Update minerva to handle “maximal-causal-chain-length” and “display-as-pathway-override”

[kltm]

Update minerva to handle “maximal-causal-chain-length” and “display-as-pathway-override”, including returning them on results and automatically updating “maximal-causal-chain-length”.

Tagging @balhoff

[balhoff]

Am I correct that the maximal-causal-chain-length of this graph would be 2, since activity 4 has no enabler defined?

flowchart LR
A1(activity 1) --enabled by--> G1(gene 1);
A2(activity 2) --enabled by--> G2(gene 2);
A3(activity 3) --enabled by--> G3(gene 3);
A1 --regulates--> A2;
A2 --causally upstream of--> A3;
A3 --positively regulates--> A4(activity 4);

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cc @vanaukenk @ukemi @cmungall @sierra-moxon

[ukemi]

I've been making models with placeholder activities when I know an activity occurs, but I don't know exactly which gene product enables it. I think this would be useful to display and should be counted, but it's just my 2 cents.

[balhoff]

Another question: should all the nodes in the chain being counted be molecular functions (vs. processes)?

[ukemi]

I would vote yes.