0) Download the HomoSapiens release of Reactome at http://www.pathwaycommons.org/pc/dbSnapshot.do?snapshot_id=1
1) Select the analysis context: Reactome-Human-As-Interaction-Graph
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 already have prompted the computation of custom axioms + RDFS inference. A new property an:interacts is available for query and browsing.
You may try a few things like:
extracting all interactions Go on the pattern panel and select add pattern
querying for interacting elements write a query eg.: select ?x ?y where ?x an:inetarcts ?y (this example uses RDQL) in the proper query panel. Follow the help and list the results. You may now plot results to a network and browse thorugh them. Try to change configurations in namespaces (visibility, colors,...)