SBGN extension - Revision history

Axec@dote.ru at 13:02, 4 February 2022

2022-02-04T13:02:12Z

Axec@dote.ru at 12:40, 4 February 2022

2022-02-04T12:40:10Z

Axec@dote.ru at 12:31, 4 February 2022

2022-02-04T12:31:55Z

Axec@dote.ru at 12:22, 4 February 2022

2022-02-04T12:22:20Z

Axec@dote.ru at 12:00, 4 February 2022

2022-02-04T12:00:17Z

Axec@dote.ru at 11:43, 4 February 2022

2022-02-04T11:43:58Z

Axec@dote.ru at 11:42, 4 February 2022

2022-02-04T11:42:56Z

Axec@dote.ru at 11:02, 4 February 2022

2022-02-04T11:02:59Z

Axec@dote.ru: Created page with " BioUML fully supports SBML standard for mathematical models it also utilizes Visual modeling as one of its core features. Thus each SBML model is represented visually in BioU..."

2022-02-04T10:44:26Z

Created page with " BioUML fully supports SBML standard for mathematical models it also utilizes Visual modeling as one of its core features. Thus each SBML model is represented visually in BioU..."

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BioUML fully supports SBML standard for mathematical models it also utilizes Visual modeling as one of its core features. Thus each SBML model is represented visually in BioUML interface.
As a standard for visual description of mathematical models\systems we use SBGN (Systems Biology Graphic Notation). It is compatible with SBML description however it does not cover all SBML elements, i.e. no any SBML object have glyph or arc representation in SBGN. It mainly concerns purely mathematical objects: equations, functions, events.

@@ Line 2: / Line 2: @@
 [[File:sbgn_extension_cvs_1.png|thumb|Fig. 2. Model of the human Cardiovascular system in BioUML.]]
 [[File:sbgn_extension_cvs_2.png|thumb|Fig. 3.  Model of the human Cardiovascular system in BioUML, concize form.]]
 BioUML fully supports and heavily utilizes SBML (Systems Biology Markup Language) as a standard for description of mathematical models with ODE and discrete events (https://sbml.org/).
@@ Line 12: / Line 11: @@
 Example of the model using only mathematical elements ([[Short term model of the heart output regulation]]) is represented on Fig.1.
 More concise way is to omit equations right hand side is represented on Fig.2.
 ===New elements added to SBGN notation in BioUML===

@@ Line 1: / Line 1: @@
-[[File:cwl_document.png|thumb|Fig. 1. Model of the human Cardiovascular system in BioUML.]]
+[[File:sbgn_extension_example.png|thumb|Fig. 1. Example of relations between equations.]]
-[[File:cwl_import.png|thumb|Fig. 2.  Model of the human Cardiovascular system in BioUML, concize form.]]
+[[File:sbgn_extension_cvs_1.png|thumb|Fig. 2. Model of the human Cardiovascular system in BioUML.]]
-[[File:cwl_import.png|thumb|Fig. 3.  Model containing both entities with reactions and mathematical objects.]]
+[[File:sbgn_extension_cvs_2.png|thumb|Fig. 3.  Model of the human Cardiovascular system in BioUML, concize form.]]
 BioUML fully supports and heavily utilizes SBML (Systems Biology Markup Language) as a standard for description of mathematical models with ODE and discrete events (https://sbml.org/).

@@ Line 20: / Line 20: @@
 |- style="background-color: Lavender"
 |Equations
-|[[File:sbgn_extension_equations.png]]
+|[[File:equations.png]]
 |Mathematical equation in the model: <ul><li>assignment<li>initial asssignment<li>algebraic<li>ODE</ul>
 |-

@@ Line 1: / Line 1: @@
 BioUML fully supports and heavily utilizes SBML (Systems Biology Markup Language) as a standard for description of mathematical models with ODE and discrete events (https://sbml.org/).
@@ Line 5: / Line 8: @@
 The most well known graphical notation in the systems biology is SBGN (Systems Biology Graphic Notation). It has three different versions, here we will concern only with Process description notation which describes the temporal courses of biochemical interactions in a network (https://sbgn.github.io/). It is compatible with SBML although it more relies on pathways comprising of entities and processes between them. Thus it does not cover every single object in SBML models. Particularly there is no visual representations for "mathematical" objects: equations, functions, events, etc.
-In BioUML we fully support SBGN Process Description notation, however we decided to extend notation we use in BioUML to fully represent SBML models. Additional motivation for that is the fact that there are many mathematical objects of biological systems (in particular - physiological model) that are not represented by a network of biochemical reactions but rather contain a set of ODE equations. For example:
+In BioUML we fully support SBGN Process Description notation, however we decided to extend notation we use in BioUML to fully represent SBML models. Additional motivation for that is the fact that there are many mathematical objects of biological systems (in particular - physiological model) that are not represented by a network of biochemical reactions but rather contain a set of ODE equations.
-<ul>
+Example of the model using only mathematical elements ([[Short term model of the heart output regulation]]) is represented on Fig.1.
-<li>[[Long-term model of the CVS/Renal system]],
+More concise way is to omit equations right hand side is represented on Fig.2.
-<li>[[Short term model of the heart output regulation]].
+Another example contains both SBGN classical elements (enities and processes) and mathematical objects such as equations and events (fig. 3).
-</ul>
 ===New elements added to SBGN notation in BioUML===
@@ Line 17: / Line 19: @@
 !Name!!Notation!!Description
 |- style="background-color: Lavender"
-|Equations| dsdd |Mathematical equation in the model: <ul><li>assignment<li>initial asssignment<li>algebraic<li>ODE</ul> |-
+|Equations
-|v. 2016.2|                        |               |}
+|[[File:sbgn_extension_equations.png]]

@@ Line 5: / Line 5: @@
 The most well known graphical notation in the systems biology is SBGN (Systems Biology Graphic Notation). It has three different versions, here we will concern only with Process description notation which describes the temporal courses of biochemical interactions in a network (https://sbgn.github.io/). It is compatible with SBML although it more relies on pathways comprising of entities and processes between them. Thus it does not cover every single object in SBML models. Particularly there is no visual representations for "mathematical" objects: equations, functions, events, etc.
-In BioUML we fully support SBGN Process Description notation, however we decided to extend notation we use in BioUML to fully represent SBML models.
+In BioUML we fully support SBGN Process Description notation, however we decided to extend notation we use in BioUML to fully represent SBML models. Additional motivation for that is the fact that there are many mathematical objects of biological systems (in particular - physiological model) that are not represented by a network of biochemical reactions but rather contain a set of ODE equations. For example:
-Here is the list of new elements:
-−
 <ul>
-<li> Equations: [[File:equations.png]]
+<li>[[Long-term model of the CVS/Renal system]],

← Older revision		Revision as of 11:43, 4 February 2022
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	<ul>		<ul>
−	<li> Equations: [[File:~~Example~~.~~jpg~~]]	+	<li> Equations: [[File:equations.png]]

← Older revision		Revision as of 11:42, 4 February 2022
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	In BioUML we fully support SBGN Process Description notation, however we decided to extend notation we use in BioUML to fully represent SBML models.		In BioUML we fully support SBGN Process Description notation, however we decided to extend notation we use in BioUML to fully represent SBML models.
		+	Here is the list of new elements:
		+
		+	<ul>
		+	<li> Equations: [[File:Example.jpg]]

← Older revision		Revision as of 11:02, 4 February 2022
Line 1:		Line 1:

−	BioUML fully supports SBML standard for mathematical models it also utilizes Visual modeling as one of its core features. Thus each SBML model is represented visually in BioUML interface.	+	BioUML fully supports and heavily utilizes SBML (Systems Biology Markup Language) as a standard for description of mathematical models with ODE and discrete events (https://sbml.org/).
−	~~As a standard for~~ visual ~~description~~ of ~~mathematical models\~~systems ~~we use~~ SBGN (Systems Biology Graphic Notation). It is compatible with SBML ~~description however~~ it does not cover ~~all SBML elements, i.e. no any SBML~~ object ~~have glyph or arc representation~~ in ~~SBGN~~. ~~It mainly concerns purely~~ mathematical objects: equations, functions, events.	+	BioUML also utilizes Visual modeling as one of its core features. Thus each SBML model is represented visually in BioUML interface. Main component of visual modeling is formal graphic notation which defines how particular elements of the model should be represented visually.
		+
		+	The most well known graphical notation in the systems biology is SBGN (Systems Biology Graphic Notation). It has three different versions, here we will concern only with Process description notation which describes the temporal courses of biochemical interactions in a network (https://sbgn.github.io/). It is compatible with SBML although it more relies on pathways comprising of entities and processes between them. Thus it does not cover every single object in SBML models. Particularly there is no visual representations for "mathematical" objects: equations, functions, events, etc.
		+
		+	In BioUML we fully support SBGN Process Description notation, however we decided to extend notation we use in BioUML to fully represent SBML models.