SBGN-ML. Milestone 1
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1 SBGN-ML Milestone 1
2 Generalities SBGN-ML is XML based cf. schema SBGN.xsd SBGN-ML files represent SBGN maps PD (Process Description) only in milestone 1
3 Basic geometry and labels COMMON TYPES AND ELEMENTS
4 Point PointAttributes attribute group absolute 2D Cartesian coordinates x (float) : horizontal, from left to right y (float) : vertical, from top to bottom origin in top-left corner of map no unit (scale free) (0,0) (0,y) point element: has PointAttributes <point x= 25.4 y= 12.3 /> (x,0) (x,y)
5 Bounding box bbox element describes a rectangle PointAttributes = top left corner (x,y) width & height (float) = dimensions <bbox x= 23 y= 11 width= 75 height= 43 > outer limit of a shape (can be irregular) applies to glyph and label elements for process nodes = central shape only (not input/output ports) width height
6 Label label element = text of a glyph element text attribute (string, mandatory) can be multiline: use line break bbox child (optional) = position the text is centered in the bbox use parent glyph s bbox when omitted represents text size hint when explicit <label text= inherited bbox > <label text= explicit bbox > <bbox x= 34 y= 9 width= 60 height= 10 > </label> inherited bbox explicit bbox
7 General structure of a SBGN-ML file HIGH LEVEL ELEMENTS
8 Structure of a SBGN-ML file sbgn root element single map element: SBGN PD map list of glyph elements (can be empty) list of arc elements (can be empty) <sbgn> <map> <glyph > </glyph> <glyph > </glyph> <arc > </arc> <arc > </arc> </map> </sbgn>
9 Stand-alone high level SBGN nodes, and sub-nodes GLYPH ELEMENT
10 class attribute (optional) Semantic of the glyph: Shape visual appearance Map syntactic validity Entity Pool Nodes (EPN): unspecified entity [DEFAULT] simple chemical macromolecule nucleic acid feature complex simple chemical multimer macromolecule multimer nucleic acid feature multimer complex multimer source and sink perturbing agent Process Nodes (PN): process omitted process uncertain process association dissociation phenotype Logic Operator Nodes (LON): and, or, not Sub-glyphs on Nodes: state variable, unit of information Sub-glyphs on Arcs: stoichiometry Other glyphs: compartment, submap, tag
11 Other attributes id attribute (mandatory) alphanumeric identifier, starting with a letter usually meaningless: <glyph id= glyph1234 > </glyph> orientation attribute (optional) Process node: horizontal, vertical Tag: left, right, up, down <glyph class= tag orientation= right id= g1 > </glyph> Label text here
12 Text inside a glyph: label or state state (optional): state variables only value attribute variable attribute <glyph class= state variable id= g1 > <state value= P variable= 42 /> </glyph> P@42 Parent glyph label (optional): all others, except PN and LON <glyph > <label text= my label /> </glyph>
13 clone element Optional Means the glyph has a clone marker <glyph class= simple chemical id= g1 > <clone /> </glyph> Can contain a label Glyph label <glyph class= complex id= g1 > <clone> <label text= clone label /> </clone> </glyph>
14 Geometry of a glyph: bbox Mandatory <glyph id= g1 > <bbox x= 2 y= 5 width= 67 height= 24 /> </glyph> Cf. definition of bbox
15 Children elements: glyph list Optional, any size <glyph id= g1 > <glyph id= g1.1 > </glyph> <glyph id= g1.2 > </glyph> </glyph> Examples: Unit of information of a compartment State variable of an EPN Inner EPN-like component of a complex
16 Children elements: port list Optional, any size 2 port elements required for PN (in & out ends) Attributes: PointAttributes absolute 2D Cartesian coordinates id: alphanumeric identifier starting with a letter <glyph class= process node id= g1 orientation= horizontal > <port x= 23 y= 4 id= g1.1 /> <port x= 56 y= 4 id= g1.2 /> bbox </glyph> g1.1 g1.2
17 Visible link between two nodes ARC ELEMENT
18 class attribute Semantic of the arc: Line visual appearance (usually, decorators at the end) Map syntactic validity (cf. class of source and target) production and consumption arcs all types of modification arcs: modulation stimulation catalysis inhibition necessary stimulation logic arc equivalence arc
19 source and target attributes Mandatory Can refer to the id of a glyph or a port <arc class= consumption source= epn1 target= pn1.1 > </arc>
20 stoichiometry of an arc Optional child element glyph of class stoichiometry <arc class= production source= pn1.2 target= epn2 > <glyph class= stoichiometry id= s1 > <label text= 3 /> <bbox x= 23 y= 45 width= 10 height= 10 > </glyph> 3 </arc>
21 Geometric path of an arc start element PointAttributes: start point of the path optional list of next elements PointAttributes: next point in the path point elements (between 0 and 2) control points of the Bezier curve (1: quadratic, 2: cubic) end element PointAttributes: end point of the path point elements (between 0 and 2) control points of the curve (1: quadratic, 2: cubic)
22 Example of paths (straight lines) Single straight line <arc > <start x= 10 y= 20 /> <end x= 60 y= 20 /> </arc> start end Polyline <arc > <start x= 10 y= 20 /> <next x= 30 y= 30 /> <next x= 50 y= 10 /> <end x= 60 y= 20 /> </arc> start next next end
23 Example of paths (curves) Quadratic Bezier curve <arc > <start x= 10 y= 20 /> <end x= 60 y= 20 > <point x= 34 y= 23 /> </end> </arc> Cubic Bezier curve <arc > <start x= 10 y= 20 /> <end x= 60 y= 20 > <point x= 12 y= 23 /> <point x= 34 y= 21 /> </end> </arc>
24 Example of paths (mixed) <arc > <start x= 10 y= 20 /> <next x= 30 y= 30 /> <next x= 50 y= 10 > <point x= 14 y= 53 > </next> <end x= 60 y= 20 > <point x= 12 y= 23 /> <point x= 34 y= 21 /> </end> </arc>
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