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libGPML is a library for reading, writing, manipulation, and conversion of files and data streams in the GPML (Graphical Pathway Markup Language) format.
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Centering (position) and dimension properties for an object.
The middle of an object in the x-direction.
The middle of an object in the y-direction.
The pixel value for the x-dimensional length of an object.
The pixel value for the y-dimensional length of an object.
Common font properties.
The hexadecimal color of text, default black.
The name of the collection of characters with a similar design, e.g. Arial (default)...
The thickness of the font used, e.g Normal (default) or Bold. A bold font has more weight.
The typographic style for Italic or Normal (default).
The typographic style for Underline or Normal (default).
The typographic style for Strikethru or Normal (default).
The point value for the size of the font.
The horizontal alignment of displayed text: Left, Center (default), or Right.
The vertical alignment of displayed text: Top, Middle (default), or Bottom.
Visual appearance of a two-dimensional object.
The hexadecimal color of a border, default black.
The visual appearance of a line, e.g. Solid (default), Dashed...
The pixel value for the width of a given border.
The hexadecimal color contained within the line or border of an object, default white.
The visual appearance of a two dimensional object, e.g. Rectangle (default), Nucleus...
The order of an object along the z-axis.
A float value (rotation in radians).
Visual appearance of a line.
The hexadecimal color of a line, default black.
The visual appearance of a line, e.g. Solid (default), Dashed...
The pixel value for the width of a given line.
Specifies a set of rules to govern layout of lines, e.g. Straight (default), Elbow...
The order of an object along the z-axis.
Style type for a line or border, e.g. Solid, Dashed...
Dimension for width or height. Cannot be a negative value.
One or more comments, properties, or references.
Descriptions or arbitrary notes for an object.
The source for a comment.
Key-value pair information for an object.
The key of a key-value pair.
The value of a key-value pair.
Reference to a gpml:Annotation.
Reference to a gpml:Citation.
Reference to a gpml:Evidence.
A graph diagram representing a biological process as a set of interactions and relationships among genes, proteins, metabolites, and other factors in the context of cellular compartments, tissues and organisms.
Textual description of the pathway.
The people who created or edited a pathway.
Reference to a database entry for an author, e.g. ORCID.
The name of an author.
The username of an author.
The authorship order of an author.
The width of a pathway.
The height of a pathway.
The hexadecimal color for the background of a pathway, default white.
The title of a pathway.
The scientific name of the species being described by a pathway, e.g. Homo sapiens...
The source of a pathway, e.g. WikiPathways, KEGG...
The version of a pathway.
The license of a pathway.
List of Data nodes. A data node denotes a biological entity that forms a node in a pathway.
Denotes a biological entity that forms a node in a pathway.
The states linked to this data node.
The internal gpml unique identifier for an element.
The text label for a data node.
The data node type, e.g. Undefined (default), GeneProduct, Metabolite, Alias...
When a pathway element is part of a gpml:Group, groupRef refers to the elementId of the parent group.
An aliasRef indicates a child/parent relationship between objects. A DataNode can have type "Alias" and refer to a gpml:Group.
List of States. A state represents a specific state of the biological entity (e.g. phosphorylation, genetic variants, etc). A state is linked to a data node.
The state of a biological entity (e.g. Undefined (default), Protein modification...) linked to a parent gpml:DataNode.
The relative x coordinates on the parent gpml:DataNode, where 0,0 is at the center and 1,1 is at the bottom-right corner of the data node.
The relative y coordinates on the parent gpml:DataNode, where 0,0 is at the center and 1,1 is at the bottom-right corner of the data node.
The pixel value for the x-dimensional length of a state.
The pixel value for the y-dimensional length of a state.
The internal gpml unique identifier for an element.
The text label for a state.
The state type, e.g. Undefined (default), Protein modification, Genetic variant...
List of Interactions. An interaction represents the biological relation between entities. An Xref can be specified for Interactions (in contrast to GraphicalLines).
Interactions represent biological relation between entities. An Xref can be specified for Interactions (in contrast to GraphicalLines).
The internal gpml unique identifier for an element.
When a pathway element is part of a gpml:Group, groupRef refers to the elementId of the parent group.
List of Graphical lines. A graphical line is a visual annotation without semantic meaning. It is often used to partition space or connect other pathway elements. An Xref cannot be specified for GraphicalLines (in contrast to Interactions).
Graphical line are visual annotations without semantic meaning. An Xref cannot be specified for GraphicalLines (in contrast to Interactions).
The internal gpml unique identifier for an element.
When a pathway element is part of a gpml:Group, groupRef refers to the elementId of the parent group.
List of Labels. A label is a text field which can be used to annotate any aspect of a pathway.
A text field which can be used to annotate any aspect of a pathway.
The internal gpml unique identifier for an element.
The text for a label.
When a pathway element is part of a gpml:Group, groupRef refers to the elementId of the parent group.
The hyperlink for a reference to an url.
List of Shapes. A shape is a visual annotation or graphical element.
A visual annotation or graphical element.
The internal gpml unique identifier for an element.
The text label for a shape.
When a pathway element is part of a gpml:Group, groupRef refers to the elementId of the parent group.
List of Groups. A group is a collection of structurally or functionally similar or related pathway elements.
A collection of structurally or functionally similar or related pathway elements.
The internal gpml unique identifier for an element.
The text label for a group.
The group type, e.g. Group (default), Complex, Pathway...
When a pathway element is part of a gpml:Group, groupRef refers to the elementId of the parent group.
List of Annotations. An annotation is a reference with additional information, e.g. some Ontology.
An annotation reference, e.g. Ontology (e.g.subcellular location), Taxonomy (e.g.organism)...
Reference to a database entry. An Annotation can have an Xref.
Link to a web address. An Annotation can have an Url.
The internal gpml unique identifier for an element.
The name, term, or text of an annotation. An Annotation must have a value and type.
The type of an annotation, e.g. Undefined (default), Ontology, Taxonomy...
Reference to a gpml:Annotation.
Reference to a citation for an annotation.
Reference to an evidence for an annotation.
A elementRef indicates a child/parent relationship between objects. The elementRef of the child refers to the elementId of the parent.
List of Citations. A citation is a reference to a source of information.
A literature reference, citation, or work.
Reference to a database entry. A Citation must have either an Xref or Url, or both.
Link to a web address. A Citation must have either an Xref or Url, or both.
The internal gpml unique identifier for an element.
Reference to a gpml:Citation.
Reference to an annotation for a citation.
A elementRef indicates a child/parent relationship between objects. The elementRef of the child refers to the elementId of the parent.
List of Evidence. An evidence provides information on type of scientific evidence.
Evidence in biological research.
Reference to a database entry. An Evidence must have an Xref.
Link to a web address. An Evidence can have an Url.
The internal gpml unique identifier for an element.
The name, term, or text of an evidence.
Reference to a gpml:Evidence.
A elementRef indicates a child/parent relationship between objects. The elementRef of the child refers to the elementId of the parent.
Reference to a database entry.
The identifier of a PublicationXref or Xref object.
Specifies the datasource prefix (see BridgeDb DataSource Ontology at https://github.com/bridgedb/datasources/blob/main/datasources.tsv) for the identifier provided as an Xref.
Link to a web address.
The link to a web address.
A location in 2-dimensional space defined by x and y coordinates.
The internal gpml unique identifier for an element.
The glyph at the ends of lines and interactions.
The x coordinate of a point.
The y coordinate of a point.
An elementRef indicates a child/parent relationship between objects. The elementRef of the child refers to the elementId of the parent.
When a point is linked to an object, relX and relY are the relative coordinates on the object, where 0,0 is at the center and 1,1 at the bottom-right corner of the object.
When a point is linked to an object, relX and relY are the relative coordinates on the object, where 0,0 is at the center and 1,1 at the bottom-right corner of the object.
A connection point on a graphical line or an interaction, where another graphical line or interaction can be connected.
Proportional distance of an anchor along the line it belongs to, between 0 and 1.
The visual representation of an anchor, e.g. Square (default), Circle, None...
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