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focus enabled_by edges on gene products rather than complexes #20

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goodb opened this issue Sep 5, 2018 · 3 comments
Closed

focus enabled_by edges on gene products rather than complexes #20

goodb opened this issue Sep 5, 2018 · 3 comments
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@goodb
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goodb commented Sep 5, 2018

If a complex has only one gene product in it, you can remove the small molecules/ions in the complex and just make the node a single gene product instead of a complex. For example, see the pathway “glycolysis”, the reaction “PGM:Mg2+ isomerise G6P to G1P” should just be enabled_by PGM (one gene product).

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goodb commented Sep 5, 2018

To see the reaction mentioned in the ticket, look instead at the more specific glycogen synthesis pathway. http://noctua-dev.berkeleybop.org/editor/graph/gomodel:-670700788

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goodb commented Sep 5, 2018

Looking at the complex named PGM:Mg2+ it is actually composed of 3 proteins (PGM1, PGM2L1, PGM2) and 1 small molecule (Mg2+). See the proteins and compounds listed at https://reactome.org/PathwayBrowser/#/R-HSA-8982491&SEL=R-HSA-453132&PATH=R-HSA-1430728,R-HSA-71387&DTAB=MT

I don't see any way to infer which of the proteins should be made the enabler. Looking for another example.

@goodb goodb self-assigned this Sep 5, 2018
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goodb commented Sep 10, 2018

This rule is already in effect. Documented as an optimization to support the Noctua 1.0 UI in https://docs.google.com/presentation/d/1_UAQN09WPCA5win5mbMs1ORMALNwiRwMBgZDPuyJEW8/edit?slide=id.g355425beec_0_3#slide=id.g374a8668ea_0_0

Closing, re-open if an example with only 1 protein in a complex comes through as a complex (and not a protein) is detected.

@goodb goodb closed this as completed Sep 10, 2018
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