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sbgn

Python bindings of the SBGN-ML schema.

Generated from libsbgnpy/schema/SBGN.xsd with xsdata, see libsbgnpy/schema/README.md; do not edit by hand. The classes mirror the schema, so the SBGN specifications are the reference for what an element means, and the docstrings are the documentation of the schema.

An SBGN document is an Sbgn holding Map objects, a map holds Glyph and Arc objects, and every element inherits from Sbgnbase, which carries the notes and the extension. See the user guide for how they are used.

Sbgnbase dataclass 

Sbgnbase(*, notes=None, extension=None)

The SBGNBase type is the base type of all main components in SBGN.

It supports attaching notes and extensions to components, with metadata and annotations encoded in the extension element. .

Notes dataclass 

Notes(*, w3_org_1999_xhtml_element=list())

The notes element stores notes. .

Extension dataclass 

Extension(*, any_element=list())

The extension element stores extension information like render information, metadata or annotations. .

Bbox dataclass 

Bbox(*, notes=None, extension=None, x, y, w, h)

Bases: Sbgnbase

The bbox element describes a rectangle.

This rectangle is defined by: PointAttributes corresponding to the 2D coordinates of the top left corner, width and height attributes. The rectangle corresponds to the outer bounding box of a shape. The shape itself can be irregular (for instance in the case of some compartments). In the case of process nodes, the bounding box only concerns the central glyph (square, or circle), the input/output ports are not included, and neither are the lines connecting them to the central glyph. A bbox is required for all glyphs, and is optional for labels. .

Point dataclass 

Point(*, notes=None, extension=None, x, y)

Bases: Sbgnbase

The point element is characterized by PointAttributes, which describe absolute 2D cartesian coordinates.

Namely: x (horizontal, from left to right), y (vertical, from top to bottom). The origin is located in the top-left corner of the map. There is no unit: proportions must be preserved, but the maps can be drawn at any scale. In the test files examples, to obtain a drawing similar to the reference *.png file, values in the corresponding *.sbgn file should be read as pixels. .

Port dataclass 

Port(*, notes=None, extension=None, x, y, id)

Bases: Sbgnbase

The port element describes an anchor point to which arcs can refer as a source or target.

It consists of: absolute 2D cartesian coordinates (PointAttribute), a unique id attribute. Two port elements are required for process nodes. They represent the extremity of the two "arms" which protrude on both sides of the core of the glyph (= square or circle shape). Other glyphs don't need ports (but can use them if desired). .

:ivar x: :ivar y: :ivar id: The xsd:ID type is an alphanumeric identifier, starting with a letter. Port IDs often contain the ID of their glyph, followed by a local port number (e.g. glyph4.1, glyph4.2, etc.) However, this style convention is not mandatory, and IDs should never be interpreted as carrying any meaning.

Label dataclass 

Label(*, notes=None, extension=None, bbox=None, text)

Bases: Sbgnbase

The label element describes the text accompanying a glyph.

The text attribute is mandatory. Its position can be specified by a bbox (optional). Tools are free to display the text in any style (font, font-size, etc.) .

:ivar bbox: :ivar text: Multi- line labels are allowed. Line breaks are encoded as 
 as specified by the XML standard.

Glyph dataclass 

Glyph(
    *,
    notes=None,
    extension=None,
    label=None,
    state=None,
    clone=None,
    callout=None,
    entity=None,
    bbox,
    glyph=list(),
    port=list(),
    class_value,
    orientation=HORIZONTAL,
    id,
    compartment_ref=None,
    compartment_order=None,
    map_ref=None,
    tag_ref=None,
)

Bases: Sbgnbase

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. .

:ivar label: :ivar state: The state element should only be used for state variables. It replaces the label element used for other glyphs. It describes the text to be drawn inside the state variable. A state must have a value, a variable, or both. If it has both, they are rendered as a concatenated string with @ in between. :ivar clone: The clone element (which is optional) means the glyph carries a clone marker. It can contain an optional label. :ivar callout: The callout element is only used for glyphs with class annotation. It contains the coordinate of the point where the annotation points to, as well as a reference to the element that is pointed to. :ivar entity: The entity is only used in activity flow diagrams. It can only be used on a unit of information glyph on a biological activity glyph, where it is compulsory. It is used to indicate the shape of this unit of information. :ivar bbox: The bbox element is mandatory and unique: exactly one per glyph. It defines the outer bounding box of the glyph. The actual shape of the glyph can be irregular (for instance in the case of some compartments) In the case of process nodes, the bounding box only concerns the central glyph (square, or circle): the input/output ports are not included, and neither are the lines connecting them to the central glyph. :ivar glyph: A glyph element can contain any number of children glyph elements. In practice, this should only happen in the following cases: a compartment with unit of information children, an EPN with states variables and/or unit of information children, a complex, with state variables, unit of info, and/or EPN children. :ivar port: :ivar class_value: 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 :ivar 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. :ivar 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") :ivar compartment_ref: 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. For AF, this should be used only for Activity Nodes. 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. :ivar compartment_order: 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. :ivar map_ref: This attribute is only used on a submap glyph. It is required. Reference to the ID of the map which provides the content of the submap. If no map is available providing the content of the submap an omitted process should be used instead of the submap. Submaps are only used in PD and AF, and thus this attribute as well. :ivar tag_ref: This attribute is only used on a terminal glyph. It is required. Reference to the ID of a tag on a map providing the content of a submap. The terminal glyph is defined as sub-glyph of this submap. Submaps and therefore terminals are only used in PD and AF, and thus this attribute as well.

State dataclass 

State(*, value=None, variable=None)

:ivar value: The value attribute represents the state of the variable. It can be: either from a predefined set of string (P, S, etc.) which correspond to specific SBO terms (cf. SBGN specs), or any arbitrary string. :ivar variable: The variable attribute describes the site where the modification described by the value attribute occurs. It is: optional when there is only one state variable on the parent EPN, required when there is more than one state variable the parent EPN.

Arc dataclass 

Arc(
    *,
    notes=None,
    extension=None,
    glyph=list(),
    port=list(),
    start,
    next=list(),
    end,
    class_value,
    id,
    source,
    target,
)

Bases: Sbgnbase

The arc element describes an SBGN arc between two SBGN nodes.

It contains: For PD: an optional stoichiometry marker, For ER: an optional cardinality marker, zero or more ports (influence targets), and zero or more outcomes, a mandatory source and target (glyph or port), a geometric description of its whole path, from start to end. This path can involve any number of straight lines or quadratic/cubic Bezier curves. .

:ivar glyph: In PD, an arc can contain a single optional sub-glyph. This glyph must be a stoichiometry marker (square with a numeric label) In ER, an arc can contain several sub-glyphs. This can be zero or one cardinality glyphs (e.g. cis or trans), plus zero to many outcome glyphs (black dot) :ivar port: Ports are only allowed in ER. :ivar start: The start element represents the starting point of the arc's path. It is unique and mandatory. :ivar next: The next element represents the next point in the arc's path. Between the start and the end of the path, there can be any number (even zero) of next elements (intermediate points). They are read consecutively: start, next, next, ..., next, end. When the path from the previous point to this point is not straight, this element also contains a list of control points (between 1 and 2) describing a Bezier curve (quadratic if 1 control point, cubic if 2) between the previous point and this point. :ivar end: The end element represents the ending point of the arc's path. It is unique and mandatory. When the path from the previous point to this point is not straight, this element also contains a list of control points (between 1 and 2) describing a Bezier curve (quadratic if 1 control point, cubic if 2) between the previous point and this point. :ivar class_value: The class attribute defines the semantic of the arc, and influences: the way that arc should be rendered, the overall syntactic validity of the map. The various classes encompass all possible types of SBGN arcs: production and consumption arcs, all types of modification arcs, logic arcs, equivalence arcs. To express a reversible reaction, use production arcs on both sides of the Process Node. :ivar id: The xsd:ID type is an alphanumeric identifier, starting with a letter. :ivar source: The source attribute can refer: either to the id of a glyph, or to the id of a port on a glyph. :ivar target: The target attribute can refer: either to the id of a glyph, or to the id of a port on a glyph.

Arcgroup dataclass 

Arcgroup(
    *,
    notes=None,
    extension=None,
    glyph=list(),
    arc=list(),
    class_value,
)

Bases: Sbgnbase

The arc group describes a set of arcs and glyphs that together have a relation.

For example For ER: interaction arcs around an interaction glyph, ... Note that, in spite of the name, an arcgroup contains both arcs and glyphs. .

:ivar glyph: An arcgroup can contain glyphs. For example, in an interaction arcgroup, there must be one interaction glyph. :ivar arc: An arcgroup can have multiple arcs. They are all assumed to form a single hyperarc-like structure. :ivar class_value: The class attribute defines the semantic of the arcgroup.

Map dataclass 

Map(
    *,
    notes=None,
    extension=None,
    bbox=None,
    glyph=list(),
    arc=list(),
    arcgroup=list(),
    version=None,
    language=None,
    id,
)

Bases: Sbgnbase

The map element describes a single SBGN PD map.

It contains a list of glyph elements and a list of arc elements. These lists can be of any size (possibly empty). .

:ivar bbox: The bbox element on a map is not mandatory, it allows the application to define a canvas, and at the same time define a whitespace margin around the glyphs. If a bbox is defined on a map, all glyphs and arcs must be inside this bbox, otherwise they could be clipped off by applications. :ivar glyph: :ivar arc: :ivar arcgroup: :ivar version: Version of the map: URI identifier that gives the language, level and version defined by SBGN. Different languages/levels/versions have different restrictions on the usage of sub-elements (that are not encoded in this schema but must be validated with an external validator) :ivar language: Language of the map: one of three sublanguages defined by SBGN. Different languages have different restrictions on the usage of sub-elements (that are not encoded in this schema but must be validated with an external validator) :ivar id: The xsd:ID type is an alphanumeric identifier, starting with a letter. It is recommended to generate meaningless IDs (e.g. "map1234") and avoid IDs with a meaning (e.g. "MAPK cascade")

Sbgn dataclass 

Sbgn(*, notes=None, extension=None, map=list())

Bases: Sbgnbase

The sbgn element is the root of any SBGNML document.

Currently each document must contain exactly one map element. .