GRIN into Chado

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GRIN into Chado

Cannon, Ethalinda K [COM S]

Has anyone tried loading GRIN data into Chado? I seem to recall mention of this having been done or planned to be done, but don't remember by whom.


Ethy



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Re: GRIN into Chado

Chris Mungall-5
Hi Ethy,

I believe there are two parts here

  1. Extracting relevant info for GRIN, including mapping their
descriptors onto TO terms
  2. Loading this into Chado

I believe the bulk of the work would be in 1. This is something we have
been looking into in the Planteome project. Pankaj, is this something
we're going to tackle soon? We don't want to duplicate effort here

Once 1 is done, it can pipe the results to 2 in a format like GAF or
Phenopackets (phenopackets.org). There is a GAF loader for Chado, but no
phenopackets one yet. Either way part 2 should be turning the handle.

On 2 Jun 2016, at 11:48, Cannon, Ethalinda K [COM S] wrote:

> Has anyone tried loading GRIN data into Chado? I seem to recall
> mention of this having been done or planned to be done, but don't
> remember by whom.
>
>
> Ethy
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and
> protocols are
> consuming the most bandwidth. Provides multi-vendor support for
> NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports.
> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: GRIN into Chado

Pankaj Jaiswal (OSU)


On 6/2/2016 12:30 PM, Chris Mungall wrote:

> Hi Ethy,
>
> I believe there are two parts here
>
>  1. Extracting relevant info for GRIN, including mapping their
> descriptors onto TO terms
>  2. Loading this into Chado
>
> I believe the bulk of the work would be in 1. This is something we
> have been looking into in the Planteome project. Pankaj, is this
> something we're going to tackle soon? We don't want to duplicate
> effort here
>
Yes. As soon as Plant Disease work is done by Jorrit, he can move on to
mapping GRIN descriptors.

Pankaj

> Once 1 is done, it can pipe the results to 2 in a format like GAF or
> Phenopackets (phenopackets.org). There is a GAF loader for Chado, but
> no phenopackets one yet. Either way part 2 should be turning the handle.
>
> On 2 Jun 2016, at 11:48, Cannon, Ethalinda K [COM S] wrote:
>
>> Has anyone tried loading GRIN data into Chado? I seem to recall
>> mention of this having been done or planned to be done, but don't
>> remember by whom.
>>
>>
>> Ethy
>>
>> ------------------------------------------------------------------------------
>>
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and
>> protocols are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning reports.
>> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema

--
Pankaj Jaiswal, PhD
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: [hidden email]
Web: http://jaiswallab.cgrb.oregonstate.edu
      http://icbo-conference.org


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: GRIN into Chado

Cannon, Ethalinda K [COM S]
Thanks Chris and Pankaj!

I had just arrived at the sinking realization about part 1 below literally seconds before your notes arrived. Not a trivial task, and not one I want to attempt independently of the Planteome project.

Ethy

________________________________________
From: Jaiswal, Pankaj - OSU <[hidden email]>
Sent: Thursday, June 2, 2016 2:39 PM
To: Chris Mungall; Cannon, Ethalinda K [COM S]
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-schema] GRIN into Chado

On 6/2/2016 12:30 PM, Chris Mungall wrote:

> Hi Ethy,
>
> I believe there are two parts here
>
>  1. Extracting relevant info for GRIN, including mapping their
> descriptors onto TO terms
>  2. Loading this into Chado
>
> I believe the bulk of the work would be in 1. This is something we
> have been looking into in the Planteome project. Pankaj, is this
> something we're going to tackle soon? We don't want to duplicate
> effort here
>
Yes. As soon as Plant Disease work is done by Jorrit, he can move on to
mapping GRIN descriptors.

Pankaj

> Once 1 is done, it can pipe the results to 2 in a format like GAF or
> Phenopackets (phenopackets.org). There is a GAF loader for Chado, but
> no phenopackets one yet. Either way part 2 should be turning the handle.
>
> On 2 Jun 2016, at 11:48, Cannon, Ethalinda K [COM S] wrote:
>
>> Has anyone tried loading GRIN data into Chado? I seem to recall
>> mention of this having been done or planned to be done, but don't
>> remember by whom.
>>
>>
>> Ethy
>>
>> ------------------------------------------------------------------------------
>>
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and
>> protocols are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning reports.
>> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema

--
Pankaj Jaiswal, PhD
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: [hidden email]
Web: http://jaiswallab.cgrb.oregonstate.edu
      http://icbo-conference.org

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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