|
Project Wiki
|
How to tune visualization optionsRDFScape presents several options to tune visualization of information. Some are discussed are presented in Selecting namespaces, also relevant is How to use inference. Instructions 0 Visualization options are under Options-> Browser. However, only the option described in 1 is specific to the browsing functionality. They other apply in al visualizations of ontologies in RDFScape. 1 Namespace selection in and. For each item in the menu, each statement in the relative context menu (see How to browse ontologies) present up to two namespaces. These can be selected namespace or not. If this options is not selected all statements that have at least one element in a selected namespace are shown. If this option is selected, only the statement with both namespaces selected are shown. Note that namespace of the node the menu is relevant is not relevant to this option. Blank nodes are always considered as not selected. 2 Treat datatype as attributes. If this option is selected, when adding a node, all its datatype properties are also added as attributes of the node (the datatype property becomess the attribute name, the corresponding object its value). 3 Use labels instead of URIs. Use rdfs:label as node or edges label instead of URIs. 4,5,6 This function allows to specify under which condition some elements shoule be visualized as a distinct node each time they are added to the network (the corresponding URI is unique). This is useful for instance when visualizing currency metabolites, that would be displayed as hubs is the correspondence URI to nodes was always 1 to 1. When 4 is selected, the are in 5' becomes active. Here it is possible to specify conditions that ientify elements that should always be visualized as unique nodes. This specification is in the form of a list of RDQL queries, separated by a string "OR CONDITION" (note that this is merely syntactic sugar, there is not an AND CONDITION, or anythig else than "CONDITION"). An example of specification is given below. When selected 6 the specifications shown are registered in the system (not yet in the filesystem, this happens when "save context" is selected, see How to work with analysis contexts). Note that this specification may be complex to input interectively, it should be almost always provided in the analysis context SELECT ?z WHERE (?z <http://www.biopax.org/release/biopax-level1.owl#NAME> ?h) AND ?h eq "H2O" OR CONDITION SELECT ?z WHERE (?z <http://www.biopax.org/release/biopax-level1.owl#NAME> ?h) AND ?h eq "ATP" OR CONDITION SELECT ?z WHERE (?z <http://www.biopax.org/release/biopax-level1.owl#NAME> ?h) AND ?h eq "CO2" FAQ |