http://sbgn.org/libsbgn/0.2
element glyph

Documentation

The glyph element is:

• either a stand-alone, high-level SBGN glyph (EPN, PN, compartment, etc),
• or a sub-glyph (state variable, unit of information, inside of a complex, ...)

In the first case, it appears directly in the glyph list of the map. In the second case, it is a child of another glyph element.

The text inside a glyph is described:

• either by a label element (optional) [process nodes can't have one],
• or by a state element (optional) [for state variables only].

Properties

This component is not nillable.

Model

<glyph
  class = xsd:string
  compartmentOrder = xsd:float
  compartmentRef = xsd:IDREF
  id = xsd:ID
  orientation = xsd:string : horizontal>
(notes, extension ) ((label? | state) , clone, callout, entity, bbox, glyph*, port* )
</glyph>

class

The class attribute defines the semantic of the glyph, and influences: the way that glyph should be rendered, the overall syntactic validity of the map. The various classes encompass the following PD SBGN elements: Entity Pool Nodes (EPN), Process Nodes (PN), Logic Operator Nodes, Sub-glyphs on Nodes (State Variable, Unit of Information), Sub-glyphs on Arcs (Stoichiometry Label), Other glyphs (Compartment, Submap, Tag, Terminal). And the following ER SBGN elements Entities (Entity, Outcome) Other (Annotation, Phenotype) Auxiliary on glyps (Existence, Location) Auxiliary on arcs (Cardinality) Delay operator implicit xor

Type:

based on
with :

Use:

required

Form:

unqualified

compartmentOrder

The compartment order attribute can be used to define a drawing order for compartments. It enables tools to draw compartments in the correct order especially in the case of overlapping compartments. Compartments are only used in PD and AF, and thus this attribute as well. The attribute is of type float, the attribute value has not to be unique. Compartments with higher compartment order are drawn on top. The attribute is optional and should only be used for compartments.

Type:

xsd:float

Use:

optional

Form:

unqualified

compartmentRef

Reference to the ID of the compartment that this glyph is part of. Only use this if there is at least one explicit compartment present in the diagram. Compartments are only used in PD and AF, and thus this attribute as well. For PD, this should be used only for EPN's. In case there are no compartments, entities that can have a location, such as EPN's, are implicit member of an invisible compartment that encompasses the whole map. In that case, this attribute must be omitted.

Type:

xsd:IDREF

Use:

optional

Form:

unqualified

id

The xsd:ID type is an alphanumeric identifier, starting with a letter. It is recommended to generate meaningless IDs (e.g. "glyph1234") and avoid IDs with a meaning (e.g. "epn_ethanol")

Type:

xsd:ID

Use:

required

Form:

unqualified

orientation

The orientation attribute is used to express how to draw asymmetric glyphs. In PD, the orientation of Process Nodes is either horizontal or vertical. It refers to an (imaginary) line connecting the two in/out sides of the PN. In PD, the orientation of Tags and Terminals can be left, right, up or down. It refers to the direction the arrow side of the glyph is pointing at.

Type:

based on
with :

Default:

horizontal

Use:

optional

Form:

unqualified

Source

<xsd:element name="glyph">
  <xsd:complexType>
    <xsd:complexContent>
      <xsd:extension base="SBGNBase">
        <xsd:sequence>
          <xsd:choice>
            <xsd:element maxOccurs="1" minOccurs="0" ref="sbgn:label"/>
            <xsd:element maxOccurs="1" minOccurs="0" name="state">
              <xsd:complexType>
                <xsd:attribute name="value" type="xsd:string" use="optional">
                </xsd:attribute>
                <xsd:attribute name="variable" type="xsd:string" use="optional">
                </xsd:attribute>
              </xsd:complexType>
            </xsd:element>
          </xsd:choice>
          <xsd:element maxOccurs="1" minOccurs="0" name="clone">
            <xsd:complexType>
              <xsd:sequence>
                <xsd:element maxOccurs="1" minOccurs="0" ref="sbgn:label"/>
              </xsd:sequence>
            </xsd:complexType>
          </xsd:element>
          <xsd:element maxOccurs="1" minOccurs="0" name="callout">
            <xsd:complexType>
              <xsd:sequence>
                <xsd:element maxOccurs="1" minOccurs="1" ref="sbgn:point"/>
              </xsd:sequence>
              <xsd:attribute name="target" type="xsd:IDREF" use="optional"/>
            </xsd:complexType>
          </xsd:element>
          <xsd:element maxOccurs="1" minOccurs="0" name="entity">
            <xsd:complexType>
              <xsd:attribute name="name" use="required">
                <xsd:simpleType>
                  <xsd:restriction base="xsd:string">
                    <xsd:enumeration value="unspecified entity"/>
                    <xsd:enumeration value="simple chemical"/>
                    <xsd:enumeration value="macromolecule"/>
                    <xsd:enumeration value="nucleic acid feature"/>
                    <xsd:enumeration value="complex"/>
                  </xsd:restriction>
                </xsd:simpleType>
              </xsd:attribute>
            </xsd:complexType>
          </xsd:element>
          <xsd:element maxOccurs="1" minOccurs="1" ref="sbgn:bbox">
          </xsd:element>
          <xsd:element maxOccurs="unbounded" minOccurs="0" ref="sbgn:glyph">
          </xsd:element>
          <xsd:element maxOccurs="unbounded" minOccurs="0" ref="sbgn:port"/>
        </xsd:sequence>
        <xsd:attribute name="class" use="required">
          <xsd:simpleType>
            <xsd:restriction base="xsd:string">
              <xsd:enumeration value="unspecified entity"/>
              <xsd:enumeration value="simple chemical"/>
              <xsd:enumeration value="macromolecule"/>
              <xsd:enumeration value="nucleic acid feature"/>
              <xsd:enumeration value="simple chemical multimer"/>
              <xsd:enumeration value="macromolecule multimer"/>
              <xsd:enumeration value="nucleic acid feature multimer"/>
              <xsd:enumeration value="complex"/>
              <xsd:enumeration value="complex multimer"/>
              <xsd:enumeration value="source and sink"/>
              <xsd:enumeration value="perturbation"/>
              <xsd:enumeration value="biological activity"/>
              <xsd:enumeration value="perturbing agent"/>
              <xsd:enumeration value="compartment"/>
              <xsd:enumeration value="submap"/>
              <xsd:enumeration value="tag"/>
              <xsd:enumeration value="terminal"/>
              <xsd:enumeration value="process"/>
              <xsd:enumeration value="omitted process"/>
              <xsd:enumeration value="uncertain process"/>
              <xsd:enumeration value="association"/>
              <xsd:enumeration value="dissociation"/>
              <xsd:enumeration value="phenotype"/>
              <xsd:enumeration value="and"/>
              <xsd:enumeration value="or"/>
              <xsd:enumeration value="not"/>
              <xsd:enumeration value="state variable"/>
              <xsd:enumeration value="unit of information"/>
              <xsd:enumeration value="entity"/>
              <xsd:enumeration value="outcome"/>
              <xsd:enumeration value="interaction"/>
              <xsd:enumeration value="influence target"/>
              <xsd:enumeration value="annotation"/>
              <xsd:enumeration value="variable value"/>
              <xsd:enumeration value="implicit xor"/>
              <xsd:enumeration value="delay"/>
              <xsd:enumeration value="existence"/>
              <xsd:enumeration value="location"/>
              <xsd:enumeration value="cardinality"/>
              <xsd:enumeration value="observable"/>
            </xsd:restriction>
          </xsd:simpleType>
        </xsd:attribute>
        <xsd:attribute default="horizontal" name="orientation">
          <xsd:simpleType>
            <xsd:restriction base="xsd:string">
              <xsd:enumeration value="horizontal"/>
              <xsd:enumeration value="vertical"/>
              <xsd:enumeration value="left"/>
              <xsd:enumeration value="right"/>
              <xsd:enumeration value="up"/>
              <xsd:enumeration value="down"/>
            </xsd:restriction>
          </xsd:simpleType>
        </xsd:attribute>
        <xsd:attribute name="id" type="xsd:ID" use="required">
        </xsd:attribute>
        <xsd:attribute name="compartmentRef" type="xsd:IDREF" use="optional">
        </xsd:attribute>
        <xsd:attribute name="compartmentOrder" type="xsd:float" use="optional">
        </xsd:attribute>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>
</xsd:element>