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sbgn / libsbgn

Libraries for the Systems Biology Graphical Notation (SBGN); Java and C++
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Implement submaps #13

Open cannin opened 14 years ago

cannin commented 14 years ago

Implement a submap. A test-case is already available.

Reported by: amarillion

cannin commented 12 years ago

Original comment by: amarillion

matthiaskoenig commented 7 years ago

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

amazein commented 7 years ago

Thank you, Matthias

We care about submaps and in general about complexity management (cc Ugur, Inna and Marek). We need semantic zooming and builiding multilevel representations hierarchically organised for disease maps. I am sure there are others who would like to explore submaps for that.

Cheers,

Alexander

On Fri, Sep 30, 2016 at 11:38 AM, Matthias König notifications@github.com wrote:

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250702938, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i .

ghost commented 7 years ago

I agree. I think support of submaps is very important. A big critic of SBGN maps being "a mess" would be addressed by submaps, enabling good engineering design. Moreover, models using SBML Comp need them.

On 30/09/16 10:58, amazein wrote:

Thank you, Matthias

We care about submaps and in general about complexity management (cc Ugur, Inna and Marek). We need semantic zooming and builiding multilevel representations hierarchically organised for disease maps. I am sure there are others who would like to explore submaps for that.

Cheers,

Alexander

On Fri, Sep 30, 2016 at 11:38 AM, Matthias König notifications@github.com wrote:

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250702938, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i .

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Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT Tel: +441223496433 Mob:+447833147074 n.lenovere@gmail.com orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/ Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/

matthiaskoenig commented 7 years ago

Hi Alexander,

I also am very interested in submaps, but I am completely unaware of the current status in SBGN & SBGN-ML dealing with that. For me it would mainly be about pathways in a large metabolic network, with the submaps representing the individual pathways

Is there already a proposal how to encode submaps in SBGN-ML? Are there any discussions about this anywhere?

M

On Fri, Sep 30, 2016 at 11:58 AM, amazein notifications@github.com wrote:

Thank you, Matthias

We care about submaps and in general about complexity management (cc Ugur, Inna and Marek). We need semantic zooming and builiding multilevel representations hierarchically organised for disease maps. I am sure there are others who would like to explore submaps for that.

Cheers,

Alexander

On Fri, Sep 30, 2016 at 11:38 AM, Matthias König <notifications@github.com

wrote:

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250702938, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_ qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i .

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Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com konigmatt@googlemail.com Tel: +49 30 20938450 Tel: +49 176 81168480

matthiaskoenig commented 7 years ago

@Nicolas Exactly what I thought. I would use it to render my comp submodels.

On Fri, Sep 30, 2016 at 12:15 PM, Matthias König konigmatt@googlemail.com wrote:

Hi Alexander,

I also am very interested in submaps, but I am completely unaware of the current status in SBGN & SBGN-ML dealing with that. For me it would mainly be about pathways in a large metabolic network, with the submaps representing the individual pathways

Is there already a proposal how to encode submaps in SBGN-ML? Are there any discussions about this anywhere?

M

On Fri, Sep 30, 2016 at 11:58 AM, amazein notifications@github.com wrote:

Thank you, Matthias

We care about submaps and in general about complexity management (cc Ugur, Inna and Marek). We need semantic zooming and builiding multilevel representations hierarchically organised for disease maps. I am sure there are others who would like to explore submaps for that.

Cheers,

Alexander

On Fri, Sep 30, 2016 at 11:38 AM, Matthias König < notifications@github.com> wrote:

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250702938, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7- ycOTw_qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250706817, or mute the thread https://github.com/notifications/unsubscribe-auth/AA29uphZneTb7b3T71azp5NLSqbWNJkuks5qvN1XgaJpZM4KK56i .

Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com konigmatt@googlemail.com Tel: +49 30 20938450 Tel: +49 176 81168480

Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com konigmatt@googlemail.com Tel: +49 30 20938450 Tel: +49 176 81168480

ghost commented 7 years ago

Submaps are part of SBGN PD. IMHO they should be part of all SBGN languages.

Regarding Pathways, note that another mechanism has been introduced in SBGN PD L1V2 and ER L1V2, the "groups". They correspond more or less to groups in SBML and pathways in BioPAX.

The big difference is that groups are not meant to fold/unfold or lead to another map as SubMaps. They are means to highlight a pathway within a given map (e.g. with a colored background). There is no support in SBGN-ML/libSBGN. I think we would need to create the element group that would contain a list of references to the nodes it contains, and a description of the highlighting (background, node colouring or contour, and the colour)

On 30/09/16 11:15, Matthias König wrote:

Hi Alexander,

I also am very interested in submaps, but I am completely unaware of the current status in SBGN & SBGN-ML dealing with that. For me it would mainly be about pathways in a large metabolic network, with the submaps representing the individual pathways

Is there already a proposal how to encode submaps in SBGN-ML? Are there any discussions about this anywhere?

M

On Fri, Sep 30, 2016 at 11:58 AM, amazein notifications@github.com wrote:

Thank you, Matthias

We care about submaps and in general about complexity management (cc Ugur, Inna and Marek). We need semantic zooming and builiding multilevel representations hierarchically organised for disease maps. I am sure there are others who would like to explore submaps for that.

Cheers,

Alexander

On Fri, Sep 30, 2016 at 11:38 AM, Matthias König <notifications@github.com

wrote:

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250702938, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_ qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250706817, or mute the thread https://github.com/notifications/unsubscribe-auth/AA29uphZneTb7b3T71azp5NLSqbWNJkuks5qvN1XgaJpZM4KK56i .

Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com konigmatt@googlemail.com Tel: +49 30 20938450 Tel: +49 176 81168480

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250709945, or mute the thread https://github.com/notifications/unsubscribe-auth/ADhftnFc-sikaSQpI1D-tW8OrzMsJ3yKks5qvOFHgaJpZM4KK56i.

Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT Tel: +441223496433 Mob:+447833147074 n.lenovere@gmail.com orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/ Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/

amazein commented 7 years ago

Hi Matthias,

If there is a proposal, I do not know about it. I guess in general this direction is not very developed at the moment. Probably partly because we would need a software support for that to actually work - switching to another diagram after clicking on a submap for example.

BW,

Alexander

On Fri, Sep 30, 2016 at 12:15 PM, Matthias König notifications@github.com wrote:

Hi Alexander,

I also am very interested in submaps, but I am completely unaware of the current status in SBGN & SBGN-ML dealing with that. For me it would mainly be about pathways in a large metabolic network, with the submaps representing the individual pathways

Is there already a proposal how to encode submaps in SBGN-ML? Are there any discussions about this anywhere?

M

On Fri, Sep 30, 2016 at 11:58 AM, amazein notifications@github.com wrote:

Thank you, Matthias

We care about submaps and in general about complexity management (cc Ugur, Inna and Marek). We need semantic zooming and builiding multilevel representations hierarchically organised for disease maps. I am sure there are others who would like to explore submaps for that.

Cheers,

Alexander

On Fri, Sep 30, 2016 at 11:38 AM, Matthias König < notifications@github.com

wrote:

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250702938, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_ qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250706817, or mute the thread https://github.com/notifications/unsubscribe-auth/ AA29uphZneTb7b3T71azp5NLSqbWNJkuks5qvN1XgaJpZM4KK56i .

Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com konigmatt@googlemail.com Tel: +49 30 20938450 Tel: +49 176 81168480

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ghost commented 7 years ago

Some software are ready for it though! See:

http://mimoza.bordeaux.inria.fr/

And of course historically, the software pushing for modularity in SBML such as ProMot http://www2.mpi-magdeburg.mpg.de/projects/promot/

On 30/09/16 11:37, amazein wrote:

Hi Matthias,

If there is a proposal, I do not know about it. I guess in general this direction is not very developed at the moment. Probably partly because we would need a software support for that to actually work - switching to another diagram after clicking on a submap for example.

BW,

Alexander

On Fri, Sep 30, 2016 at 12:15 PM, Matthias König notifications@github.com wrote:

Hi Alexander,

I also am very interested in submaps, but I am completely unaware of the current status in SBGN & SBGN-ML dealing with that. For me it would mainly be about pathways in a large metabolic network, with the submaps representing the individual pathways

Is there already a proposal how to encode submaps in SBGN-ML? Are there any discussions about this anywhere?

M

On Fri, Sep 30, 2016 at 11:58 AM, amazein notifications@github.com wrote:

Thank you, Matthias

We care about submaps and in general about complexity management (cc Ugur, Inna and Marek). We need semantic zooming and builiding multilevel representations hierarchically organised for disease maps. I am sure there are others who would like to explore submaps for that.

Cheers,

Alexander

On Fri, Sep 30, 2016 at 11:38 AM, Matthias König < notifications@github.com

wrote:

Does anybody care about submaps? Would this be the way to have hierarchical maps?

It should be sufficient to have an attribute submap on the glyph which can reference map ids.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250702938, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_ qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250706817, or mute the thread https://github.com/notifications/unsubscribe-auth/ AA29uphZneTb7b3T71azp5NLSqbWNJkuks5qvN1XgaJpZM4KK56i .

Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com konigmatt@googlemail.com Tel: +49 30 20938450 Tel: +49 176 81168480

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sbgn/libsbgn/issues/13#issuecomment-250709945, or mute the thread https://github.com/notifications/unsubscribe-auth/AS7-yUpIjkXqrigS2Eo1WM0wThlq4ADKks5qvOFHgaJpZM4KK56i .

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Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT Tel: +441223496433 Mob:+447833147074 n.lenovere@gmail.com orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/ Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/

vtoure commented 7 years ago

Hi Matthias, Submaps are supported by SBGN PD and SBGN AF. Regarding libSBGN/SBGN-ML, there will be a complete support for submaps (already implemented in the milestone 3 - not released yet).

How it's done with an example: Map2 is a submap of Map1

The submap glyph carries terminal glyphs. The terminal glyphs will basically link to the tag glyphs (usually Entity Pool Nodes and Compartments for PD, Activity Nodes and Compartments for AF) in the submap Map2.

Hope this helps.

Best, Vasundra