Provides input for OR positive regulates about pathways2go HOT 7 CLOSED

@ukemi I'm looking at 'activated TAK1 mediates p38 MAPK activation https://reactome.org/PathwayBrowser/#/R-HSA-450294&SEL=R-HSA-450302&PATH=R-HSA-168256,R-HSA-168249,R-HSA-168898,R-HSA-168164 as a test case for this one. The first cut only puts one regulates relation in between 'Phosphorylated MKK3/MKK6 migrates to nucleus' and 'Activated human MKK3/MKK6 phosphorylates p38 MAPK complexed with MAPKAPK2 or MAPKAPK3'. Which reactions in this pathway should be linked by positive regulates (and which by provides input for) ? Just want to set up a test.

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There is already a test case in the canonical glycolysis pathway. I'm seeing individuals that are given parents to both the terms and to the regulation terms. Peter and I are focusing on glycolysis as the test case. @huaiyumi is looking at the MAPK pathway.

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Okay fair enough @ukemi .

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@balhoff if you look at the text of the issue linked here, I'm wondering if the rules for deepening the specificity of the relations in question should fall out of property chains in the RO rather than custom rules. It looks like there is already one in place that would cover the 'directly provides input for' case but it uses an obsolete relation: 'obsolete has direct output' o 'has direct input' ?

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How specific is this to Reactome's representation? I think that would be the deciding factor.

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For the moment I went ahead and added the rules locally. Even if/when the property chains exist, Noctua users don't really have a good way of seeing their results and I think that is important at this stage.

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@balhoff if you look at the text of the issue linked here, I'm wondering if the rules for deepening the specificity of the relations in question should fall out of property chains in the RO rather than custom rules.

@goodb I think that would be good but I'm not sure where to look. It sounds like this is resolved for the time being though.

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