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Add new MF-MF relations to graph editor for creating example models for documentation #801
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The new relations have been added to the graph editor pop-up window on noctua-dev, but the label for two of the relations reflects an alternative label, not the main label currently listed in the latest RO release. In the screenshot above, the labels for: RO:0002407 (indirectly positively regulates) uses an alternative label, (indirectly activates) and RO:0002409 (indirectly negatively regulates) uses an alternative label, (indirectly inhibits). |
Apparently there is something I'm missing. Going back to the source, minerva is sending this back:
These are the correct labels for the three listed relations, so not minerva. I did another complete rebuild and restart of the system, including destroying all journals, and mystery labels persist. Hm. |
@vanaukenk The good news is that I believe I've traced the problem back to the source; the bad news it that the fix isn't trivial and requires messing with some annoying old software and configurations. The fix should not take too long, but I wanted to give you the option to go ahead with the bad labels for these and I can follow up with the label fix after that. How much pressure is there here for the final fix? |
@kltm |
@vanaukenk Yes, maybe I didn't explain myself well here. Let's try and touch bases a little. I'll ping you on another channel. |
Noting #804 |
Tested on production and all appears to be working as expected. Thanks @kltm |
In order to write curator documentation for using the new MF-MF relations, we'd like to add them to the graph editor pop-up window. The relations will also be added to the pathway editor with a separate ticket in that repo (coming).
For ease of display, I suggest that we not try to recapitulate all the new relations parentage in the upper section of the graph editor pop-up window, but @ukemi feel free to comment here if you think otherwise.
Here's a suggested display (only including direct parents and siblings here):
negatively regulates (RO:0002212)
-directly negatively regulates (RO:0002630)
-indirectly negatively regulates (RO:0002409)
positively regulates (RO:0002213)
-directly positively regulates (RO:0002629)
-indirectly positively regulates (RO:0002407)
causally upstream of, positive effect (RO:0002304)
-constitutively upstream of (RO:0012009)
causally upstream of, negative effect (RO:0002305)
-removes input for (RO:0012010)
Note that 'indirectly negatively regulates' (RO:0002409) and 'indirectly positively regulates' (RO:0002407) currently exist in the pop-up window but they aren't included in the upper section with the more commonly used GO-CAM relations and they have their old labels, 'indirectly inhibits' and 'indirectly activates', respectively.
Also note that 'directly inhibits' (RO:0002408) and 'directly activates' (RO:0002406), which are also both in the full list of relations in the pop-up window, are now obsolete.
Thank you.
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