ways to implement cross-species links in apollo/jbrowse?

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ways to implement cross-species links in apollo/jbrowse?

Michael Poeschla
Hi all,

I want to implement something with our apollo browser and was hoping that someone could point me in the right direction to get started, or let me know if a solution already exists. We have a browser loaded with closely related teleost species. I also have a table with orthologous genes between the species and their genomic locations that I want to use as the basis for a new feature, where I could click on an annotation in apollo (or jbrowse track) and then be able to click through to orthologous sites in other species. Not sure if this is a jbrowse or apollo issue so posting it to both lists per the developer's advice (thanks Nathan!).

Any advice/suggestions would be appreciated.

Thanks in advance!
Michael




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Re: ways to implement cross-species links in apollo/jbrowse?

adf_ncgr
Hi Michael-
we have similar comparative genomics interests within our project (which happens to deal with more or less closely related plant species); and we've approached it in a couple of different ways, one of which might be able to work for you too.

The first way is simplest and perhaps appropriate for your case since you already have precomputed orthology; we've simply injected an AJAX service callout into the gene details dialog in JBrowse, and the implementation of the service is responsible for providing links to other resources for the gene (which in your case could be a set of links to each of the orthologs).
You can see it in action here:
http://www.medicagohapmap2.org/jbrowse/?data=medtr%2FA17_HM341.gnm4&loc=medtr.A17_HM341.gnm4.ann2.Medtr5g089110&tracks=A17_HM341.gnm4.ann2
(after you click on the glyph for the gene model, there might be a slight pause before the links appear while the AJAX call is being handled; we should probably have an indicator of sorts there)

The second way is having JBrowse working in conjunction with a multi-genome micro/macro synteny comparison app we've been developing (the Genome Context Viewer (GCV): https://github.com/legumeinfo/lis_context_viewer/wiki/Examples);
this allows on-the-fly parameterized determination of syntelogs, which can be communicated to drive JBrowse using messaging via a BroadcastChannel; although we're still pretty much just exploring this mechanism for effecting inter-application communication it so far seems promising. But actually, even without this event-based approach, the mechanism in the first option I described above can also just linkout to the GCV app (as we've done among our links in that example, just see the one described as "similar genomic contexts"). One possible merit of this approach is that it can take you to related regions of genomes via synteny even when an ortholog for the gene in question appears to be missing (which is sometimes just an artifact of assembly/annotation).

If any of this seems to merit further discussion, I'd happy to discuss further (and/or point you to someone from my group who can give more implementation details).

hope it helps, in any case
Andrew

On 1/21/19 9:48 AM, Michael Poeschla wrote:
Hi all, 

I want to implement something with our apollo browser and was hoping that someone could point me in the right direction to get started, or let me know if a solution already exists. We have a browser loaded with closely related teleost species. I also have a table with orthologous genes between the species and their genomic locations that I want to use as the basis for a new feature, where I could click on an annotation in apollo (or jbrowse track) and then be able to click through to orthologous sites in other species. Not sure if this is a jbrowse or apollo issue so posting it to both lists per the developer's advice (thanks Nathan!). 

Any advice/suggestions would be appreciated.

Thanks in advance!
Michael 



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 






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Re: ways to implement cross-species links in apollo/jbrowse?

Michael Poeschla
Hi Andrew, thanks for your response. Both of these methods look pretty promising, and it'd be great to try the first way first, and the GCV looks really cool and I'd love to try it too at some point as you guys develop it. 

I'm not too familiar with AJAX so it'd be really great to chat further with you or someone over there and see how you guys implemented that.

I'm also wondering, if anyone knows, how easy it is to generate a bunch of links in apollo based on genome locations. I believe this would be scriptable in jbrowse.. would the url structure let me do this easily in apollo?   


Thanks so much, 
Michael Poeschla
From: "Andrew Farmer" <[hidden email]>
To: "apollo" <[hidden email]>, "Michael Poeschla" <[hidden email]>, "gmod-ajax" <[hidden email]>
Sent: Tuesday, January 22, 2019 7:31:35 AM
Subject: Re: [apollo] ways to implement cross-species links in apollo/jbrowse?

Hi Michael-
we have similar comparative genomics interests within our project (which happens to deal with more or less closely related plant species); and we've approached it in a couple of different ways, one of which might be able to work for you too.

The first way is simplest and perhaps appropriate for your case since you already have precomputed orthology; we've simply injected an AJAX service callout into the gene details dialog in JBrowse, and the implementation of the service is responsible for providing links to other resources for the gene (which in your case could be a set of links to each of the orthologs).
You can see it in action here:
http://www.medicagohapmap2.org/jbrowse/?data=medtr%2FA17_HM341.gnm4&loc=medtr.A17_HM341.gnm4.ann2.Medtr5g089110&tracks=A17_HM341.gnm4.ann2
(after you click on the glyph for the gene model, there might be a slight pause before the links appear while the AJAX call is being handled; we should probably have an indicator of sorts there)

The second way is having JBrowse working in conjunction with a multi-genome micro/macro synteny comparison app we've been developing (the Genome Context Viewer (GCV): https://github.com/legumeinfo/lis_context_viewer/wiki/Examples);
this allows on-the-fly parameterized determination of syntelogs, which can be communicated to drive JBrowse using messaging via a BroadcastChannel; although we're still pretty much just exploring this mechanism for effecting inter-application communication it so far seems promising. But actually, even without this event-based approach, the mechanism in the first option I described above can also just linkout to the GCV app (as we've done among our links in that example, just see the one described as "similar genomic contexts"). One possible merit of this approach is that it can take you to related regions of genomes via synteny even when an ortholog for the gene in question appears to be missing (which is sometimes just an artifact of assembly/annotation).

If any of this seems to merit further discussion, I'd happy to discuss further (and/or point you to someone from my group who can give more implementation details).

hope it helps, in any case
Andrew

On 1/21/19 9:48 AM, Michael Poeschla wrote:
Hi all, 

I want to implement something with our apollo browser and was hoping that someone could point me in the right direction to get started, or let me know if a solution already exists. We have a browser loaded with closely related teleost species. I also have a table with orthologous genes between the species and their genomic locations that I want to use as the basis for a new feature, where I could click on an annotation in apollo (or jbrowse track) and then be able to click through to orthologous sites in other species. Not sure if this is a jbrowse or apollo issue so posting it to both lists per the developer's advice (thanks Nathan!). 

Any advice/suggestions would be appreciated.

Thanks in advance!
Michael 

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 






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RE: ways to implement cross-species links in apollo/jbrowse?

Cook, Malcolm
In reply to this post by adf_ncgr

Lurking here, but, mightn’t a perhaps useful interface to navigating such syntelogs/orthologues be to (somehow) extend the mafviewer plugin to allow linking to precomputed multiple alignments…???

 

 

From: [hidden email] <[hidden email]> On Behalf Of Andrew Farmer
Sent: Tuesday, January 22, 2019 12:32 AM
To: [hidden email]; Michael Poeschla <[hidden email]>; [hidden email]
Subject: Re: [apollo] ways to implement cross-species links in apollo/jbrowse?

 

**CAUTION: Non-Stowers email**

Hi Michael-
we have similar comparative genomics interests within our project (which happens to deal with more or less closely related plant species); and we've approached it in a couple of different ways, one of which might be able to work for you too.

The first way is simplest and perhaps appropriate for your case since you already have precomputed orthology; we've simply injected an AJAX service callout into the gene details dialog in JBrowse, and the implementation of the service is responsible for providing links to other resources for the gene (which in your case could be a set of links to each of the orthologs).
You can see it in action here:
http://www.medicagohapmap2.org/jbrowse/?data=medtr%2FA17_HM341.gnm4&loc=medtr.A17_HM341.gnm4.ann2.Medtr5g089110&tracks=A17_HM341.gnm4.ann2
(after you click on the glyph for the gene model, there might be a slight pause before the links appear while the AJAX call is being handled; we should probably have an indicator of sorts there)

The second way is having JBrowse working in conjunction with a multi-genome micro/macro synteny comparison app we've been developing (the Genome Context Viewer (GCV): https://github.com/legumeinfo/lis_context_viewer/wiki/Examples);
this allows on-the-fly parameterized determination of syntelogs, which can be communicated to drive JBrowse using messaging via a BroadcastChannel; although we're still pretty much just exploring this mechanism for effecting inter-application communication it so far seems promising. But actually, even without this event-based approach, the mechanism in the first option I described above can also just linkout to the GCV app (as we've done among our links in that example, just see the one described as "similar genomic contexts"). One possible merit of this approach is that it can take you to related regions of genomes via synteny even when an ortholog for the gene in question appears to be missing (which is sometimes just an artifact of assembly/annotation).

If any of this seems to merit further discussion, I'd happy to discuss further (and/or point you to someone from my group who can give more implementation details).

hope it helps, in any case
Andrew

On 1/21/19 9:48 AM, Michael Poeschla wrote:

Hi all, 
 
I want to implement something with our apollo browser and was hoping that someone could point me in the right direction to get started, or let me know if a solution already exists. We have a browser loaded with closely related teleost species. I also have a table with orthologous genes between the species and their genomic locations that I want to use as the basis for a new feature, where I could click on an annotation in apollo (or jbrowse track) and then be able to click through to orthologous sites in other species. Not sure if this is a jbrowse or apollo issue so posting it to both lists per the developer's advice (thanks Nathan!). 
 
Any advice/suggestions would be appreciated.
 
Thanks in advance!
Michael 



 
 
 
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
 

 





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Re: ways to implement cross-species links in apollo/jbrowse?

adf_ncgr
In reply to this post by Michael Poeschla
Hi Michael-
sure, we'd be happy to chat with you further, either on-list or off, just let me know what seems like
the best mechanism and I can try to set something up with the right people on my end involved.

And we'd be more than happy also to help get you set up with GCV on your data. The current implementation
of the services layer is using a m chado-based backend with a Django layer, but we have an alternative
implementation in progress using redis and a "microservices"-oriented approach (primarily to help with scaling
some of the heavier back-end operations).

looking forward to further discussion

Andrew


On 1/23/19 3:05 PM, Michael Poeschla wrote:
Hi Andrew, thanks for your response. Both of these methods look pretty promising, and it'd be great to try the first way first, and the GCV looks really cool and I'd love to try it too at some point as you guys develop it. 

I'm not too familiar with AJAX so it'd be really great to chat further with you or someone over there and see how you guys implemented that.

I'm also wondering, if anyone knows, how easy it is to generate a bunch of links in apollo based on genome locations. I believe this would be scriptable in jbrowse.. would the url structure let me do this easily in apollo?   


Thanks so much, 
Michael Poeschla
From: "Andrew Farmer" [hidden email]
To: "apollo" [hidden email], "Michael Poeschla" [hidden email], "gmod-ajax" [hidden email]
Sent: Tuesday, January 22, 2019 7:31:35 AM
Subject: Re: [apollo] ways to implement cross-species links in apollo/jbrowse?

Hi Michael-
we have similar comparative genomics interests within our project (which happens to deal with more or less closely related plant species); and we've approached it in a couple of different ways, one of which might be able to work for you too.

The first way is simplest and perhaps appropriate for your case since you already have precomputed orthology; we've simply injected an AJAX service callout into the gene details dialog in JBrowse, and the implementation of the service is responsible for providing links to other resources for the gene (which in your case could be a set of links to each of the orthologs).
You can see it in action here:
http://www.medicagohapmap2.org/jbrowse/?data=medtr%2FA17_HM341.gnm4&loc=medtr.A17_HM341.gnm4.ann2.Medtr5g089110&tracks=A17_HM341.gnm4.ann2
(after you click on the glyph for the gene model, there might be a slight pause before the links appear while the AJAX call is being handled; we should probably have an indicator of sorts there)

The second way is having JBrowse working in conjunction with a multi-genome micro/macro synteny comparison app we've been developing (the Genome Context Viewer (GCV): https://github.com/legumeinfo/lis_context_viewer/wiki/Examples);
this allows on-the-fly parameterized determination of syntelogs, which can be communicated to drive JBrowse using messaging via a BroadcastChannel; although we're still pretty much just exploring this mechanism for effecting inter-application communication it so far seems promising. But actually, even without this event-based approach, the mechanism in the first option I described above can also just linkout to the GCV app (as we've done among our links in that example, just see the one described as "similar genomic contexts"). One possible merit of this approach is that it can take you to related regions of genomes via synteny even when an ortholog for the gene in question appears to be missing (which is sometimes just an artifact of assembly/annotation).

If any of this seems to merit further discussion, I'd happy to discuss further (and/or point you to someone from my group who can give more implementation details).

hope it helps, in any case
Andrew

On 1/21/19 9:48 AM, Michael Poeschla wrote:
Hi all, 

I want to implement something with our apollo browser and was hoping that someone could point me in the right direction to get started, or let me know if a solution already exists. We have a browser loaded with closely related teleost species. I also have a table with orthologous genes between the species and their genomic locations that I want to use as the basis for a new feature, where I could click on an annotation in apollo (or jbrowse track) and then be able to click through to orthologous sites in other species. Not sure if this is a jbrowse or apollo issue so posting it to both lists per the developer's advice (thanks Nathan!). 

Any advice/suggestions would be appreciated.

Thanks in advance!
Michael 

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 







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Re: ways to implement cross-species links in apollo/jbrowse?

adf_ncgr
In reply to this post by Cook, Malcolm
Hi Malcom-
thanks for pointing that out! if I ever knew JBrowse had that plugin, I had totallt forgotten it (though I've recently been using
the similar functionality that is present in IGV for MAF files). This could definitely come in handy for us.

I guess the main difference between going this route and what I was describing would be the requirement to generate whole-genome pre-computed nucleotide-level alignments; the things I was describing earlier were more or less just based on the idea  that genes had been assigned into families by some method (e.g. we typically just match proteins against HMMs representing some standardized set of gene families), and then only "aligning" at the level of the gene order and orientation. But integrating the two approaches would certainly be quite powerful, and we've been thinking about such approaches a bit recently; knowing that JBrowse supports this feature is definitely helpful.

thanks again

Andrew



On 1/24/19 12:21 PM, Cook, Malcolm wrote:

Lurking here, but, mightn’t a perhaps useful interface to navigating such syntelogs/orthologues be to (somehow) extend the mafviewer plugin to allow linking to precomputed multiple alignments…???

 

 

From: [hidden email] [hidden email] On Behalf Of Andrew Farmer
Sent: Tuesday, January 22, 2019 12:32 AM
To: [hidden email]; Michael Poeschla [hidden email]; [hidden email]
Subject: Re: [apollo] ways to implement cross-species links in apollo/jbrowse?

 

**CAUTION: Non-Stowers email**

Hi Michael-
we have similar comparative genomics interests within our project (which happens to deal with more or less closely related plant species); and we've approached it in a couple of different ways, one of which might be able to work for you too.

The first way is simplest and perhaps appropriate for your case since you already have precomputed orthology; we've simply injected an AJAX service callout into the gene details dialog in JBrowse, and the implementation of the service is responsible for providing links to other resources for the gene (which in your case could be a set of links to each of the orthologs).
You can see it in action here:
http://www.medicagohapmap2.org/jbrowse/?data=medtr%2FA17_HM341.gnm4&loc=medtr.A17_HM341.gnm4.ann2.Medtr5g089110&tracks=A17_HM341.gnm4.ann2
(after you click on the glyph for the gene model, there might be a slight pause before the links appear while the AJAX call is being handled; we should probably have an indicator of sorts there)

The second way is having JBrowse working in conjunction with a multi-genome micro/macro synteny comparison app we've been developing (the Genome Context Viewer (GCV): https://github.com/legumeinfo/lis_context_viewer/wiki/Examples);
this allows on-the-fly parameterized determination of syntelogs, which can be communicated to drive JBrowse using messaging via a BroadcastChannel; although we're still pretty much just exploring this mechanism for effecting inter-application communication it so far seems promising. But actually, even without this event-based approach, the mechanism in the first option I described above can also just linkout to the GCV app (as we've done among our links in that example, just see the one described as "similar genomic contexts"). One possible merit of this approach is that it can take you to related regions of genomes via synteny even when an ortholog for the gene in question appears to be missing (which is sometimes just an artifact of assembly/annotation).

If any of this seems to merit further discussion, I'd happy to discuss further (and/or point you to someone from my group who can give more implementation details).

hope it helps, in any case
Andrew

On 1/21/19 9:48 AM, Michael Poeschla wrote:

Hi all, 
 
I want to implement something with our apollo browser and was hoping that someone could point me in the right direction to get started, or let me know if a solution already exists. We have a browser loaded with closely related teleost species. I also have a table with orthologous genes between the species and their genomic locations that I want to use as the basis for a new feature, where I could click on an annotation in apollo (or jbrowse track) and then be able to click through to orthologous sites in other species. Not sure if this is a jbrowse or apollo issue so posting it to both lists per the developer's advice (thanks Nathan!). 
 
Any advice/suggestions would be appreciated.
 
Thanks in advance!
Michael 



 
 
 
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
 

 




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.