$ref not showing up in chado database

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$ref not showing up in chado database

sjyap
Hi all,

 I am currently using Chado database and Gbrowse version 2.14. While using
the mouse over feature, the pop up balloon are not able to to display $ref
as show in the image attached. I have tried to upload the gff3 file from the
yeast data to the chado database, the $ref able to show up in the balloon
using gff3 file, but not the chado database. For example "YAL014C is a gene
spanning from xxx..xxx" in chado database and  "YAL014C is a gene spanning
chrI from xxx..xxx" for gff3 flat file.

Anybody facing the similar problem? Appreciate your help!

http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5015889/screenshot.305.jpg 
http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5015889/screenshot.304.jpg 

Best regards,
Soon Joo


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Re: $ref not showing up in chado database

Scott Cain
Hi Soon Joo, 

The best place to ask about this is on the GBrowse mailing list (cc'ed here).

I wonder if the chromsome entries in the SGD GFF3 file have both ID and Name entries in the lines that define them.  While it is not required by the GFF3 spec, the Chado adaptor has a few quirks that make having both necessary.  So for chrI, the line should look something like this:

chrI   .   chromosome   1   512345   .    .    .    Name=chrI;ID=chrI;...

Scott


On Wed, Nov 23, 2011 at 3:24 AM, sjyap <[hidden email]> wrote:
Hi all,

 I am currently using Chado database and Gbrowse version 2.14. While using
the mouse over feature, the pop up balloon are not able to to display $ref
as show in the image attached. I have tried to upload the gff3 file from the
yeast data to the chado database, the $ref able to show up in the balloon
using gff3 file, but not the chado database. For example "YAL014C is a gene
spanning from xxx..xxx" in chado database and  "YAL014C is a gene spanning
chrI from xxx..xxx" for gff3 flat file.

Anybody facing the similar problem? Appreciate your help!

http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5015889/screenshot.305.jpg
http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5015889/screenshot.304.jpg

Best regards,
Soon Joo


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Sent from the gmod-devel mailing list archive at Nabble.com.

------------------------------------------------------------------------------
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contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
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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

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
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Re: $ref not showing up in chado database

sjyap
Hi Scott,

 Thanks for your input. Yes, the gff3 file I used is the demo yeast gff3 located in the databases that came with the gbrowse installer. The gff3 file does contain Name and ID like you mentioned. Like you suggested before, I have installed Bio::DB::Das::Chado to version 0.33, and put in the '- srcfeatureslice 1' in the database stanza like below:


db_adaptor    = Bio::DB::Das::Chado
db_args       =  -dsn dbi:Pg:dbname=chado_genomedb_03;host=localhost;port=5432
                -user postgres
                -srcfeatureslice 1
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       =  -dsn dbi:Pg:dbname=chado_genomedb_03;host=localhost;port=5432
                -user postgres
                -srcfeatureslice 1
search options = default +autocomplete

It finally works, the mouse over manage to show the $ref, and without showing other genes from other chromosomes. However, when I try to search the database, I can only search the keyword limited to starting of the keyword, but not middle of the kBesaeyword, for example:

endosomal snare related to mammalian syntaxin 8

It will return with a result if I search for endosomal, but if I search for syntaxin there will be no result. I don't know what is the error why I can't search the full text input?

Best regards,
Soon Joo


On Tue, Nov 29, 2011 at 3:23 AM, Scott Cain <[hidden email]> wrote:
Hi Soon Joo, 

The best place to ask about this is on the GBrowse mailing list (cc'ed here).

I wonder if the chromsome entries in the SGD GFF3 file have both ID and Name entries in the lines that define them.  While it is not required by the GFF3 spec, the Chado adaptor has a few quirks that make having both necessary.  So for chrI, the line should look something like this:

chrI   .   chromosome   1   512345   .    .    .    Name=chrI;ID=chrI;...

Scott


On Wed, Nov 23, 2011 at 3:24 AM, sjyap <[hidden email]> wrote:
Hi all,

 I am currently using Chado database and Gbrowse version 2.14. While using
the mouse over feature, the pop up balloon are not able to to display $ref
as show in the image attached. I have tried to upload the gff3 file from the
yeast data to the chado database, the $ref able to show up in the balloon
using gff3 file, but not the chado database. For example "YAL014C is a gene
spanning from xxx..xxx" in chado database and  "YAL014C is a gene spanning
chrI from xxx..xxx" for gff3 flat file.

Anybody facing the similar problem? Appreciate your help!

http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5015889/screenshot.305.jpg
http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5015889/screenshot.304.jpg

Best regards,
Soon Joo


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View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/ref-not-showing-up-in-chado-database-tp5015889p5015889.html
Sent from the gmod-devel mailing list archive at Nabble.com.

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel



--
------------------------------------------------------------------------
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


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel