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feature_cvterm Empty

sganesh02
I created a test instance of Chado and loaded the features for about 23 genomes from GFF files.
 
I just noticed that the feature tables are being loaded fine but the feature_cvterm table is empty. So I am not able to distinguish the features.
I was able to sucessfully load ontologies.
 
Any hints on where I should start troubleshooting from ?
 
Thanks
Ganesh

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Re: feature_cvterm Empty

Scott Cain
Hi Ganesh,

Did the GFF have ontology annotations in the ninth column?  What did they look like?  Did you get any warning messages while the GFF files were loading?  What loader did you use?

Scott


On Fri, Mar 29, 2013 at 12:34 PM, Ganesh S Moorthy <[hidden email]> wrote:
I created a test instance of Chado and loaded the features for about 23 genomes from GFF files.
 
I just noticed that the feature tables are being loaded fine but the feature_cvterm table is empty. So I am not able to distinguish the features.
I was able to sucessfully load ontologies.
 
Any hints on where I should start troubleshooting from ?
 
Thanks
Ganesh

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Ontario Institute for Cancer Research
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Re: feature_cvterm Empty

sganesh02
what should be the name of the attribute ? ontology_term ? or dbxref ? the GFF file has no ontology_terms. I converted it from a GenBank file, it does have DbXref for some features.
 
Ganesh

From: Scott Cain <[hidden email]>
To: Ganesh S Moorthy <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Sent: Friday, March 29, 2013 12:37 PM
Subject: Re: [Gmod-schema] feature_cvterm Empty

Hi Ganesh,

Did the GFF have ontology annotations in the ninth column?  What did they look like?  Did you get any warning messages while the GFF files were loading?  What loader did you use?

Scott


On Fri, Mar 29, 2013 at 12:34 PM, Ganesh S Moorthy <[hidden email]> wrote:
I created a test instance of Chado and loaded the features for about 23 genomes from GFF files.
 
I just noticed that the feature tables are being loaded fine but the feature_cvterm table is empty. So I am not able to distinguish the features.
I was able to sucessfully load ontologies.
 
Any hints on where I should start troubleshooting from ?
 
Thanks
Ganesh

------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
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Re: feature_cvterm Empty

Scott Cain
Hi Ganesh,

The table feature_cvterm is for linking features to controlled vocabulary or ontology terms.  Something has to provide that link; in GFF, it would be the Ontology_term attribute (the capital "O" is important).  Typically, it would look something like:

  ...;Ontology_term=GO:0012345,GO:0012346;...

Providing Dbxref entries will create entries in the feature_dbxref table.

Scott


On Fri, Mar 29, 2013 at 2:25 PM, Ganesh S Moorthy <[hidden email]> wrote:
what should be the name of the attribute ? ontology_term ? or dbxref ? the GFF file has no ontology_terms. I converted it from a GenBank file, it does have DbXref for some features.
 
Ganesh

From: Scott Cain <[hidden email]>
To: Ganesh S Moorthy <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Sent: Friday, March 29, 2013 12:37 PM
Subject: Re: [Gmod-schema] feature_cvterm Empty

Hi Ganesh,

Did the GFF have ontology annotations in the ninth column?  What did they look like?  Did you get any warning messages while the GFF files were loading?  What loader did you use?

Scott


On Fri, Mar 29, 2013 at 12:34 PM, Ganesh S Moorthy <[hidden email]> wrote:
I created a test instance of Chado and loaded the features for about 23 genomes from GFF files.
 
I just noticed that the feature tables are being loaded fine but the feature_cvterm table is empty. So I am not able to distinguish the features.
I was able to sucessfully load ontologies.
 
Any hints on where I should start troubleshooting from ?
 
Thanks
Ganesh

------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
_______________________________________________
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Own the Future-Intel(R) Level Up Game Demo Contest 2013
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Re: feature_cvterm Empty

sganesh02
Thanks a lot Scott!
 
I think I dont have those in the official annottations in the GenBank file.
 
I think what I was really looking for is where is the fact that feature is "exon" / "cds" / "m rna"/ "gene" stored ?
 
Thanks
Ganesh

From: Scott Cain <[hidden email]>
To: Ganesh S Moorthy <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Sent: Friday, March 29, 2013 2:50 PM
Subject: Re: [Gmod-schema] feature_cvterm Empty

Hi Ganesh,

The table feature_cvterm is for linking features to controlled vocabulary or ontology terms.  Something has to provide that link; in GFF, it would be the Ontology_term attribute (the capital "O" is important).  Typically, it would look something like:

  ...;Ontology_term=GO:0012345,GO:0012346;...

Providing Dbxref entries will create entries in the feature_dbxref table.

Scott


On Fri, Mar 29, 2013 at 2:25 PM, Ganesh S Moorthy <[hidden email]> wrote:
what should be the name of the attribute ? ontology_term ? or dbxref ? the GFF file has no ontology_terms. I converted it from a GenBank file, it does have DbXref for some features.
 
Ganesh

From: Scott Cain <[hidden email]>
To: Ganesh S Moorthy <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Sent: Friday, March 29, 2013 12:37 PM
Subject: Re: [Gmod-schema] feature_cvterm Empty

Hi Ganesh,

Did the GFF have ontology annotations in the ninth column?  What did they look like?  Did you get any warning messages while the GFF files were loading?  What loader did you use?

Scott


On Fri, Mar 29, 2013 at 12:34 PM, Ganesh S Moorthy <[hidden email]> wrote:
I created a test instance of Chado and loaded the features for about 23 genomes from GFF files.
 
I just noticed that the feature tables are being loaded fine but the feature_cvterm table is empty. So I am not able to distinguish the features.
I was able to sucessfully load ontologies.
 
Any hints on where I should start troubleshooting from ?
 
Thanks
Ganesh

------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
_______________________________________________
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
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Re: feature_cvterm Empty

Scott Cain
Oh, that's different.  This is in the feature table itself, via feature.type_id, which is a foreign key back to the cvterm table, and in practice, should be a link to a term in the Sequence Ontology.

Scott


On Fri, Mar 29, 2013 at 3:39 PM, Ganesh S Moorthy <[hidden email]> wrote:
Thanks a lot Scott!
 
I think I dont have those in the official annottations in the GenBank file.
 
I think what I was really looking for is where is the fact that feature is "exon" / "cds" / "m rna"/ "gene" stored ?
 
Thanks
Ganesh

From: Scott Cain <[hidden email]>
To: Ganesh S Moorthy <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Sent: Friday, March 29, 2013 2:50 PM

Subject: Re: [Gmod-schema] feature_cvterm Empty

Hi Ganesh,

The table feature_cvterm is for linking features to controlled vocabulary or ontology terms.  Something has to provide that link; in GFF, it would be the Ontology_term attribute (the capital "O" is important).  Typically, it would look something like:

  ...;Ontology_term=GO:0012345,GO:0012346;...

Providing Dbxref entries will create entries in the feature_dbxref table.

Scott


On Fri, Mar 29, 2013 at 2:25 PM, Ganesh S Moorthy <[hidden email]> wrote:
what should be the name of the attribute ? ontology_term ? or dbxref ? the GFF file has no ontology_terms. I converted it from a GenBank file, it does have DbXref for some features.
 
Ganesh

From: Scott Cain <[hidden email]>
To: Ganesh S Moorthy <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Sent: Friday, March 29, 2013 12:37 PM
Subject: Re: [Gmod-schema] feature_cvterm Empty

Hi Ganesh,

Did the GFF have ontology annotations in the ninth column?  What did they look like?  Did you get any warning messages while the GFF files were loading?  What loader did you use?

Scott


On Fri, Mar 29, 2013 at 12:34 PM, Ganesh S Moorthy <[hidden email]> wrote:
I created a test instance of Chado and loaded the features for about 23 genomes from GFF files.
 
I just noticed that the feature tables are being loaded fine but the feature_cvterm table is empty. So I am not able to distinguish the features.
I was able to sucessfully load ontologies.
 
Any hints on where I should start troubleshooting from ?
 
Thanks
Ganesh

------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
_______________________________________________
Gmod-schema mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-schema




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
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