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geneontology / wc-gocam-viz

Web component to visualize GO-CAMs
BSD 3-Clause "New" or "Revised" License
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Biological Process GO terms displayed with GO-CAMs not following part_of chains (Alliance KANBAN-126) #7

Open kltm opened 2 years ago

kltm commented 2 years ago

Shadowing for our accounting: https://agr-jira.atlassian.net/browse/KANBAN-126

kltm commented 2 years ago

Tagging @vanaukenk @tmushayahama @dustine32

dustine32 commented 2 years ago

@vanaukenk Using example model epidermal growth factor receptor signaling pathway via MAPK cascade (C. elegans) and concentrating on GP let-60 here: image This GP is currently only displayed in the pathway widget right-side pane under its directly-connected process, "Ras protein signal transduction": image Sounds like this GP should really be added under BP GO:0005006 "epidermal growth factor receptor signaling pathway via MAPK cascade", which it's indirectly-connected to via the part_of chain: image Two questions:

  1. Should the above arrow represent a copy or a move of let-60 into the indirectly-connected BP GO:0005006 "epidermal growth factor receptor signaling pathway via MAPK cascade"?
  2. If all GPs in this model are all indirectly connected to GO:0005006, should GO:0005006 be the only BP grouping in the pathway widget right-side pane?
kltm commented 2 years ago

@tmushayahama Has this work underway.

vanaukenk commented 1 year ago

Needs testing on noctua-dev Alliance Pathway Preview workbench @vanaukenk @ukemi