has_parts for iron assimilation processes

[gocentral]

   is_a GO:0033212 ! iron assimilation *** 
             is_a GO:0033213 ! iron assimilation by capture and transport [has_part: "iron ion transmembrane transport"]
             is_a GO:0033214 ! iron assimilation by chelation and transport [has_part: "iron ion transmembrane transport"]
             is_a GO:0033215 ! iron assimilation by reduction and transport [has_part: "iron ion transmembrane transport"]
             po GO:0006881 ! extracellular sequestering of iron ion

1. The part_of child seems odd. If iron assimilation ends_with iron ions inside the cell, is sequesting outside the cell really part of this process?
2. Judging by the def of the parent, can we not make the has_part relationships to the more specific GO:0097459 ! iron ion import into cell?
3. Can we have additional has_part relationships to distinguish the 3 cases? E.g. GO:0033215 has_part GO:0000293 ! ferric-chelate reductase activity

Reported by: cmungall

Original Ticket: geneontology/ontology-requests/10390

[gocentral]

• labels: --> Other term-related request
• assigned_to: Paola Roncaglia

Original comment by: paolaroncaglia

[gocentral]

Hi Chris,

The part_of child seems odd. If iron assimilation ends_with iron ions inside the cell, is sequesting outside the cell really part of this process?

I think that GO:0006881 ! extracellular sequestering of iron ion should be part_of 'cellular iron ion homeostasis' (and therefore sibling of 'intracellular sequestering of iron ion'). Its current location makes no sense to me. (There are no other 'extracellular sequestering' terms, so we're good.) The link was added back in 2008, but I think it's safe to remove it. I'll do that.

Judging by the def of the parent, can we not make the has_part relationships to the more specific GO:0097459 ! iron ion import into cell?

I'd say yes... will do.

Can we have additional has_part relationships to distinguish the 3 cases? E.g. GO:0033215 has_part GO:0000293 ! ferric-chelate reductase activity

a) 'iron assimilation by capture and transport' is defined as 'A process in which iron (Fe3+) is solubilized by binding to a receptor or transport protein and transported into a cell.' so the only one that comes to my mind is 'iron binding'... but this has specific children for 'ferric iron binding', 'ferrous iron binding' and above all 'iron chaperone activity' ('Assists in the delivery of iron ions to target proteins or compartments.') so would we get TPVs? Can't think of other has_part links...

b) 'iron assimilation by chelation and transport' is defined as 'A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors.'. Possibly create new term 'siderophore import into cell' and add link 'iron assimilation by chelation and transport' has_part 'siderophore import into cell'. What do you think?

c) 'iron assimilation by reduction and transport' is defined as '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.' so yes adding a has_part link to GO:0000293 ! ferric-chelate reductase activity sounds right.

Let me know what you think and I'll do the edits, thanks. Paola

Original comment by: paolaroncaglia

[gocentral]

Hi again Chris, I've done the first couple of edits to start with:

Made GO:0006881 ! extracellular sequestering of iron ion part_of 'cellular iron ion homeostasis' (rather than GO:0033212 ! iron assimilation)

Added link: GO:0033212 ! iron assimilation has_part GO:0097459 ! iron ion import into cell

As for a) in my previous comment, I see now that we wouldn't get TPVs, but on second thought 'iron binding' wouldn't be right anyway (iron ions must be bound for the assimilation to occur, but 'iron binding' would be used to annotate the proteins that actually bind iron). Can't think of other has_part links.

I'll wait to hear from you about b) above - then I'll implement that, and the link in c).

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Chris,

I've added the link: GO:0033215 ! iron assimilation by reduction and transport has_part GO:0000293 ! ferric-chelate reductase activity

May I close this ticket now? Or if you can think of further links you'd like to be added, let me know. Thanks! Paola

Original comment by: paolaroncaglia

[gocentral]

wonderful, thank you. Yes, can be closed.

Original comment by: cmungall

[gocentral]

I feel there should be some way we can distinguish the siblings based on their parts but this is not a priority for me

Original comment by: cmungall

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia