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wormjam-consortium / wormjam

Website/Repository containing the WormJam genome scale model
https://wormjam.life
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Missing gene reference #103

Open cfrainay opened 2 years ago

cfrainay commented 2 years ago

Some genes are referenced in reactions' fbc:geneProductAssociation but absent from the fbc:listOfGeneProducts list, causing errors in model build from sbml.

Here is the list of 'dangling' gene references: "G_ND" "G_Unknown" "G_TBD" "G_NA" "WBGene00009407"

Except for the last one, they all seems to correspond to missing genes, maybe this could be harmonized under a single entity, to make spotting these gaps easier? or, even better, in order to avoid unrelated reactions sharing GPR, use numbered entities (G_Unknown_1, G_Unknown_2 ...)?

michaelwitting commented 2 years ago

Yes, you are right. That should be corrected. I will check in my fork and changed it.

michaelwitting commented 2 years ago

How do you typically annotated GPR for transport reactions? Shall we just leave them empty?

cfrainay commented 2 years ago

For diffuse transports it seems that HumanGEM and BIGG's Recon3 do not define any fbc:geneProductAssociation. I have also a Xylella fastidiosa model with dummy genes like "spontaneous" and "no_assignement". I'm not sure what is the community consensus here... I would say that not being able to know when a gene association point to a "real" gene or not is a red flag and that no association at all is better

I checked the fbc package documentation and I don't find any recommendations regarding reactions without known or existing genes associations. It is not listed either that having a fbc:geneProductAssociation is a requirement for reactions. However if there is a fbc:geneProductAssociation it can not be empty and must contains at least one fbc:Association with a fbc:GeneProductRef.