update of interaction types

[egonw]

Can you please have a look at this code and tell me if we can/should update this:

	private static Resource getLineTypeResource(LineType lt) {
		if(lt.equals(LineType.ARROW)) {
			return null;
		} else if (lt.equals(LineType.TBAR)) {
			return Wp.Inhibition;
		} else if (lt.equals(MIMShapes.MIM_CATALYSIS)) {
			return Wp.Catalysis;
		} else if (lt.equals(MIMShapes.MIM_CONVERSION)) {
			return Wp.Conversion;
		} else if (lt.equals(MIMShapes.MIM_INHIBITION)) {
			return Wp.Inhibition;
		} else if (lt.equals(MIMShapes.MIM_STIMULATION)) {
			return Wp.Stimulation;
		} else if (lt.equals(MIMShapes.MIM_TRANSLATION)) {
			return Wp.TranscriptionTranslation;
		} else if (lt.equals(MIMShapes.MIM_NECESSARY_STIMULATION)) {
			System.out.println("TODO: necessary stimulation");
		} else if (lt.equals(MIMShapes.MIM_MODIFICATION)) {
			System.out.println("TODO: modification");
		} else {
			System.out.println("Unknown and unsupported interaction type: " + lt);
		}
		return null;
	}

I think we might have to. This is what I find in the output of the RDF generation

778x "Unknown and unsupported interaction type: mim-binding"
30x "Unknown and unsupported interaction type: mim-cleavage"
9x "Unknown and unsupported interaction type: ReceptorSquare"
6x "Unknown and unsupported interaction type: Receptor"

[egonw]

@DeniseSl22, @mkutmon, what does your outline of interactions have for these three mim types?

1. mim-cleavage
2. MIM_NECESSARY_STIMULATION
3. MIM_MODIFICATION

Was there a reason why that one was missing in the current WikiPathways Ontology/Vocabulary?

[DeniseSl22]

Hi @egonw , @mkutmon and @RyAMiller ,

I think we should leave the current GPML2RDF conversion for the existing MIM-types in PWs.
We will not have a new interaction panel in the next PV release, because then we would need to do (major) updates to the WPs website as well (and it's better to do this for the new dev site, than for the old one)....

For the unsupported ones: the ReceptorSquare and Receptor should not be used; could you make a unit test for these in Jenkins, so we can find them and change them to whatever it should mean?
For the MIM-binding and cleavage, these do exist and people are allowed to use them.
In the new panel, I'm proposing the following:
Mim-cleavage: becomes "Conversion"
Mim-necessary-stimulation: becomes "Stimulation"
mim-modification: become "Modification" .

And may I draw your attention to the latest addition of the MIM panel, translocation? This was originally mentioned in the paper describing the MIMs in PV, but never implemented. It is part of the code now (and will be part of PV in the next release @mkutmon and me are working on).

Hope this gives @egonw enough info to go in, if not let me know!

[DeniseSl22]

See this document for details: https://docs.google.com/document/d/1YhaqPVznPyn270skwmEcDBWzezsu1lOClEG4eIKyTQM/edit?usp=sharing