!!!Queries on ontologies

!!! Link ontologies to a networks in Cytoscape

(:keywords rdfscape, cytoscape, plugin, features, ontology, owl, rdf, visualiziation, interactive,browsing, inference, reasoning :)

!! RDFScape features list

!!!Queries of ontologies
RDFScape supports:
* '''SPARQL''' queries
* '''RDQL''' queries
* queries based on '''Class''' membership
* queries based on '''string''' similiarity

In addition to these standard queries, RDFScape supports also:
* Interactive '''context-based browsing''' of ontologies (right selecting a node prompts all statemente associated to this node, and their selection "drives" the expansion of the network").
* '''Visual queries'''. Elements of a network can be declared as "variables", and the resulting "pattern" can be used as a visual query.

!!! Visualization of ontologies
* ''' Visualize''' and '''search''' results of queries on a network.
* Select '''resources''' to be '''visualized''' by '''namaspace''' (as well as their '''color''').
* Fine '''tune visulization options''': show datatypes as attributes, show rdf:label or URIs as node labels, show nodes corresponding to the same URIs as distinct nodes (ex. currency metabolites).

!!! Reasoning
* Apply '''RDFS'''/'''OWL''' inference with varying levels of axiom coverage, add you own axioms as '''inference rules''' to evaluate your interpretation of the domain.
* Use also the inferred knowledge in all your queries, visualization and so on...
* You can filter the inferred knowledge, and derive semantic tranformation of the original ontologies (pathway ontologies as interaction networks, pathway ontologies as causal networks...)

!!! Link ontologies to a network in cytoscape
* Map ontologies (and the facts they entails) to a Cytoscape network.

!!! Coming next
* ''Extension of term scoring function (From terms enrichment to ontology patterns enrichment) (under development)''
* ''Inference of statements from data (under development)''

(:keywords rdfscape, cytoscape, plugin, features, ontology, owl, rdf, visualiziation, interactiv, inference, reasoning :)

(: keywords rdfscape, cytoscape, plugin, features, ontology, owl, rdf, visualiziation, interactiv, inference, reasoning :)