Meta data from evidence tracks

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

Meta data from evidence tracks

Marc Höppner-3
Hi,

I think my first attempt at sending this ended up in data nirvana… next try then:

Question/Issue 1:
-----------------------
I noticed that when creating transcripts from evidence, that all meta data (like ‘description, dbxref) are lost. This is a bit of a problem, since my workflow/rationale looks like this:

- create annotation with maker
- functionally annotate maker annotation
- load as track into WebApollo
- Manual verify transcript structures/meta data and add to user-curated track (changing the models significantly would of course require the curator to remove the meta data)
- Save curated annotations to Chado DB
- Load curated annotations to Jbrowse portal from Chado

So I hadn’t intended to ever take the annotations out of the database again - but if the meta data is always lost in this processing chain, I would basically have to dump out the WebApollo annotation, functionally annotate it and then load it into JBrowse as a flat file. Which to me defeats the purpose a little bit of being able to store WebApollo transcript models to chado and so on (in my use case anyway).

Is there any solution to this?

Question/Issue 2:
———————————

When following the existing tutorials on how to load data into WebApollo (like mRNAs), the gene-level feature is only ever created when one or more transcripts are added to the user track. Does that mean that I can’t import gene-level information at all (this sort of related to the issue above, i.e. loosing meta data that I have created prior to importing into WebApollo or when moving it to the user-curated track)?

I am guessing this is a quite difficult from a technical point of view?


Regards,

Marc
Reply | Threaded
Open this post in threaded view
|

Re: Meta data from evidence tracks

nathandunn

> On Oct 22, 2014, at 11:19 PM, Marc Höppner <[hidden email]> wrote:
>
> Hi,
>
> I think my first attempt at sending this ended up in data nirvana… next try then:
>
> Question/Issue 1:
> -----------------------
> I noticed that when creating transcripts from evidence, that all meta data (like ‘description, dbxref) are lost. This is a bit of a problem, since my workflow/rationale looks like this:
>
> - create annotation with maker
> - functionally annotate maker annotation
> - load as track into WebApollo
> - Manual verify transcript structures/meta data and add to user-curated track (changing the models significantly would of course require the curator to remove the meta data)
> - Save curated annotations to Chado DB
> - Load curated annotations to Jbrowse portal from Chado
>
> So I hadn’t intended to ever take the annotations out of the database again - but if the meta data is always lost in this processing chain, I would basically have to dump out the WebApollo annotation, functionally annotate it and then load it into JBrowse as a flat file. Which to me defeats the purpose a little bit of being able to store WebApollo transcript models to chado and so on (in my use case anyway).
>
> Is there any solution to this?

This needs to be fixed with the new release (in my opinion).   I would like for the GFF3 and Chado exporters to do a round-trip export.   I’m going to open a bug for this and assign it to the new release.  

https://github.com/GMOD/Apollo/issues/52

I want to discuss this internally, as I don’t necessarily thing that this is trivial and we are in the process of rewriting how we interact with Chado.  

> Question/Issue 2:
> ———————————
>
> When following the existing tutorials on how to load data into WebApollo (like mRNAs), the gene-level feature is only ever created when one or more transcripts are added to the user track. Does that mean that I can’t import gene-level information at all (this sort of related to the issue above, i.e. loosing meta data that I have created prior to importing into WebApollo or when moving it to the user-curated track)?
>
> I am guessing this is a quite difficult from a technical point of view?

Can you be more specific as to how you are loading the data (from GFF3 files?)?    I think that you should be able to import gene-level information.  

Nathan

>
> Regards,
>
> Marc


Reply | Threaded
Open this post in threaded view
|

Re: Meta data from evidence tracks

Suzanna Lewis-3
Can we add this to the topic items for this Thursday's call.

On Thu, Oct 23, 2014 at 7:13 PM, Nathan Dunn <[hidden email]> wrote:

> On Oct 22, 2014, at 11:19 PM, Marc Höppner <[hidden email]> wrote:
>
> Hi,
>
> I think my first attempt at sending this ended up in data nirvana… next try then:
>
> Question/Issue 1:
> -----------------------
> I noticed that when creating transcripts from evidence, that all meta data (like ‘description, dbxref) are lost. This is a bit of a problem, since my workflow/rationale looks like this:
>
> - create annotation with maker
> - functionally annotate maker annotation
> - load as track into WebApollo
> - Manual verify transcript structures/meta data and add to user-curated track (changing the models significantly would of course require the curator to remove the meta data)
> - Save curated annotations to Chado DB
> - Load curated annotations to Jbrowse portal from Chado
>
> So I hadn’t intended to ever take the annotations out of the database again - but if the meta data is always lost in this processing chain, I would basically have to dump out the WebApollo annotation, functionally annotate it and then load it into JBrowse as a flat file. Which to me defeats the purpose a little bit of being able to store WebApollo transcript models to chado and so on (in my use case anyway).
>
> Is there any solution to this?

This needs to be fixed with the new release (in my opinion).   I would like for the GFF3 and Chado exporters to do a round-trip export.   I’m going to open a bug for this and assign it to the new release.

https://github.com/GMOD/Apollo/issues/52

I want to discuss this internally, as I don’t necessarily thing that this is trivial and we are in the process of rewriting how we interact with Chado.

> Question/Issue 2:
> ———————————
>
> When following the existing tutorials on how to load data into WebApollo (like mRNAs), the gene-level feature is only ever created when one or more transcripts are added to the user track. Does that mean that I can’t import gene-level information at all (this sort of related to the issue above, i.e. loosing meta data that I have created prior to importing into WebApollo or when moving it to the user-curated track)?
>
> I am guessing this is a quite difficult from a technical point of view?

Can you be more specific as to how you are loading the data (from GFF3 files?)?    I think that you should be able to import gene-level information.

Nathan

>
> Regards,
>
> Marc



Reply | Threaded
Open this post in threaded view
|

Re: Meta data from evidence tracks

nathandunn

If you want.  I know that this needs to happen for the new release.  If there is some nuance we can talk about it, but Chado / GFF3 with complete and correct metadata needs to work properly.

Nathan



On Oct 28, 2014, at 9:08 AM, Suzanna Lewis <[hidden email]> wrote:

Can we add this to the topic items for this Thursday's call.

On Thu, Oct 23, 2014 at 7:13 PM, Nathan Dunn <[hidden email]> wrote:

> On Oct 22, 2014, at 11:19 PM, Marc Höppner <[hidden email]> wrote:
>
> Hi,
>
> I think my first attempt at sending this ended up in data nirvana… next try then:
>
> Question/Issue 1:
> -----------------------
> I noticed that when creating transcripts from evidence, that all meta data (like ‘description, dbxref) are lost. This is a bit of a problem, since my workflow/rationale looks like this:
>
> - create annotation with maker
> - functionally annotate maker annotation
> - load as track into WebApollo
> - Manual verify transcript structures/meta data and add to user-curated track (changing the models significantly would of course require the curator to remove the meta data)
> - Save curated annotations to Chado DB
> - Load curated annotations to Jbrowse portal from Chado
>
> So I hadn’t intended to ever take the annotations out of the database again - but if the meta data is always lost in this processing chain, I would basically have to dump out the WebApollo annotation, functionally annotate it and then load it into JBrowse as a flat file. Which to me defeats the purpose a little bit of being able to store WebApollo transcript models to chado and so on (in my use case anyway).
>
> Is there any solution to this?

This needs to be fixed with the new release (in my opinion).   I would like for the GFF3 and Chado exporters to do a round-trip export.   I’m going to open a bug for this and assign it to the new release.

https://github.com/GMOD/Apollo/issues/52

I want to discuss this internally, as I don’t necessarily thing that this is trivial and we are in the process of rewriting how we interact with Chado.

> Question/Issue 2:
> ———————————
>
> When following the existing tutorials on how to load data into WebApollo (like mRNAs), the gene-level feature is only ever created when one or more transcripts are added to the user track. Does that mean that I can’t import gene-level information at all (this sort of related to the issue above, i.e. loosing meta data that I have created prior to importing into WebApollo or when moving it to the user-curated track)?
>
> I am guessing this is a quite difficult from a technical point of view?

Can you be more specific as to how you are loading the data (from GFF3 files?)?    I think that you should be able to import gene-level information.

Nathan

>
> Regards,
>
> Marc