Examples¶

In this section example use cases of libsbgnpy are provided.

In [1]:

from IPython.display import Image, display
import os
import tempfile
from libsbgnpy import Sbgn

def sbgn_to_jupyter_image(sbgn: Sbgn):
    """Render the SBGN to image in the notebook."""
    f_png = tempfile.NamedTemporaryFile(suffix=".png", delete=False)
    render_sbgn(sbgn, image_file=f_png.name, 
                       file_format="png")
    display(Image(f_png.name, width=500))
    f_png.close()
    os.unlink(f_png.name)

from IPython.display import Image, display import os import tempfile from libsbgnpy import Sbgn def sbgn_to_jupyter_image(sbgn: Sbgn): """Render the SBGN to image in the notebook.""" f_png = tempfile.NamedTemporaryFile(suffix=".png", delete=False) render_sbgn(sbgn, image_file=f_png.name, file_format="png") display(Image(f_png.name, width=500)) f_png.close() os.unlink(f_png.name)

Create SBGN¶

The example demonstrates how to create a Sbgn document from scratch. This includes creation of the following objects.

• Map: SBGN map
• Bbox: bounding boxes
• Glyph: glyph (nodes)
• Arc: arc (edges)

The full map consists of a simple reaction catalysed via ADH1 which converts Ethanol + NAD+ --> Ethanal + NADH + H+.

In [2]:

from libsbgnpy import *

# create new map
map = Map(
	language=MapLanguage.PROCESS_DESCRIPTION,
	bbox=Bbox(x=0, y=0, w=363, h=253),
)
sbgn = Sbgn(map=[map])

# create glyphs and add to map
map.glyph.extend([
	Glyph(
		class_value=GlyphClass.SIMPLE_CHEMICAL,
		id="glyph1",
		label=Label(text="Ethanol"),
		bbox=Bbox(x=40, y=120, w=60, h=60),
	),
	Glyph(
		class_value=GlyphClass.SIMPLE_CHEMICAL,
		id="glyph_ethanal",
		label=Label(text="Ethanal"),
		bbox=Bbox(x=220, y=110, w=60, h=60),
	),
	Glyph(
		class_value=GlyphClass.MACROMOLECULE,
		id="glyph_adh1",
		label=Label(text="ADH1"),
		bbox=Bbox(x=106, y=20, w=108, h=60),
	),
	Glyph(
		class_value=GlyphClass.SIMPLE_CHEMICAL,
		id="glyph_h",
		label=Label(text="H+"),
		bbox=Bbox(x=220, y=190, w=60, h=60),
	),
	Glyph(
		class_value=GlyphClass.SIMPLE_CHEMICAL,
		id="glyph_nad",
		label=Label(text="NAD+"),
		bbox=Bbox(x=40, y=190, w=60, h=60),
	),
	Glyph(
		class_value=GlyphClass.SIMPLE_CHEMICAL,
		id="glyph_nadh",
		label=Label(text="NADH"),
		bbox=Bbox(x=300, y=150, w=60, h=60),
	),
	# glyph with ports (process)
	Glyph(
		class_value=GlyphClass.PROCESS,
		id="pn1",
		orientation=GlyphOrientation.HORIZONTAL,
		bbox=Bbox(x=148, y=168, w=24, h=24),
		port=[
			Port(x=136, y=180, id="pn1.1"),
			Port(x=184, y=180, id="pn1.2"),
		],
	)
])

# arcs
# create arcs and set the start and end points
map.arc.extend([
	Arc(
		class_value=ArcClass.CONSUMPTION,
		source="glyph1",
		target="pn1.1",
		id="a01",
		start=Arc.Start(x=98, y=160),
		end=Arc.End(x=136, y=180),
	),
	Arc(
		class_value=ArcClass.PRODUCTION,
		source="pn1.2",
		target="glyph_nadh",
		id="a02",
		start=Arc.Start(x=184, y=180),
		end=Arc.End(x=300, y=180),
	),
	Arc(
		class_value=ArcClass.CATALYSIS,
		source="glyph_adh1",
		target="pn1",
		id="a03",
		start=Arc.Start(x=160, y=80),
		end=Arc.End(x=160, y=168),
	),
	Arc(
		class_value=ArcClass.PRODUCTION,
		source="pn1.2",
		target="glyph_h",
		id="a04",
		start=Arc.Start(x=184, y=180),
		end=Arc.End(x=224, y=202),
	),
	Arc(
		class_value=ArcClass.PRODUCTION,
		source="pn1.2",
		target="glyph_ethanal",
		id="a05",
		start=Arc.Start(x=184, y=180),
		end=Arc.End(x=224, y=154),
	),
	Arc(
		class_value=ArcClass.CONSUMPTION,
		source="glyph_nad",
		target="pn1.1",
		id="a06",
		start=Arc.Start(x=95, y=202),
		end=Arc.End(x=136, y=180),
	),
])

# write SBGN to file
f_out = tempfile.NamedTemporaryFile(suffix=".sbgn")
write_sbgn_to_file(sbgn, f_out.name)

# show xml
console.print(write_sbgn_to_string(sbgn))

# render SBGN
sbgn_to_jupyter_image(sbgn)

from libsbgnpy import * # create new map map = Map( language=MapLanguage.PROCESS_DESCRIPTION, bbox=Bbox(x=0, y=0, w=363, h=253), ) sbgn = Sbgn(map=[map]) # create glyphs and add to map map.glyph.extend([ Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph1", label=Label(text="Ethanol"), bbox=Bbox(x=40, y=120, w=60, h=60), ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_ethanal", label=Label(text="Ethanal"), bbox=Bbox(x=220, y=110, w=60, h=60), ), Glyph( class_value=GlyphClass.MACROMOLECULE, id="glyph_adh1", label=Label(text="ADH1"), bbox=Bbox(x=106, y=20, w=108, h=60), ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_h", label=Label(text="H+"), bbox=Bbox(x=220, y=190, w=60, h=60), ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nad", label=Label(text="NAD+"), bbox=Bbox(x=40, y=190, w=60, h=60), ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nadh", label=Label(text="NADH"), bbox=Bbox(x=300, y=150, w=60, h=60), ), # glyph with ports (process) Glyph( class_value=GlyphClass.PROCESS, id="pn1", orientation=GlyphOrientation.HORIZONTAL, bbox=Bbox(x=148, y=168, w=24, h=24), port=[ Port(x=136, y=180, id="pn1.1"), Port(x=184, y=180, id="pn1.2"), ], ) ]) # arcs # create arcs and set the start and end points map.arc.extend([ Arc( class_value=ArcClass.CONSUMPTION, source="glyph1", target="pn1.1", id="a01", start=Arc.Start(x=98, y=160), end=Arc.End(x=136, y=180), ), Arc( class_value=ArcClass.PRODUCTION, source="pn1.2", target="glyph_nadh", id="a02", start=Arc.Start(x=184, y=180), end=Arc.End(x=300, y=180), ), Arc( class_value=ArcClass.CATALYSIS, source="glyph_adh1", target="pn1", id="a03", start=Arc.Start(x=160, y=80), end=Arc.End(x=160, y=168), ), Arc( class_value=ArcClass.PRODUCTION, source="pn1.2", target="glyph_h", id="a04", start=Arc.Start(x=184, y=180), end=Arc.End(x=224, y=202), ), Arc( class_value=ArcClass.PRODUCTION, source="pn1.2", target="glyph_ethanal", id="a05", start=Arc.Start(x=184, y=180), end=Arc.End(x=224, y=154), ), Arc( class_value=ArcClass.CONSUMPTION, source="glyph_nad", target="pn1.1", id="a06", start=Arc.Start(x=95, y=202), end=Arc.End(x=136, y=180), ), ]) # write SBGN to file f_out = tempfile.NamedTemporaryFile(suffix=".sbgn") write_sbgn_to_file(sbgn, f_out.name) # show xml console.print(write_sbgn_to_string(sbgn)) # render SBGN sbgn_to_jupyter_image(sbgn)

<?xml version="1.0" encoding="UTF-8"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
  <map language="process description">
    <bbox x="0" y="0" w="363" h="253"/>
    <glyph class="simple chemical" orientation="horizontal" id="glyph1">
      <label text="Ethanol"/>
      <bbox x="40" y="120" w="60" h="60"/>
    </glyph>
    <glyph class="simple chemical" orientation="horizontal" id="glyph_ethanal">
      <label text="Ethanal"/>
      <bbox x="220" y="110" w="60" h="60"/>
    </glyph>
    <glyph class="macromolecule" orientation="horizontal" id="glyph_adh1">
      <label text="ADH1"/>
      <bbox x="106" y="20" w="108" h="60"/>
    </glyph>
    <glyph class="simple chemical" orientation="horizontal" id="glyph_h">
      <label text="H+"/>
      <bbox x="220" y="190" w="60" h="60"/>
    </glyph>
    <glyph class="simple chemical" orientation="horizontal" id="glyph_nad">
      <label text="NAD+"/>
      <bbox x="40" y="190" w="60" h="60"/>
    </glyph>
    <glyph class="simple chemical" orientation="horizontal" id="glyph_nadh">
      <label text="NADH"/>
      <bbox x="300" y="150" w="60" h="60"/>
    </glyph>
    <glyph class="process" orientation="horizontal" id="pn1">
      <bbox x="148" y="168" w="24" h="24"/>
      <port x="136" y="180" id="pn1.1"/>
      <port x="184" y="180" id="pn1.2"/>
    </glyph>
    <arc class="consumption" id="a01" source="glyph1" target="pn1.1">
      <start x="98" y="160"/>
      <end x="136" y="180"/>
    </arc>
    <arc class="production" id="a02" source="pn1.2" target="glyph_nadh">
      <start x="184" y="180"/>
      <end x="300" y="180"/>
    </arc>
    <arc class="catalysis" id="a03" source="glyph_adh1" target="pn1">
      <start x="160" y="80"/>
      <end x="160" y="168"/>
    </arc>
    <arc class="production" id="a04" source="pn1.2" target="glyph_h">
      <start x="184" y="180"/>
      <end x="224" y="202"/>
    </arc>
    <arc class="production" id="a05" source="pn1.2" target="glyph_ethanal">
      <start x="184" y="180"/>
      <end x="224" y="154"/>
    </arc>
    <arc class="consumption" id="a06" source="glyph_nad" target="pn1.1">
      <start x="95" y="202"/>
      <end x="136" y="180"/>
    </arc>
  </map>
</sbgn>

SBGN rendered: /tmp/tmpj8zf3ou4.png

Iterate Arcs & Glyphs¶

Example for iterating over glyphs and arcs in given SBGN file

In [3]:

from libsbgnpy import *

# Map
sbgn: Sbgn = read_sbgn_from_file("adh.sbgn")
map: Map = sbgn.map[0]

# Map
console.print(f"Map: {map.language}, BBox: {map.bbox}")
console.rule()

# Glyphs
for g in map.glyph:
    console.print(
        f"Glyph '{g.id}' of class '{g.class_value}' and label '{g.label}'."
    )
console.rule()

# Arcs
for a in map.arc:
    console.print(f"Arc '{a.id}' with class '{a.class_value}'.")

from libsbgnpy import * # Map sbgn: Sbgn = read_sbgn_from_file("adh.sbgn") map: Map = sbgn.map[0] # Map console.print(f"Map: {map.language}, BBox: {map.bbox}") console.rule() # Glyphs for g in map.glyph: console.print( f"Glyph '{g.id}' of class '{g.class_value}' and label '{g.label}'." ) console.rule() # Arcs for a in map.arc: console.print(f"Arc '{a.id}' with class '{a.class_value}'.")

Map: MapLanguage.PROCESS_DESCRIPTION, BBox: Bbox(notes=None, extension=None, 
x=0.0, y=0.0, w=363.0, h=253.0)
────────────────────────────────────────────────────────────────────────────────
Glyph 'glyph1' of class 'GlyphClass.SIMPLE_CHEMICAL' and label 
'Label(notes=None, extension=None, bbox=None, text='Ethanol')'.
Glyph 'glyph_ethanal' of class 'GlyphClass.SIMPLE_CHEMICAL' and label 
'Label(notes=None, extension=None, bbox=None, text='Ethanal')'.
Glyph 'glyph_adh1' of class 'GlyphClass.MACROMOLECULE' and label 
'Label(notes=None, extension=None, bbox=None, text='ADH1')'.
Glyph 'glyph_h' of class 'GlyphClass.SIMPLE_CHEMICAL' and label 
'Label(notes=None, extension=None, bbox=None, text='H+')'.
Glyph 'glyph_nad' of class 'GlyphClass.SIMPLE_CHEMICAL' and label 
'Label(notes=None, extension=None, bbox=None, text='NAD+')'.
Glyph 'glyph_nadh' of class 'GlyphClass.SIMPLE_CHEMICAL' and label 
'Label(notes=None, extension=None, bbox=None, text='NADH')'.
Glyph 'pn1' of class 'GlyphClass.PROCESS' and label 'None'.
────────────────────────────────────────────────────────────────────────────────
Arc 'a01' with class 'ArcClass.CONSUMPTION'.
Arc 'a02' with class 'ArcClass.PRODUCTION'.
Arc 'a03' with class 'ArcClass.CATALYSIS'.
Arc 'a04' with class 'ArcClass.PRODUCTION'.
Arc 'a05' with class 'ArcClass.PRODUCTION'.
Arc 'a06' with class 'ArcClass.CONSUMPTION'.

SBGN notes¶

The optional SBGN element named 'notes', present on every major SBGN component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0 (http://www.w3.org/1999/xhtml).

Write SBGN notes¶

In [4]:

from libsbgnpy import *

# create map
map = Map(language=MapLanguage.PROCESS_DESCRIPTION)
sbgn = Sbgn(map=[map])

# create glyph
g = Glyph(
    id="g1",
    class_value=GlyphClass.MACROMOLECULE,
    label=Label(text="INSR"),
    bbox=Bbox(x=100, y=100, w=80, h=40),
)
map.glyph.append(g)

# set notes
g.notes = Sbgnbase.Notes(
    w3_org_1999_xhtml_element=[
        """<body xmlns="http://www.w3.org/1999/xhtml">
This is an example note describing the INSR glyph.
</body>""",
        """<body xmlns="http://www.w3.org/1999/xhtml">
A second note with more information
</body>""",
    ]
)

console.print(write_sbgn_to_string(sbgn))

from libsbgnpy import * # create map map = Map(language=MapLanguage.PROCESS_DESCRIPTION) sbgn = Sbgn(map=[map]) # create glyph g = Glyph( id="g1", class_value=GlyphClass.MACROMOLECULE, label=Label(text="INSR"), bbox=Bbox(x=100, y=100, w=80, h=40), ) map.glyph.append(g) # set notes g.notes = Sbgnbase.Notes( w3_org_1999_xhtml_element=[ """ This is an example note describing the INSR glyph. """, """ A second note with more information """, ] ) console.print(write_sbgn_to_string(sbgn))

<?xml version="1.0" encoding="UTF-8"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
  <map language="process description">
    <glyph class="macromolecule" orientation="horizontal" id="g1">
      <notes><body xmlns="http://www.w3.org/1999/xhtml">
This is an example note describing the INSR glyph.
</body></notes><body xmlns="http://www.w3.org/1999/xhtml">
A second note with more information
</body><label text="INSR"/>
      <bbox x="100" y="100" w="80" h="40"/>
    </glyph>
  </map>
</sbgn>

Read SBGN notes¶

SBGN notes can be read via the get_notes function which returns a Notes instance. We just display the note we wrote before on one of the glyphs.

In [5]:

map: Map = sbgn.map[0]

for g in map.glyph:
    if g.notes:
        console.print(g.id)
        console.print(g.notes.w3_org_1999_xhtml_element)

map: Map = sbgn.map[0] for g in map.glyph: if g.notes: console.print(g.id) console.print(g.notes.w3_org_1999_xhtml_element)

g1
[
    '<body xmlns="http://www.w3.org/1999/xhtml">\nThis is an example note 
describing the INSR glyph.\n</body>',
    '<body xmlns="http://www.w3.org/1999/xhtml">\nA second note with more 
information\n</body>'
]

SBGN extension¶

SBGN allows to write extension information. This can be any well-formed XML content. Whereas Notes is a container for content to be shown directly to humans, Extension is a container for optional software-generated content not meant to be shown to humans. Every SBGN object can have its own Extension object instance. In XML, the Extension content type is any, allowing essentially arbitrary well-formed XML data content.

Write SBGN extension¶

In [6]:

sbgn = Sbgn()
map = Map(language=MapLanguage.PROCESS_DESCRIPTION)
sbgn.map.append(map)
extension = Sbgnbase.Extension()
extension.any_element.append("""<renderInformation id="example" programName="SBML Layout" programVersion="3.0"
 xmlns="http://projects.eml.org/bcb/sbml/render/level2">
    <listOfColorDefinitions>
    <colorDefinition id="yelloComp" value="#ffffccff" />
    <colorDefinition id="grayComp" value="#e0e0e0ff" />
    <colorDefinition id="orange" value="#fa9e2fff" />
    <colorDefinition id="blue" value="#2958acff" />
    <colorDefinition id="green" value="#378f5cff" />
    <colorDefinition id="Color_0" value="#969696" />
    <colorDefinition id="Color_1" value="#ff9900" />
    <colorDefinition id="Color_2" value="#000000" />			
    </listOfColorDefinitions>
    <listOfGradientDefinitions>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="LinearGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ccffff" />
        <stop offset="100%" stop-color="#ffffff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="OrangeGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#fa9e2fff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="BlueGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#2958acff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="GreenGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#378f5cff" />
    </linearGradient>
    </listOfGradientDefinitions>
    <listOfStyles>
    <style idList="glyph0 glyph2 glyph14 glyph34 ">
        <g stroke="Color_2" stroke-width="5" fill="yelloComp"  />			
    </style>
    <style idList="glyph1">
        <g stroke="Color_2" stroke-width="5" fill="grayComp"  />			
    </style>
    </listOfStyles>
</renderInformation>""")
map.extension = extension

console.print(write_sbgn_to_string(sbgn))

sbgn = Sbgn() map = Map(language=MapLanguage.PROCESS_DESCRIPTION) sbgn.map.append(map) extension = Sbgnbase.Extension() extension.any_element.append(""" """) map.extension = extension console.print(write_sbgn_to_string(sbgn))

<?xml version="1.0" encoding="UTF-8"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
  <map language="process description">
    <extension><renderInformation id="example" programName="SBML Layout" 
programVersion="3.0"
 xmlns="http://projects.eml.org/bcb/sbml/render/level2">
    <listOfColorDefinitions>
    <colorDefinition id="yelloComp" value="#ffffccff" />
    <colorDefinition id="grayComp" value="#e0e0e0ff" />
    <colorDefinition id="orange" value="#fa9e2fff" />
    <colorDefinition id="blue" value="#2958acff" />
    <colorDefinition id="green" value="#378f5cff" />
    <colorDefinition id="Color_0" value="#969696" />
    <colorDefinition id="Color_1" value="#ff9900" />
    <colorDefinition id="Color_2" value="#000000" />                    
    </listOfColorDefinitions>
    <listOfGradientDefinitions>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="LinearGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ccffff" />
        <stop offset="100%" stop-color="#ffffff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="OrangeGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#fa9e2fff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="BlueGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#2958acff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="GreenGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#378f5cff" />
    </linearGradient>
    </listOfGradientDefinitions>
    <listOfStyles>
    <style idList="glyph0 glyph2 glyph14 glyph34 ">
        <g stroke="Color_2" stroke-width="5" fill="yelloComp"  />               
    </style>
    <style idList="glyph1">
        <g stroke="Color_2" stroke-width="5" fill="grayComp"  />                
    </style>
    </listOfStyles>
</renderInformation></extension>
  </map>
</sbgn>

Read SBGN extension¶

We now read the map extension information written in the example above.

In [7]:

# map is a container for the glyphs and arcs
map: Map = sbgn.map[0]

extension: Sbgnbase.Extension = map.extension
if extension:
    console.print(extension)
    console.print(str(extension.any_element[0]))

# map is a container for the glyphs and arcs map: Map = sbgn.map[0] extension: Sbgnbase.Extension = map.extension if extension: console.print(extension) console.print(str(extension.any_element[0]))

Extension(
    any_element=[
        '<renderInformation id="example" programName="SBML Layout" 
programVersion="3.0"\n xmlns="http://projects.eml.org/bcb/sbml/render/level2">\n
<listOfColorDefinitions>\n    <colorDefinition id="yelloComp" value="#ffffccff" 
/>\n    <colorDefinition id="grayComp" value="#e0e0e0ff" />\n    
<colorDefinition id="orange" value="#fa9e2fff" />\n    <colorDefinition 
id="blue" value="#2958acff" />\n    <colorDefinition id="green" 
value="#378f5cff" />\n    <colorDefinition id="Color_0" value="#969696" />\n    
<colorDefinition id="Color_1" value="#ff9900" />\n    <colorDefinition 
id="Color_2" value="#000000" />\t\t\t\n    </listOfColorDefinitions>\n    
<listOfGradientDefinitions>\n    <linearGradient x1="0%" y1="0%" z1="0%" 
x2="100%" y2="0%" z2="100%" id="LinearGradient_0" spreadMethod="reflect">\n     
<stop offset="0%" stop-color="#ccffff" />\n        <stop offset="100%" 
stop-color="#ffffff" />\n    </linearGradient>\n    <linearGradient x1="0%" 
y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" id="OrangeGradient_0" 
spreadMethod="reflect">\n        <stop offset="0%" stop-color="#ffffff" />\n    
<stop offset="100%" stop-color="#fa9e2fff" />\n    </linearGradient>\n    
<linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="BlueGradient_0" spreadMethod="reflect">\n        <stop offset="0%" 
stop-color="#ffffff" />\n        <stop offset="100%" stop-color="#2958acff" />\n
</linearGradient>\n    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%"
z2="100%" id="GreenGradient_0" spreadMethod="reflect">\n        <stop 
offset="0%" stop-color="#ffffff" />\n        <stop offset="100%" 
stop-color="#378f5cff" />\n    </linearGradient>\n    
</listOfGradientDefinitions>\n    <listOfStyles>\n    <style idList="glyph0 
glyph2 glyph14 glyph34 ">\n        <g stroke="Color_2" stroke-width="5" 
fill="yelloComp"  />\t\t\t\n    </style>\n    <style idList="glyph1">\n        
<g stroke="Color_2" stroke-width="5" fill="grayComp"  />\t\t\t\n    </style>\n  
</listOfStyles>\n</renderInformation>'
    ]
)
<renderInformation id="example" programName="SBML Layout" programVersion="3.0"
 xmlns="http://projects.eml.org/bcb/sbml/render/level2">
    <listOfColorDefinitions>
    <colorDefinition id="yelloComp" value="#ffffccff" />
    <colorDefinition id="grayComp" value="#e0e0e0ff" />
    <colorDefinition id="orange" value="#fa9e2fff" />
    <colorDefinition id="blue" value="#2958acff" />
    <colorDefinition id="green" value="#378f5cff" />
    <colorDefinition id="Color_0" value="#969696" />
    <colorDefinition id="Color_1" value="#ff9900" />
    <colorDefinition id="Color_2" value="#000000" />                    
    </listOfColorDefinitions>
    <listOfGradientDefinitions>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="LinearGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ccffff" />
        <stop offset="100%" stop-color="#ffffff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="OrangeGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#fa9e2fff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="BlueGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#2958acff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="GreenGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#378f5cff" />
    </linearGradient>
    </listOfGradientDefinitions>
    <listOfStyles>
    <style idList="glyph0 glyph2 glyph14 glyph34 ">
        <g stroke="Color_2" stroke-width="5" fill="yelloComp"  />               
    </style>
    <style idList="glyph1">
        <g stroke="Color_2" stroke-width="5" fill="grayComp"  />                
    </style>
    </listOfStyles>
</renderInformation>

Read & Write SBGN¶

Helper functions for reading, writing and printing SBGN are provided in the utils module.

Write SBGN to string¶

The SBGN string can be generated from the sbgn object via

In [8]:

sbgn_str = write_sbgn_to_string(sbgn)
console.print(sbgn_str)

sbgn_str = write_sbgn_to_string(sbgn) console.print(sbgn_str)

<?xml version="1.0" encoding="UTF-8"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
  <map language="process description">
    <extension><renderInformation id="example" programName="SBML Layout" 
programVersion="3.0"
 xmlns="http://projects.eml.org/bcb/sbml/render/level2">
    <listOfColorDefinitions>
    <colorDefinition id="yelloComp" value="#ffffccff" />
    <colorDefinition id="grayComp" value="#e0e0e0ff" />
    <colorDefinition id="orange" value="#fa9e2fff" />
    <colorDefinition id="blue" value="#2958acff" />
    <colorDefinition id="green" value="#378f5cff" />
    <colorDefinition id="Color_0" value="#969696" />
    <colorDefinition id="Color_1" value="#ff9900" />
    <colorDefinition id="Color_2" value="#000000" />                    
    </listOfColorDefinitions>
    <listOfGradientDefinitions>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="LinearGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ccffff" />
        <stop offset="100%" stop-color="#ffffff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="OrangeGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#fa9e2fff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="BlueGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#2958acff" />
    </linearGradient>
    <linearGradient x1="0%" y1="0%" z1="0%" x2="100%" y2="0%" z2="100%" 
id="GreenGradient_0" spreadMethod="reflect">
        <stop offset="0%" stop-color="#ffffff" />
        <stop offset="100%" stop-color="#378f5cff" />
    </linearGradient>
    </listOfGradientDefinitions>
    <listOfStyles>
    <style idList="glyph0 glyph2 glyph14 glyph34 ">
        <g stroke="Color_2" stroke-width="5" fill="yelloComp"  />               
    </style>
    <style idList="glyph1">
        <g stroke="Color_2" stroke-width="5" fill="grayComp"  />                
    </style>
    </listOfStyles>
</renderInformation></extension>
  </map>
</sbgn>

Write SBGN to file¶

In [9]:

f_out = tempfile.NamedTemporaryFile(suffix=".sbgn", delete=False)

# write SBGN
write_sbgn_to_file(sbgn=sbgn, f=f_out.name)

f_out.close()
os.unlink(f_out.name)

f_out = tempfile.NamedTemporaryFile(suffix=".sbgn", delete=False) # write SBGN write_sbgn_to_file(sbgn=sbgn, f=f_out.name) f_out.close() os.unlink(f_out.name)

Read SBGN from file¶

In [10]:

sbgn = read_sbgn_from_file("glycolysis.sbgn")

sbgn = read_sbgn_from_file("glycolysis.sbgn")

Create SBGN images¶

SBGN images can be renderd via the render_sbgn function. This uses the service provided by Frank Bergmann available from http://sysbioapps.spdns.org/.

In [11]:

# Render SBGN
sbgn = read_sbgn_from_file("glycolysis.sbgn")
f_png = tempfile.NamedTemporaryFile(suffix=".png", delete=False)
render_sbgn(sbgn, image_file=f_png.name, 
                   file_format="png")
display(Image(f_png.name, width=500))
f_png.close()
os.unlink(f_png.name)

# Render SBGN sbgn = read_sbgn_from_file("glycolysis.sbgn") f_png = tempfile.NamedTemporaryFile(suffix=".png", delete=False) render_sbgn(sbgn, image_file=f_png.name, file_format="png") display(Image(f_png.name, width=500)) f_png.close() os.unlink(f_png.name)

SBGN rendered: /tmp/tmp6_2wijv0.png

Write special characters¶

SBGN supports UTF-8 and all characters can be used in the labels.

In [12]:

map = Map(
    language=MapLanguage.PROCESS_DESCRIPTION,
    bbox=Bbox(x=0, y=0, w=600, h=200),
)
sbgn = Sbgn(map=[map])

# create some glyphs
map.glyph = [
    # simple glyph
    Glyph(
        class_value=GlyphClass.MACROMOLECULE,
        id="glyph1",
        label=Label(text="α/β hydrolase"),
        bbox=Bbox(x=5, y=70, w=160, h=60),
    ),
    Glyph(
        class_value=GlyphClass.MACROMOLECULE,
        id="glyph2",
        label=Label(text="5′-3′; exoribonuclease"),
        bbox=Bbox(x=435, y=70, w=160, h=60),
    ),
    Glyph(
        class_value=GlyphClass.PROCESS,
        id="glyph3",
        bbox=Bbox(x=300, y=90, w=20, h=20),
        port=[
            Port(id="glyph3.1", x=285, y=100),
            Port(id="glyph3.2", x=315, y=100),
        ],
    ),
]
map.arc = [
    Arc(
        id="arc1",
        class_value=ArcClass.CONSUMPTION,
        source="glyph1",
        target="glyph3.1",
        start=Arc.Start(x=165, y=100),
        end=Arc.End(x=285, y=100),
    ),
    Arc(
        id="arc2",
        class_value=ArcClass.PRODUCTION,
        source="glyph3.2",
        target="glyph2",
        start=Arc.Start(x=315, y=100),
        end=Arc.End(x=435, y=100),
    ),
]
sbgn_to_jupyter_image(sbgn)

map = Map( language=MapLanguage.PROCESS_DESCRIPTION, bbox=Bbox(x=0, y=0, w=600, h=200), ) sbgn = Sbgn(map=[map]) # create some glyphs map.glyph = [ # simple glyph Glyph( class_value=GlyphClass.MACROMOLECULE, id="glyph1", label=Label(text="α/β hydrolase"), bbox=Bbox(x=5, y=70, w=160, h=60), ), Glyph( class_value=GlyphClass.MACROMOLECULE, id="glyph2", label=Label(text="5′-3′; exoribonuclease"), bbox=Bbox(x=435, y=70, w=160, h=60), ), Glyph( class_value=GlyphClass.PROCESS, id="glyph3", bbox=Bbox(x=300, y=90, w=20, h=20), port=[ Port(id="glyph3.1", x=285, y=100), Port(id="glyph3.2", x=315, y=100), ], ), ] map.arc = [ Arc( id="arc1", class_value=ArcClass.CONSUMPTION, source="glyph1", target="glyph3.1", start=Arc.Start(x=165, y=100), end=Arc.End(x=285, y=100), ), Arc( id="arc2", class_value=ArcClass.PRODUCTION, source="glyph3.2", target="glyph2", start=Arc.Start(x=315, y=100), end=Arc.End(x=435, y=100), ), ] sbgn_to_jupyter_image(sbgn)

SBGN rendered: /tmp/tmpnzuayi1d.png

Render information¶

Render information can be encoded directly with the libsbgnpy library. The following example shows how to do this.

In [13]:

map = Map(language=MapLanguage.PROCESS_DESCRIPTION)
sbgn = Sbgn(map=[map])

# create glyph
map.glyph = [
    Glyph(
        id="glyph1",
        class_value=GlyphClass.MACROMOLECULE,
        label=Label(text="INSR"),
        bbox=Bbox(x=100, y=100, w=80, h=40),
    ),
    Glyph(
        id="glyph2",
        class_value=GlyphClass.SIMPLE_CHEMICAL,
        label=Label(text="ATP"),
        bbox=Bbox(x=200, y=100, w=80, h=40),
    ),
    Glyph(
        id="glyph3",
        class_value=GlyphClass.SIMPLE_CHEMICAL,
        label=Label(text="glucose"),
        bbox=Bbox(x=300, y=100, w=80, h=40),
    ),
]

"""
Information to write:
<renderInformation id="example" programName="libsbgnpy" programVersion="1.0.0"
 xmlns="http://www.sbml.org/sbml/level3/version1/render/version1">
    <listOfColorDefinitions>
    <colorDefinition id="color0" value="#969696" />
    <colorDefinition id="color1" value="#ff9900" />
    </listOfColorDefinitions>

    <listOfGradientDefinitions>
        <linearGradient x1="0%" y1="0%" x2="100%" y2="0%" id="gradient0">
            <stop offset="0%" stop-color="#ccffff" />
            <stop offset="100%" stop-color="#ffffff" />
        </linearGradient>
    </listOfGradientDefinitions>

    <listOfStyles>
    <style idList="glyph1 glyph2">
        <g stroke="color0" stroke-width="5" fill="color1" />
    </style>
    <style idList="glyph3">
        <g stroke="color1" stroke-width="2" fill="gradient0" />
    </style>
    </listOfStyles>
</renderInformation>
"""
render_info = RenderInformation(
    id="example",
    program_name="libsbgnpy",
    program_version="1.0.0",
    list_of_color_definitions=ListOfColorDefinitions(
        color_definition=[
            ColorDefinition(id="color_blue", value="#0000FFCC"),
            ColorDefinition(id="color_red", value="#FF0000CC"),
        ]
    ),
    list_of_gradient_definitions=ListOfGradientDefinitions(
        linear_gradient=[
            LinearGradient(
                id="bw_gradient",
                x1="0%",
                y1="0%",
                x2="100%",
                y2="0%",
                stop=[
                    LinearGradient.Stop(offset="0%", stop_color="#ffffff"),
                    LinearGradient.Stop(offset="100%", stop_color="#000000"),
                ],
            )
        ]
    ),
    list_of_styles=ListOfStyles(
        [
            Style(
                id_list="glyph1",
                g=G(stroke="color_blue", stroke_width=5, fill="color_red"),
            ),
            Style(
                id_list="glyph2",
                g=G(stroke="color_red", stroke_width=5, fill="color_blue"),
            ),
            Style(
                id_list="glyph3",
                g=G(stroke="color1", stroke_width=2, fill="bw_gradient"),
            ),
        ]
    ),
)
# set extension
xml_str = write_render_to_string(render_info=render_info)
console.print(xml_str)
map.extension = Sbgn.Extension([xml_str])
# console.print(write_sbgn_to_string(sbgn))
sbgn_to_jupyter_image(sbgn)

map = Map(language=MapLanguage.PROCESS_DESCRIPTION) sbgn = Sbgn(map=[map]) # create glyph map.glyph = [ Glyph( id="glyph1", class_value=GlyphClass.MACROMOLECULE, label=Label(text="INSR"), bbox=Bbox(x=100, y=100, w=80, h=40), ), Glyph( id="glyph2", class_value=GlyphClass.SIMPLE_CHEMICAL, label=Label(text="ATP"), bbox=Bbox(x=200, y=100, w=80, h=40), ), Glyph( id="glyph3", class_value=GlyphClass.SIMPLE_CHEMICAL, label=Label(text="glucose"), bbox=Bbox(x=300, y=100, w=80, h=40), ), ] """ Information to write: """ render_info = RenderInformation( id="example", program_name="libsbgnpy", program_version="1.0.0", list_of_color_definitions=ListOfColorDefinitions( color_definition=[ ColorDefinition(id="color_blue", value="#0000FFCC"), ColorDefinition(id="color_red", value="#FF0000CC"), ] ), list_of_gradient_definitions=ListOfGradientDefinitions( linear_gradient=[ LinearGradient( id="bw_gradient", x1="0%", y1="0%", x2="100%", y2="0%", stop=[ LinearGradient.Stop(offset="0%", stop_color="#ffffff"), LinearGradient.Stop(offset="100%", stop_color="#000000"), ], ) ] ), list_of_styles=ListOfStyles( [ Style( id_list="glyph1", g=G(stroke="color_blue", stroke_width=5, fill="color_red"), ), Style( id_list="glyph2", g=G(stroke="color_red", stroke_width=5, fill="color_blue"), ), Style( id_list="glyph3", g=G(stroke="color1", stroke_width=2, fill="bw_gradient"), ), ] ), ) # set extension xml_str = write_render_to_string(render_info=render_info) console.print(xml_str) map.extension = Sbgn.Extension([xml_str]) # console.print(write_sbgn_to_string(sbgn)) sbgn_to_jupyter_image(sbgn)

<renderInformation 
xmlns="http://www.sbml.org/sbml/level3/version1/render/version1" id="example" 
programName="libsbgnpy" programVersion="1.0.0">
  <listOfColorDefinitions>
    <colorDefinition id="color_blue" value="#0000FFCC"/>
    <colorDefinition id="color_red" value="#FF0000CC"/>
  </listOfColorDefinitions>
  <listOfGradientDefinitions>
    <linearGradient id="bw_gradient" x1="0%" x2="100%" y1="0%" y2="0%">
      <stop offset="0%" stop-color="#ffffff"/>
      <stop offset="100%" stop-color="#000000"/>
    </linearGradient>
  </listOfGradientDefinitions>
  <listOfStyles>
    <style idList="glyph1">
      <g stroke="color_blue" stroke-width="5" fill="color_red"/>
    </style>
    <style idList="glyph2">
      <g stroke="color_red" stroke-width="5" fill="color_blue"/>
    </style>
    <style idList="glyph3">
      <g stroke="color1" stroke-width="2" fill="bw_gradient"/>
    </style>
  </listOfStyles>
</renderInformation>

SBGN rendered: /tmp/tmph8nnu87y.png

Clone marker example¶

Clone markers can be set via the Glyph.Clone() on glyphs. In the example we are adding clone markers to NAD+, NADH and H+ as cofactors.

In [14]:

"""Clone marker example."""
from libsbgnpy import *
# create new map
map = Map(
    language=MapLanguage.PROCESS_DESCRIPTION,
    bbox=Bbox(x=0, y=0, w=363, h=253),
)
# add map to new sbgn
sbgn = Sbgn(map=[map])

# create glyphs and add to map
map.glyph.extend(
    [
        Glyph(
            class_value=GlyphClass.SIMPLE_CHEMICAL,
            id="glyph1",
            label=Label(text="Ethanol"),
            bbox=Bbox(x=40, y=120, w=60, h=60),
        ),
        Glyph(
            class_value=GlyphClass.SIMPLE_CHEMICAL,
            id="glyph_ethanal",
            label=Label(text="Ethanal"),
            bbox=Bbox(x=220, y=110, w=60, h=60),
        ),
        Glyph(
            class_value=GlyphClass.MACROMOLECULE,
            id="glyph_adh1",
            label=Label(text="ADH1"),
            bbox=Bbox(x=106, y=20, w=108, h=60),
        ),
        Glyph(
            class_value=GlyphClass.SIMPLE_CHEMICAL,
            id="glyph_h",
            label=Label(text="H+"),
            bbox=Bbox(x=220, y=190, w=60, h=60),
            clone=Glyph.Clone(),  # clone marker
        ),
        Glyph(
            class_value=GlyphClass.SIMPLE_CHEMICAL,
            id="glyph_nad",
            label=Label(text="NAD+"),
            bbox=Bbox(x=40, y=190, w=60, h=60),
            clone=Glyph.Clone(),  # clone marker
        ),
        Glyph(
            class_value=GlyphClass.SIMPLE_CHEMICAL,
            id="glyph_nadh",
            label=Label(text="NADH"),
            bbox=Bbox(x=300, y=150, w=60, h=60),
            clone=Glyph.Clone(),  # clone marker
        ),
        # glyph with ports (process)
        Glyph(
            class_value=GlyphClass.PROCESS,
            id="pn1",
            orientation=GlyphOrientation.HORIZONTAL,
            bbox=Bbox(x=148, y=168, w=24, h=24),
            port=[
                Port(x=136, y=180, id="pn1.1"),
                Port(x=184, y=180, id="pn1.2"),
            ],
        ),
    ]
)

# arcs
# create arcs and set the start and end points
map.arc.extend(
    [
        Arc(
            class_value=ArcClass.CONSUMPTION,
            source="glyph1",
            target="pn1.1",
            id="a01",
            start=Arc.Start(x=98, y=160),
            end=Arc.End(x=136, y=180),
        ),
        Arc(
            class_value=ArcClass.PRODUCTION,
            source="pn1.2",
            target="glyph_nadh",
            id="a02",
            start=Arc.Start(x=184, y=180),
            end=Arc.End(x=300, y=180),
        ),
        Arc(
            class_value=ArcClass.CATALYSIS,
            source="glyph_adh1",
            target="pn1",
            id="a03",
            start=Arc.Start(x=160, y=80),
            end=Arc.End(x=160, y=168),
        ),
        Arc(
            class_value=ArcClass.PRODUCTION,
            source="pn1.2",
            target="glyph_h",
            id="a04",
            start=Arc.Start(x=184, y=180),
            end=Arc.End(x=224, y=202),
        ),
        Arc(
            class_value=ArcClass.PRODUCTION,
            source="pn1.2",
            target="glyph_ethanal",
            id="a05",
            start=Arc.Start(x=184, y=180),
            end=Arc.End(x=224, y=154),
        ),
        Arc(
            class_value=ArcClass.CONSUMPTION,
            source="glyph_nad",
            target="pn1.1",
            id="a06",
            start=Arc.Start(x=95, y=202),
            end=Arc.End(x=136, y=180),
        ),
    ]
)

f_png = tempfile.NamedTemporaryFile(suffix=".png", delete=False)
render_sbgn(sbgn, image_file=f_png.name, 
                   file_format="png")
display(Image(f_png.name, width=500))
f_png.close()
os.unlink(f_png.name)

"""Clone marker example.""" from libsbgnpy import * # create new map map = Map( language=MapLanguage.PROCESS_DESCRIPTION, bbox=Bbox(x=0, y=0, w=363, h=253), ) # add map to new sbgn sbgn = Sbgn(map=[map]) # create glyphs and add to map map.glyph.extend( [ Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph1", label=Label(text="Ethanol"), bbox=Bbox(x=40, y=120, w=60, h=60), ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_ethanal", label=Label(text="Ethanal"), bbox=Bbox(x=220, y=110, w=60, h=60), ), Glyph( class_value=GlyphClass.MACROMOLECULE, id="glyph_adh1", label=Label(text="ADH1"), bbox=Bbox(x=106, y=20, w=108, h=60), ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_h", label=Label(text="H+"), bbox=Bbox(x=220, y=190, w=60, h=60), clone=Glyph.Clone(), # clone marker ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nad", label=Label(text="NAD+"), bbox=Bbox(x=40, y=190, w=60, h=60), clone=Glyph.Clone(), # clone marker ), Glyph( class_value=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nadh", label=Label(text="NADH"), bbox=Bbox(x=300, y=150, w=60, h=60), clone=Glyph.Clone(), # clone marker ), # glyph with ports (process) Glyph( class_value=GlyphClass.PROCESS, id="pn1", orientation=GlyphOrientation.HORIZONTAL, bbox=Bbox(x=148, y=168, w=24, h=24), port=[ Port(x=136, y=180, id="pn1.1"), Port(x=184, y=180, id="pn1.2"), ], ), ] ) # arcs # create arcs and set the start and end points map.arc.extend( [ Arc( class_value=ArcClass.CONSUMPTION, source="glyph1", target="pn1.1", id="a01", start=Arc.Start(x=98, y=160), end=Arc.End(x=136, y=180), ), Arc( class_value=ArcClass.PRODUCTION, source="pn1.2", target="glyph_nadh", id="a02", start=Arc.Start(x=184, y=180), end=Arc.End(x=300, y=180), ), Arc( class_value=ArcClass.CATALYSIS, source="glyph_adh1", target="pn1", id="a03", start=Arc.Start(x=160, y=80), end=Arc.End(x=160, y=168), ), Arc( class_value=ArcClass.PRODUCTION, source="pn1.2", target="glyph_h", id="a04", start=Arc.Start(x=184, y=180), end=Arc.End(x=224, y=202), ), Arc( class_value=ArcClass.PRODUCTION, source="pn1.2", target="glyph_ethanal", id="a05", start=Arc.Start(x=184, y=180), end=Arc.End(x=224, y=154), ), Arc( class_value=ArcClass.CONSUMPTION, source="glyph_nad", target="pn1.1", id="a06", start=Arc.Start(x=95, y=202), end=Arc.End(x=136, y=180), ), ] ) f_png = tempfile.NamedTemporaryFile(suffix=".png", delete=False) render_sbgn(sbgn, image_file=f_png.name, file_format="png") display(Image(f_png.name, width=500)) f_png.close() os.unlink(f_png.name)

SBGN rendered: /tmp/tmpyd1lj3iy.png