fix taxon restriction 'iron ion import across cell outer membrane'

[ValWood]

'iron ion import across cell outer membrane' SubClassOf 'only in taxon' some Bacteria

from https://github.com/geneontology/go-ontology/issues/16776

[ukemi]

Since both organelles and bacteria can have outer membranes, I will remove the TR.

-D

[ValWood]

This term is still unavailable to us?

[ukemi]

Looks like it is coming from the restriction on 'cell envelope'. Are you sure you want the 'cell outer membrane' taxon restriction removed? 'Cell outer membrane' is a part_of 'cell envelope'.

Cell outer membrane: A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.

[ValWood]

I'm not sure what the problem is. All I know is that there is a taxon restriction somewhere that prevents us from using the term? But I can't see what the taxon restriction is.

[ValWood]

I just rechecked and the term is still unavailable to us

[ukemi]

I see the taxon restriction, but do yeast have an outer CELL membrane and is it part_of a 'cell envelope'? Is this really the term you want to use?

[ukemi]

Don't they just have a plasma membrane and a cell wall?

[ValWood]

Oh I see what you mean, blind spot. It's the wrong term. @Antonialock

[ukemi]

cell envelope: An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.

[mah11]

I think the taxon restriction for 'iron ion import across cell outer membrane' is correct - from what I recall, the 'cell outer membrane' business really is meant to apply to Bacteria (probably only Gram-negative bacteria at that). Other species don't have double cell membranes.

I wonder if the actual problem is this link (from #16776):

'high-affinity ferric iron transmembrane transporter activity' SubClassOf 'part of' some 'iron ion import across cell outer membrane'

because PMID:16522632, which is one of the papers cited in the GO:0033573 def, leads off with "The high affinity iron uptake complex in the yeast plasma membrane (PM) consists of the ferroxidase, Fet3p, and the ferric iron permease, Ftr1p." in the abstract, implying that some instances of 'high-affinity ferric iron transmembrane transporter activity' execution can be part of transport across yeast cell membranes.

[mah11]

... it would be good to have @Antonialock confirm, though, because she's been working on iron transport in pombe and I haven't ;)

[ValWood]

Actually the term I can't approve is this one GO:0033573 high-affinity iron permease complex

[mah11]

yeah, that's all part of the chain from https://github.com/geneontology/go-ontology/issues/16776#issuecomment-449491917 ... and it's the GO:0015092 part_of GO:0098706 link that looks most suspect to me

[ValWood]

See the comment from @balhoff in the previous ticket:

"Sorry for the slow reply! This one is due to an actual taxon constraint:

'high-affinity iron permease complex' SubClassOf 'capable of' some 'high-affinity ferric iron transmembrane transporter activity' 'high-affinity ferric iron transmembrane transporter activity' SubClassOf 'part of' some 'iron ion import across cell outer membrane' 'iron ion import across cell outer membrane' SubClassOf 'only in taxon' some Bacteria"

[ukemi]

I think @mah11 is correct.

Based on the def:

'high-affinity ferric iron transmembrane transporter activity' SubClassOf 'part of' some 'iron ion import across cell outer membrane'

should be: 'high-affinity ferric iron transmembrane transporter activity' SubClassOf 'part of' some 'iron ion transmembrane transport'

[mah11]

@ukemi - yes, that sounds good. phew!

[Antonialock]

yep sounds good

[ukemi]

OK. I will fix this. I can actually do it with some shuffling of terms further up the graph that don't seem to have necessary and sufficient definitions. Thanks Everyone.