Loading RefSeq/Uniprot into CHADO

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

Loading RefSeq/Uniprot into CHADO

Josep F Abril
First of all, Happy new year,

in order to upload a set of genes from RefSeq, I've been following the
instructions found at:

   http://gmod.org/wiki/Load_RefSeq_Into_Chado

There it is explained how to loaad RefSeq annotations into an organism database.
However, my question is if it is possible to upload ALL the annotation/sequences
on a separate table, not associated to a given organism but to a generic "NCBI"
or "RefSeq" entity. I wonder then if I can request the corresponding information
(i.e. sequence) to the CHADO pg database instead of linking the gene names to an
external URL, like in the "ballon" example below.

   balloon click = <h2>Gene $name</h2>
          <a href='http://www.google.com/search?q=$name'>Search Google</a><br>
          <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed 
term=$name'>Search NCBI</a><br>


Thanks in advance for your help... Best wishes...

---->8---->8---->8---->8---->8---->8---->8---->8---->8----
             Josep Francesc ABRIL FERRANDO, PhD
   COMPUTATIONAL GENOMICS LAB @ GENETICS DEPARTMENT / IBUB
      FACULTAT de BIOLOGIA - UNIVERSITAT de BARCELONA
  Av Diagonal, 645 - 08028 - Barcelona - Catalonia - SPAIN
  Ph: +34 93 4031305 / Fax: +34 93 4034420 / [hidden email]
  **************  http://compgen.bio.ub.es  **************
  *************  http://planarian.bio.ub.es  *************
  ***************  http://europlannet.org  ***************
----8<----8<----8<----8<----8<----8<----8<----8<----8<----

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel
Reply | Threaded
Open this post in threaded view
|

Re: Loading RefSeq/Uniprot into CHADO

Scott Cain
Hi Josep,

I cc'ed your email to the schema (Chado) mailing list; the devel list
can be trimmed off of replies after this.

Can you please describe in a little more detail what your goals are?
Of course, you are free to do anything you want with your database, so
creating a "generic" organism is certainly doable, and I've heard of
people doing that for various reasons.  The issue of display (like in
GBrowse) is really only peripherally related; GBrowse is very flexible
and can do pretty much anything you want as long as you plan for it
ahead of time.

Happy New Year,
Scott


On Mon, Jan 2, 2012 at 11:54 AM, Josep F Abril <[hidden email]> wrote:

> First of all, Happy new year,
>
> in order to upload a set of genes from RefSeq, I've been following the
> instructions found at:
>
>   http://gmod.org/wiki/Load_RefSeq_Into_Chado
>
> There it is explained how to loaad RefSeq annotations into an organism database.
> However, my question is if it is possible to upload ALL the annotation/sequences
> on a separate table, not associated to a given organism but to a generic "NCBI"
> or "RefSeq" entity. I wonder then if I can request the corresponding information
> (i.e. sequence) to the CHADO pg database instead of linking the gene names to an
> external URL, like in the "ballon" example below.
>
>   balloon click = <h2>Gene $name</h2>
>          <a href='http://www.google.com/search?q=$name'>Search Google</a><br>
>          <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed
> term=$name'>Search NCBI</a><br>
>
>
> Thanks in advance for your help... Best wishes...
>
> ---->8---->8---->8---->8---->8---->8---->8---->8---->8----
>             Josep Francesc ABRIL FERRANDO, PhD
>   COMPUTATIONAL GENOMICS LAB @ GENETICS DEPARTMENT / IBUB
>      FACULTAT de BIOLOGIA - UNIVERSITAT de BARCELONA
>  Av Diagonal, 645 - 08028 - Barcelona - Catalonia - SPAIN
>  Ph: +34 93 4031305 / Fax: +34 93 4034420 / [hidden email]
>  **************  http://compgen.bio.ub.es  **************
>  *************  http://planarian.bio.ub.es  *************
>  ***************  http://europlannet.org  ***************
> ----8<----8<----8<----8<----8<----8<----8<----8<----8<----
>
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual
> desktops for less than the cost of PCs and save 60% on VDI infrastructure
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> _______________________________________________
> 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/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel