Re: storing mutants in Chado

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: storing mutants in Chado

Stephen Ficklin-2
HI All,

I'm responding to a question posed by Andrew Block on the Tripal mailing list and I thought I'd CC the gmod-schema list for input from others.  His question is: 

"As I stated before, we will have many mutants for individual species.  Looking at several websites that use GMOD, there does not seem to be a way to have different mutants just version of the same species.  How would I set up Tripal/Chado to allow for mutants? "

My recommendation would be to store the species that these mutants belong to in the 'organism' table and then each mutant stored in the 'stock' table. The foreign key constraint (stock.organism_id) links the mutant back to the organism.  Genotypes and Phenotypes are related to the  mutant in the following way:  a record for each mutant is added to the the nd_experiment_stock table, with a corresponding foreign key relationship to the nd_experiment_table.  Using the common nd_experiment_id value he can then link in phenotypes and genotypes using the nd_experiment_phenotype and nd_experiment_genotype tables.  Any features associated with the genotypes are associated using the feature_genotype table.

Thanks,
Stephen

On 2/13/2013 4:00 PM, Block,Andrew wrote:
Hello Trupal,

I have installed Tripal and am starting to set up our database.  I am creating a website for RNA dependent RNA polymerases (RdRp) with many different mutants for different viruses species.  The goal of the database is to analysis structure, sequences, & molecular data and keep track of storage through a webpage.

When I run the "Load OBO Gene Ontology" using cron I get an error.  I was able to instal other OBOs after this one, but for some reason I can not install this OBO.  I went into the obo_loader.php file to change line 564, but could not see how to change the file.  How would I fix this problem?

The error code is: Calling: tripal_cv_load_obo_v1_2_id(4, 15)
Downloading URL http://www.geneontology.org/ontology/gene_ontology.obo, saving to /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx
Opening File /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx

Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to allocate 71 bytes) in /Users/andrew/Sites/drupal/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 564

I also keep getting: Invalid argument supplied for foreach() in /Users/andrew/Sites/drupal/includes/form.inc on line 1217.  Does anybody know about this error?

As I stated before, we will have many mutants for individual species.  Looking at several websites that use GMOD, there does not seem to be a way to have different mutants just version of the same species.  Ho would I set up Tripal/Chado to allow for mutants?  How would I remove the other species that are found in Tripal?

Thank you,

Andrew Block

Research Associate
-------------------------------------------------------
Colorado State University
Dept. of Biochemistry & Molecular Biology
Molecular and Radiological Biosciences 139
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
-------------------------------------------------------
(970) 491-0271    Lab
-------------------------------------------------------



------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013 
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: storing mutants in Chado

Naama Menda-3
Hi Andrew ,

Stephen's reply is exactly how we store Solanaceae mutants at SGN . 

There are a few use cases with the Natural Diversity module at the gmod wiki
http://gmod.org/wiki/Chado_Natural_Diversity_Module

The SGN use case is pretty similar to the way mutants are handled.

-Naama

Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
[hidden email]

On Wed, Feb 13, 2013 at 4:58 PM, Stephen Ficklin <[hidden email]> wrote:
HI All,

I'm responding to a question posed by Andrew Block on the Tripal mailing list and I thought I'd CC the gmod-schema list for input from others.  His question is: 

"As I stated before, we will have many mutants for individual species.  Looking at several websites that use GMOD, there does not seem to be a way to have different mutants just version of the same species.  How would I set up Tripal/Chado to allow for mutants? "

My recommendation would be to store the species that these mutants belong to in the 'organism' table and then each mutant stored in the 'stock' table. The foreign key constraint (stock.organism_id) links the mutant back to the organism.  Genotypes and Phenotypes are related to the  mutant in the following way:  a record for each mutant is added to the the nd_experiment_stock table, with a corresponding foreign key relationship to the nd_experiment_table.  Using the common nd_experiment_id value he can then link in phenotypes and genotypes using the nd_experiment_phenotype and nd_experiment_genotype tables.  Any features associated with the genotypes are associated using the feature_genotype table.

Thanks,
Stephen

On 2/13/2013 4:00 PM, Block,Andrew wrote:
Hello Trupal,

I have installed Tripal and am starting to set up our database.  I am creating a website for RNA dependent RNA polymerases (RdRp) with many different mutants for different viruses species.  The goal of the database is to analysis structure, sequences, & molecular data and keep track of storage through a webpage.

When I run the "Load OBO Gene Ontology" using cron I get an error.  I was able to instal other OBOs after this one, but for some reason I can not install this OBO.  I went into the obo_loader.php file to change line 564, but could not see how to change the file.  How would I fix this problem?

The error code is: Calling: tripal_cv_load_obo_v1_2_id(4, 15)
Downloading URL http://www.geneontology.org/ontology/gene_ontology.obo, saving to /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx
Opening File /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx

Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to allocate 71 bytes) in /Users/andrew/Sites/drupal/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 564

I also keep getting: Invalid argument supplied for foreach() in /Users/andrew/Sites/drupal/includes/form.inc on line 1217.  Does anybody know about this error?

As I stated before, we will have many mutants for individual species.  Looking at several websites that use GMOD, there does not seem to be a way to have different mutants just version of the same species.  Ho would I set up Tripal/Chado to allow for mutants?  How would I remove the other species that are found in Tripal?

Thank you,

Andrew Block

Research Associate
-------------------------------------------------------
Colorado State University
Dept. of Biochemistry & Molecular Biology
Molecular and Radiological Biosciences 139
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
-------------------------------------------------------
<a href="tel:%28970%29%20491-0271" value="+19704910271" target="_blank">(970) 491-0271    Lab
-------------------------------------------------------



------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013 
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: storing mutants in Chado

Sook Jung
Hi Andrew,
Just to add a few more comments.
If a 'stock', like a cultivar, from which the mutant was generated is known, we use stock_relationship table to store the relationship. Also wanted to clarify that nd_experiment is intended to represent each individual assay involving a stock. Below is the statement you can find in the wiki page.
Sook
------------------------------------
http://gmod.org/wiki/Chado_Natural_Diversity_Module
"This is the core table for the natural diversity module, representing each individual assay that is undertaken (nb this is usually *not* an entire experiment). Each nd_experiment should give rise to a single genotype or phenotype and be described via 1 (or more) protocols. Collections of assays that relate to each other should be linked to the same record in the project table.
Experiment.type is a cvterm that will define which records are expected for other tables. Any CV may be used but it was designed with terms such as: [phenotype_assay, genotype_assay, field_collection, cross_experiment] in mind."
-----------
On Thu, Feb 14, 2013 at 10:32 AM, Naama Menda <[hidden email]> wrote:
Hi Andrew ,

Stephen's reply is exactly how we store Solanaceae mutants at SGN . 

There are a few use cases with the Natural Diversity module at the gmod wiki
http://gmod.org/wiki/Chado_Natural_Diversity_Module

The SGN use case is pretty similar to the way mutants are handled.

-Naama

Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

<a href="tel:%28607%29%20254%203569" value="+16072543569" target="_blank">(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
[hidden email]

On Wed, Feb 13, 2013 at 4:58 PM, Stephen Ficklin <[hidden email]> wrote:
HI All,

I'm responding to a question posed by Andrew Block on the Tripal mailing list and I thought I'd CC the gmod-schema list for input from others.  His question is: 

"As I stated before, we will have many mutants for individual species.  Looking at several websites that use GMOD, there does not seem to be a way to have different mutants just version of the same species.  How would I set up Tripal/Chado to allow for mutants? "

My recommendation would be to store the species that these mutants belong to in the 'organism' table and then each mutant stored in the 'stock' table. The foreign key constraint (stock.organism_id) links the mutant back to the organism.  Genotypes and Phenotypes are related to the  mutant in the following way:  a record for each mutant is added to the the nd_experiment_stock table, with a corresponding foreign key relationship to the nd_experiment_table.  Using the common nd_experiment_id value he can then link in phenotypes and genotypes using the nd_experiment_phenotype and nd_experiment_genotype tables.  Any features associated with the genotypes are associated using the feature_genotype table.

Thanks,
Stephen

On 2/13/2013 4:00 PM, Block,Andrew wrote:
Hello Trupal,

I have installed Tripal and am starting to set up our database.  I am creating a website for RNA dependent RNA polymerases (RdRp) with many different mutants for different viruses species.  The goal of the database is to analysis structure, sequences, & molecular data and keep track of storage through a webpage.

When I run the "Load OBO Gene Ontology" using cron I get an error.  I was able to instal other OBOs after this one, but for some reason I can not install this OBO.  I went into the obo_loader.php file to change line 564, but could not see how to change the file.  How would I fix this problem?

The error code is: Calling: tripal_cv_load_obo_v1_2_id(4, 15)
Downloading URL http://www.geneontology.org/ontology/gene_ontology.obo, saving to /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx
Opening File /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx

Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to allocate 71 bytes) in /Users/andrew/Sites/drupal/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 564

I also keep getting: Invalid argument supplied for foreach() in /Users/andrew/Sites/drupal/includes/form.inc on line 1217.  Does anybody know about this error?

As I stated before, we will have many mutants for individual species.  Looking at several websites that use GMOD, there does not seem to be a way to have different mutants just version of the same species.  Ho would I set up Tripal/Chado to allow for mutants?  How would I remove the other species that are found in Tripal?

Thank you,

Andrew Block

Research Associate
-------------------------------------------------------
Colorado State University
Dept. of Biochemistry & Molecular Biology
Molecular and Radiological Biosciences 139
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
-------------------------------------------------------
<a href="tel:%28970%29%20491-0271" value="+19704910271" target="_blank">(970) 491-0271    Lab
-------------------------------------------------------



------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013 
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema