Open ukemi opened 4 years ago
To clarify a little of what is in my mind from the discussion during the call. A possible data flow, that could be followed for both reactome->go-cam and other "immutable" upstream sources (e.g. current syngo, other pathways databases), could be roughly as follows:
This would allow for the upstreams to have: 1) fairly independent lifecycles 2) to have built-in versioning and history (github).
Okay @kltm here you go. https://github.com/geneontology/reactome-go-cams Should I start making updates to that one or continue updating noctua-models with reactome changes currently bound for noctua-dev ?
@kltm @ukemi what project should this be in ?
@goodb It might be good to stick a pin in the home project for the moment. As the week progresses, we should have a better idea where we're at (hopefully). As far as the data flow goes, I think that's still TBD--what I said last week was a hasty proposal off the top of my head. I think, maybe, it goes one of two ways:
Thinking about how these would mechanically work and how fiddly it would be to have to multiple branches running around, it seems like the former would be easier, although it would require more effort upfront. How does that sound to you, and would you like to talk about this a bit more on the software call (or some other time) this week?
@goodb Another, somewhat orthogonal issue, is how to mark models like this as "immutable" (or whatever we want to call it). Naturally, coordinating the decisions there with changes in Minerva.
Also, to answer your original question to me more directly, I think the "best" thing for the moment, given infinite time at your end, would be to update here, them clobber on noctua-models in a PR until we sort out some of the other issues outlined above.
Also also, it would be easy-ish to still stream these into the the triplestore and the /go-cam interface without going through the editorial system. To answer an unasked question, it would also be easy to turn these into JSON-response-like objects and create a set of static pages a la http://noctua.geneontology.org/workbench/pathwayview/?model_id=gomodel:5ed1aab700000024 and deliver them out of GitHub pages, as there is now a separate repo.
On the Pathways2GO call May 27, we decided that the imported Reactome models and other imports should not be edited by curators. These models would be house in separate repositories where they would be immutable by curators and only be updated through the regeneration process at each Reactome release. ping @kltm This will be the paradigm forward for imported models.