Implement submaps

[cannin]

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

Reported by: amarillion

[cannin]

• milestone: 1165716 --> Milestone 3

Original comment by: amarillion

[matthiaskoenig]

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]

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 [email protected]
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
#13 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i
.

[ghost]

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 [email protected]
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
#13 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AS7-ycOTw_qiHuFn9p4uHNYibvO9fM0oks5qvNiWgaJpZM4KK56i
.

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub #13 (comment), or mute the thread https://github.com/notifications/unsubscribe-auth/ADhftoLIDARzlwbIimazfgQhkJMm7GDjks5qvN1XgaJpZM4KK56i.

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

[matthiaskoenig]

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 [email protected] 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 <[email protected]

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
#13 (comment), 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
#13 (comment), 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
[email protected]
Tel: +49 30 20938450
Tel: +49 176 81168480

[matthiaskoenig]

@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 [email protected]
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 [email protected]
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 <
[email protected]>
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
#13 (comment), 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
#13 (comment), 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
[email protected]
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
[email protected]
Tel: +49 30 20938450
Tel: +49 176 81168480

[ghost]

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 [email protected] 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 <[email protected]

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
#13 (comment), 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
#13 (comment), 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
[email protected]
Tel: +49 30 20938450
Tel: +49 176 81168480

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub #13 (comment), 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 [email protected]
orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/
Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/

[amazein]

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 [email protected]
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 [email protected]
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 <
[email protected]

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
#13 (comment), 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
#13 (comment), 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
[email protected]
Tel: +49 30 20938450
Tel: +49 176 81168480

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

[ghost]

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 [email protected]
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 [email protected]
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 <
[email protected]

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
#13 (comment), 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
#13 (comment), 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
[email protected]
Tel: +49 30 20938450
Tel: +49 176 81168480

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

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub #13 (comment), or mute the thread https://github.com/notifications/unsubscribe-auth/ADhftoD1uNZhTGujN6_LvE5DNDXYfRmNks5qvOZogaJpZM4KK56i.

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

[vtoure]

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

• a map have an ID: <map id="Map1"> , <map id="Map2">
• the submap glyph (drawn in Map1) get a mapRef: <glyph class="submap" ... mapRef="Map2">

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.

• the terminal glyphs get a tagRef - : <glyph class="terminal" ... tagRef="glyph3">
  , glyph3 being a tag glyph in the submap Map2.

Hope this helps.

Best,
Vasundra