Review annotations to 'GO:0033212 iron import into cell' and children

[pgaudet]

Hello,

There are some errors in the annotations of 'GO:0033212 iron import into cell' and children. Possibly this is because the term used to be labeled 'iron assimilation', and several mechanisms of iron import were missing.

I've added suggestions for all the annotations that need to be reviewed.
https://docs.google.com/spreadsheets/d/1bwOqVnt0QUxx1TwbdzQL22ylvOXS5xJBVLGkiuel0zA/edit#gid=0

Contributor (Assigned by)

Alzheimers_University_of_Toronto | 1 AspGD | 12 CACAO | 1 CGD | 7 EcoCyc | 5 MGI | 1 MTBBASE | 1 PomBase | 2 SGD | 1 UniProt | 2

Thanks, Pascale

[ggeorghiou]

MTBBase and UniProt changes made

[ukemi]

MGI annotation changed to homeostasis.

[ValWood]

I deleted ours, but then I added them back. @Antonialock you did the original, but at first glance this seems correct to me. The oxidase reduced the iron for transport by the transmembrane transporter?

The term used to be called "iron assimilation by reduction and transport" and I think it was for this process, at least originally.

seems to fit the def A process in which iron is solubilized by reduction from Fe3+ to Fe2+ via a cell surface reductase and subsequent transport of the iron across the membrane by iron uptake proteins.

[ValWood]

The reference for the term is this one, doesn't look right? http://europepmc.org/abstract/MED/16963626 It's a pombe paper about iron homeostasis, but not about this process?

[ValWood]

Sorry that's a different process involving the plasma membrane ferric-chelate reductase Frp1 https://www.pombase.org/gene/SPBC1683.09c

this is oxidase-permease-based iron transport (standard ferrous iron transport system?)

I'll just delete. Val

[srengel]

just now removed the one SGD annotation.

[keseler]

EcoCyc annotations changed/removed.

I have a question, though: Can the reductive removal of iron from a siderophore still be considered part of the siderophore-dependent iron import process? I.e. I would like to make annotations to both GO:0033214 and GO:0033215 for some of the enzymes.

[pgaudet]

@keseler

Can the reductive removal of iron from a siderophore still be considered part of the siderophore-dependent iron import process?

Yes, I think so. @marcfeuermann @Antonialock What does that seem right ?

[sandyl27]

CACAO changes made.

[pgaudet]

Hi @marekskrzypek Can you look at the CDG and AspGD annotations ? https://docs.google.com/spreadsheets/d/1bwOqVnt0QUxx1TwbdzQL22ylvOXS5xJBVLGkiuel0zA/edit#gid=0

Thanks, Pascale

[marekskrzypek]

Done.

Thanks, Marek

On Nov 26, 2018, at 8:58 AM, pgaudet notifications@github.com<mailto:notifications@github.com> wrote:

Hi @marekskrzypekhttps://github.com/marekskrzypek Can you look at the CDG and AspGD annotations ? https://docs.google.com/spreadsheets/d/1bwOqVnt0QUxx1TwbdzQL22ylvOXS5xJBVLGkiuel0zA/edit#gid=0

Thanks, Pascale

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[pgaudet]

Thanks !