search

geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
38 stars 12 forks source link

Ability to distingush "unknown" steps from "constitutively upstream" #908

Open ValWood opened 4 months ago

ValWood commented 4 months ago

If I have pathways with a gap, and here it would be really nice to be able to put a big red "?" instead of "constitutively upstream" (sometimes we might use constitutively upstream for committed chunks of processes like transcription), or in the case of the arginine biosynthesis pathway we know the entire metabolic pathway, but there is an unknown citrulline carrier between arg3 and arg12 so the pathway looks complete but it isn't:

Screenshot 2024-07-25 at 09 36 10

I would like to annotate as arg3 -> ? -> arg12 so that gaps in pathways can easily be identified for computational purposes (and for the projects studying unknown proteins).

CC @PCarme

thomaspd commented 2 months ago

You should be able to add an activity that has no gene product associated with it (i.e. just use "information biomacromolecule" in the enabled_by field), and connect it into your model. Screen Shot 2024-09-06 at 9 18 04 AM

ValWood commented 2 months ago

Thanks we will try this! @ CC @PCarme

ValWood commented 2 months ago

It would be cool if this displayed as a [? unknown] (information biomolecule is a bit cryptic)

Screenshot 2024-09-06 at 18 08 19
pgaudet commented 2 months ago

I think you can use ChEBI:protein (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=36080), which is a bit less cryptic