WikiPathways GPML Vocabulary Boolean property for the existence of an Anchor on a given line or interaction. hasAnchor Boolean property for the existence of an Attribute class associated with a given object. hasAttribute Boolean property for the existence of a BioPax class associated with a given pathway. hasBiopax Boolean property for the existence of a Comment class associated with a given object. hasComment Boolean property for the existence of a DataNode in a given pathway. hasDataNode Boolean property for the existence of a GraphicalLine in a given pathway. hasGraphicalLine Boolean property for the existence of a Group in a given pathway. hasGroup Boolean property for the existence of an InfroBox in a given pathway. hasInfoBox Boolean property for the existence of an Interaction in a given pathway. hasInteraction Boolean property for the existence of a Label in a given pathway. hasLabel Boolean property for the existence of a Legend in a given pathway. hasLegend Boolean property for the existence of a Point in a given line or interaction. hasPoint Boolean property for the existence of a PublicationXref associated with a given object. hasPublicationXref Boolean property for the existence of a Shape in a given pathway. hasShape Boolean property for the existence of a State in a given pathway. hasState Boolean property for the existence of an Xref associated with a given object. hasXref Horizontal alignment of displayed text, e.g., Left, Center, Right. align Specifies the glyph at the ends of lines and interactions. arrowHead The person who created or edited the pathway in question. author Range minimum is zero. boardHeight Range minimum is zero. boardWidth Deprecated: Not in use. data-Source Deprecated: An electronic mail address. Used to reference the author or maintainer of a pathway prior to WikiPathways. email The hexidecimal color value used to paint the area of an object, not including its border. fillColor Deprecated: Not in use. fontDecoration The name of the set of printable text characters to be used for visualization. fontName The point value for the size of the font. fontSize Deprecated: Not in use. fontStrikethru The typographic style or font face applied to displayed text, e.g., Arial. fontStyle Thickness of the font used, e.g a bold font would have more weight. Used for DataNodes, Labels and Shapes. fontWeight A GraphRef indicates a "depends on" or child/parent relationship between two Pathway elements. The element with the GraphRef is the child, and the element referred to by the GraphRef is the parent. The parent's GraphId will be specified by the child's GraphRef. graphRef Uniquely identifies a gpml:Group in a gpml:Pathway. groupId The pixel value for the y-dimensional length of a given object. height The hyperlink optionally specified in a Label. href The date of the last modification of the pathway. last-Modified The license of a pathway. license The maintainer of the pathway. Currently not used in WP. maintainer The name of a pathway. name The scientific name (e.g., Homo sapiens) of the species being described by the pathway. organism RelX is the x-coordinate used when a point or state is linked to a another object - relative coordinate to the object that it is linked to (0,0 - center, 1,1 - bottom-right). relX RelY is the y-coordinate used when a point or state is linked to a another object - relative coordinate to the object that it is linked to (0,0 - center, 1,1 - bottom-right). relY The degree value of angular offset relative to the center of a given object. rotation Currently: Specifies the glyph (graphical representation) to use for GPML elements (DataNode, Label, Shape, State). Proposed: Expand it to also describe Anchors. It should replace the term currently used to specify the graphical representation of an Anchor. The current term is "Shape," which conflicts with the GPML element named "Shape." See details for term "Shape." shapeType The author, reference or category of a comment. Used to help parse pathway-level comments, e.g., the descriptions displayed at WikiPathways.org are comments with source="WikiPathways-description". source A free text field to describe the nature or category of a given state. stateType The type of Group, e.g., Complex. style TextLabel of an object (DataNode, Group, Label, Shape, State). textlabel Vertical alignment of displayed text, e.g., Top, Middle, Bottom. valign The version of a Pathway (currently not used in WP). version The pixel value for the x-dimensional length of a given object. width The x-coordinate of a point in the 2-dimensional plane in which a pathway is drawn. x The y-coordinate of a point in the 2-dimensional plane in which a pathway is drawn. y A connection point on a graphical line or an interaction, where another graphical line or interaction can be connected. Anchor Element used to specify key/value paired information for a given object. Attribute Element used to embed Biopax (namespace: http://www.biopax.org/release/biopax-level3.owl) content in a GPML document. Biopax Elements used to provide descriptions and arbitrary notes for a given object. Comment A visual annotation, often used to partition space or connect other annotation, e.g., Shapes. An Xref can not be specified for GraphicalLines (in contrast to Interactions). GraphicalLine Currently just a placeholder -- not used. InfoBox Defines the biochemical relationship between DataNodes or with Anchors on other Interactions. An Xref can be specified for Interactions (in contrast to GraphicalLines). Interaction Defines a literature reference. Refers to a BioPAX definition. PublicationXref Deprecated: Not in use. RequiresCurationAttention Reference to a database entry that matches the node in the pathway. It is a combination of an identifier of the entity and an identifier of the database in which the entity is found. Xref skos:ConceptScheme WikiPathways GPML Vocabulary Denotes a biological entity that forms a node in a pathway and has some biological meaning associated with it. For a list of the gpml:DataNode types supported at WikiPathways, see subclasses of wp:DataNode or the wpTypes vocabulary defined for use in applications.. DataNode A collection of structurally or functionally similar or related pathway elements. Group Label A text field which can be used to annotate any aspect of a pathway. An explanatory list of the colors used for visualizing data on the pathway. Not currently used. Legend 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. Pathway A location in 2-dimensional space defined by x and y coordinates. Point Shape can refer to two different things in GPML, both of which are associated with graphical elements. Shape A particular condition, mode or modification of an entity, e.g., phosphorylated, activated, mutated, SNP, etc. State Reuse of references defined by BioPAX. biopaxRef Middle of a pathway element in the x-direction. centerX Middle of a pathway element in the y-direction. centerY The color to be used for visualization. color Specifies a set of rules to govern layout of Graphical Lines and Interactions. PathVisio (Java): Line Type and GPML: ConnectorType connectorType Specifies the datasource for the identifier provided as an Xref. Equivalent to http://vocabularies.bridgedb.org/ops#DataSource conventional name . database A GraphId is a unique (per Pathway) identifier for a pathway element, such as DataNode, Interaction, GraphicalLine, Label, Point, Group, Shape, State and Anchor. graphId A GroupRef indicates that its element is part of the gpml:Group with the specified GroupId. DataNode, GraphicalLine, Group, Interaction, Label and Shape can be part of a group. groupRef The identifier of a PublicationXref or Xref object. id Key of the key/value pair in the Attribute class. key The visual appearance of a line or border, e.g., Solid or Broken. lineStyle The pixel value for the width of a given line, interaction or border. lineThickness Proportional distance of an anchor along the line it belongs to, between 0 and 1. position The visual representation of an anchor, e.g., Circle or None. shape Specifies the type of an object (DataNode, GraphicalLine, Interaction). type Value of the key/value pair in the Attribute class. value Indicates the zorder of the object in the pathway. zorder