wikipathways / wikipathways/GPML2RDF
update of interaction types
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@mkutmon is already working on this.
Since May 13, 2019.
question
- Dominant language
- Java
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Description
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"
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