take out cross pathway links

[goodb]

This is an interim step before finishing #43

The view in Noctua will only show contents from the individual pathway. No links to super/sub pathways nor links to events in other pathways will be shown. These will all eventually be captured in the bridge model graph(s). Fairly significant work on the client will be needed to support the use of the bridge model in the UI. (Won't happen unless it is prioritized.)

[ukemi]

What do you mean by no links to subpathways? Does that mean that in the Reactome representation of axon guidance we won't include Netrin-1 signaling?

[goodb]

The idea is that we could only ever see one level of the hierarchy as seen in the Reactome viewer. For axon guidance, you would just see
axon guidance has_part semaphorin interactions
axon guidance has_part NCAM signaling for neurite out-growth
axon guidance has_part Netrin-1 signaling
axon guidance has_part
etc.

You would not see any events from these subpathways (that is the same as now). This change will mainly impact models (e.g. most signaling pathways) that have connections linking to events in other pathways (which are often super or sub pathways).

[goodb]

As an example of a model that is strongly affected by this change. See TCF dependent signaling in response to WNT. In order to build up the full picture of this pathway we would really need to find a way to display the information from the many inter-linked pathways from Reactome. I think the bridge model pattern would work but again, requires client development to happen. The only real alternative that I see is to do what we did before and import the connected data into the model - but then we deal with large clouded graphs (which is why Reactome broke it apart in the first place) and massive redundancy across related models.