while.
>
>      Joshua
>
>      On Mon, Sep 27, 2010 at 5:41 PM, Rachana Jain <[hidden email]>
>      wrote:
>
>        Hello,                                                                 
>                                                                               
>        I am getting started with implementing chado schema (sequence, cv,     
>        organism modules) on oracle. I would appreciate if someone could let   
>        me know:                                                               
>                                                                               
>        1) Oracle implementation of chado. I could do this by converting       
>        postgresql DDL to Oracle but I wanted to keep this my last option.     
>                                                                               
>        2) How to install SO on chado instance on Oracle.                     
>                                                                               
>        Any help is much appreciated.                                         
>        Regards                                                               
>        -Rachana                                                               
>        [hidden email]                                                     
>                                                                               
>
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Re: Chado: Oracle implemetaion

Siddhartha Basu
Hi,
I would recommend to start with ....
https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk/chado/bin/cxgn/gmod_load_cvterms.pl

You need to install Bio::Chado::Schema, it also comes with update
option. Send feedback if you face any problem with that.

thanks,
-siddhartha



On Mon, 04 Oct 2010, Rachana Jain wrote:

> Hi Siddhartha and Eric,                                                          
>                                                                                  
> Thanks a lot for your detailed replies. We have to stick with oracle due to      
> organization policies. Neverthless, I now have a decently working version of the
> chado schema (sequence and cv modules). I used SwissSQL to convert the DDL to    
> oracle DDL to generate a quick prototype version of the modules we needed.      
>                                                                                  
> I am now trying to input the sequence ontology data in the cv module. Could you  
> please direct me to the scripts I could use for that?                            
>                                                                                  
> I appreciate your help.                                                          
> -Rachana                                                                        
>                                                                                  
> --- On Wed, 9/29/10, Siddhartha Basu <[hidden email]> wrote:                  
>                                                                                  
>   From: Siddhartha Basu <[hidden email]>                                      
>   Subject: [Gmod-schema] Re: Chado: Oracle implemetaion                          
>   To: [hidden email]                                          
>   Date: Wednesday, September 29, 2010, 7:49 AM                                  
>                                                                                  
>   Following up on eric,  use of SQL-Translator is strongly recommened.          
>   Over the years,  perl's cross-rdbms tool support got excellent and so it      
>   now almost covers almost most of the corners for doing the conversion. I      
>   have used it with combination of                                              
>   Bio-Chado-Schema(http://search.cpan.org/dist/Bio-Chado-Schema/) to            
>   autogenerate a current version of cross database chado schema on the fly      
>   for automated unit testing.                                                    
>   So,  to get started, i would suggest to get a working version of core database
>   schema(table                                                                  
>   defintions,  constraints,  indexes,  datatypes,  forign keys). Then try        
>   to layer the views and database specific functions separtely if needed.        
>   Here are few oracle specific issues that you might encounter( a lot of which  
>   were being fine tuned by Eric) ....                                            
>                                                                                  
>   * synonym table is not portable and cannot be used directly. It is a reserved  
>   keyword for                                                                    
>     oracle. The SQL-Translator based conversion will create '_synonym' for      
>     you. Along the same line the *comment* column in organism table will be      
>   '_comment' in                                                                  
>     oracle.                                                                      
>   * You are going to encounter quite a handful of CLOB field(featureprop.value  
>   for example) in oracle for                                                    
>     chado. Read the oracle guideline for searching/indexing CLOB field to tune  
>   your                                                                          
>     SQL query. At least,  you have to use the LIKE operator in the WHERE        
>     clause for those field or use Oracle text for added search                  
>     functionallity.                                                              
>   * By default, oracle search with LIKE operator is case sensitive. For          
>     insensitive search follow the guideline here ...                            
>                                                                                  
>   http://www.dba-oracle.com/t_oracle10g_release_2_case_insensitive_searches.htm 
>       At dictyBase,  we employ the 'query transformation' technique (using      
>     UPPER in left hand side expression) along with an extra function based index
>     (to avoid a complete table scan,  for example in feature.name).              
>                                                                                  
>   Hope this helps,  would be happy to share any code or ideas.                  
>                                                                                  
>   thanks,                                                                        
>   -siddhartha                                                                    
>                                                                                  
>   On Tue, 28 Sep 2010, Eric Just wrote:                                          
>                                                                                  
> >    Hi Rachana,                                                              
> >    We at dictyBase have been using Chado in Oracle for about 5 years.  To    
> >    generate the Oracle DDL, we used SQL Translator on the original          
>   PostgreSQL                                                                    
> >    DDL.   There are a couple of GMOD scripts that load ontologies, so        
>   loading                                                                        
> >    SO should not be a problem.  We chose Oracle because we had a site        
>   license                                                                        
> >    and had other portions of our code accessing a legacy Oracle schema that  
> >    we wanted to run in parallel with Chado.                                  
> >    If possible, I recommend using Postgres because, like Josh said, the      
> >    community and support are better.   That said,  if you choose Oracle, we  
> >    are glad to share any of our code and lessons learned.                    
> >    I am a little rusty in the details as I've moved to another project, but  
> >    Siddhartha Basu who currently works at dictyBase on our Oracle Chado      
> >    instance can provide more current thoughts/opinions on that.              
> >    Good luck with whatever you use.  Chado and the associated tools are      
> >    great.                                                                    
> >    Eric                                                                      
> >    On Sep 27, 2010, at 6:52 PM, Joshua Orvis <[hidden email]> wrote:      
> >                                                                              
> >      Rachana -                                                              
> >                                                                              
> >      Oracle has been used for Chado by a few groups, and a notable user I    
> >      think of first is Eric Just.  I'll give him the opportunity to respond  
> >      here, but I have the DDLs for representing several of the Chado modules
> >      in Oracle from his group that we also used for a short while.          
> >                                                                              
> >      Joshua                                                                  
> >                                                                              
> >      On Mon, Sep 27, 2010 at 5:41 PM, Rachana Jain <[hidden email]>      
> >      wrote:                                                                  
> >                                                                              
> >        Hello,                                                                
>                                                                                  
> >                                                                              
>                                                                                  
> >        I am getting started with implementing chado schema (sequence, cv,    
>                                                                                  
> >        organism modules) on oracle. I would appreciate if someone could      
>   let                                                                            
> >        me know:                                                              
>                                                                                  
> >                                                                              
>                                                                                  
> >        1) Oracle implementation of chado. I could do this by converting      
>                                                                                  
> >        postgresql DDL to Oracle but I wanted to keep this my last option.    
>                                                                                  
> >                                                                              
>                                                                                  
> >        2) How to install SO on chado instance on Oracle.                    
>                                                                                  
> >                                                                              
>                                                                                  
> >        Any help is much appreciated.                                        
>                                                                                  
> >        Regards                                                              
>                                                                                  
> >        -Rachana                                                              
>                                                                                  
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> >      and start using them to simplify application deployment and            
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> > Start uncovering the many advantages of virtual appliances                  
> > and start using them to simplify application deployment and                  
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>   and start using them to simplify application deployment and                    
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