(:keywords pathways, Cytoscape, Biopax, Ontology, Semantic web, Reasoning, Inference, analysis, cause, effect :)
0) Download the HumanCyc at http://www.pathwaycommons.org/pc/dbSnapshot.do?snapshot_id=2
1) Select the analysis context: HumanCyc-Local-Causal
2) Activate the selected context
3) Select the Tab "2) Load Ontologies"
4) Select "add"
5) Input the location of your ontologies, following the URL scheme. URLs accessible from the web will start with http:// , URLs accessible on the local disk will start with file:// (On unix systems, for instance... file:///home/username/..)
6) Load my ontologies. If URLs are correct, all fields should turn green. If there are problems (red fields) delete the corresponding ontology field and input it again, with the correct URL
7) If this is the first time you are using thi analysis context, go to the tab "1) Select my analysis context" and select "save current context". This will avoid steps 4-5 next time.
8) Current settings in the default analysis context will apply custom inference rules and no reasoning at this stage. 'A new property an:affects' is available for query and browsing.
You may try a few things like:
query and browse the causal network if you system if fast enough (wait some minute on an ontology of this size) start by plotting a smallMolecule in RDFScape (either try a string search by name, or an RDQL/SPARQL query by type, or even ask directly for all elements linked by an:affects). Then just browse the ontology alng the an:affects relations!