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immature peptide region #2251

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ValWood opened this issue Oct 2, 2024 · 4 comments
Open

immature peptide region #2251

ValWood opened this issue Oct 2, 2024 · 4 comments
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@ValWood
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ValWood commented Oct 2, 2024 •
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complete this ticket. reminder (SO browsing issue)

ticket-SO browsing
@kimrutherford
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What needs to be done here?

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ValWood commented Oct 2, 2024

I'm not sure yet. I wnt to demo something on our next call. Will add discuss.

@ValWood ValWood added the discuss label Oct 2, 2024
@ValWood ValWood self-assigned this Oct 2, 2024
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ValWood commented Nov 5, 2024

For SO browsing, ignore part_of (only display is_a)

@ValWood ValWood removed the discuss label Nov 5, 2024
@ValWood ValWood assigned kimrutherford and unassigned ValWood Nov 5, 2024
kimrutherford added a commit to pombase/pombase-chado that referenced this issue Nov 6, 2024
@kimrutherford
Fix "part_of" in SO closure creation
d5259c9 
We weren't adding SO "part_of" relations to the cvtermpath table
because relation-graph was returning "part_of" as the relation instead
of the expected BFO:0000050.

Refs pombase/website#2251
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There was a bug is the way the transitive closure was stored in Chado. The code was expecting BFO:0000050 as the relation term ID, but was getting part_of. The only other ontology that had this problem was PSI-MOD but that has very few part_of relations and none connecting modification terms used by us.

For SO browsing, ignore part_of (only display is_a)

That fix probably isn't needed now but let me know what you think once the website is fixed on Thursday morning.

After fixing that the annotation appear on the immature peptide region page:

image

I'll check this on Thursday and close the issue.

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