ribosome GO:0005840 intracellular non-membrane-bounded organelle

[hattrill]

Currently, ribosome GO:0005840 is_a intracellular non-membrane-bounded organelle

I know this could be debated, but I think that most researchers would call this a complex.
Could we move this under "GO:0032991 protein-containing complex"? Especially as now we are using gp2term rels, located_in seems jarring.

[ValWood]

should be GO:1990904 ribonucleoprotein complex (like the subunits)

Can't it be both an intracellular non-membrane-bounded organelle and a complex?

[pgaudet]

I dont think this is consitent with our rules.

As @hattrill points out, for protein-containing complex the geneproduct2term relation is part_of, while for cellular anatomical strucutres, it's located_in or is_active_in (depending on whether the CC data shows where the gene is active, as opposed to just a localization assay).

So, I dont think a term can be a is_a child of BOTH complex and cellular anatomical entity.

@vanaukenk @cmungall @ukemi @balhoff

[hattrill]

And, just for fun - polysome is_a GO:1990904 ribonucleoprotein complex

[pgaudet]

That is indeed very entertaining :D Le jeu. 18 mars 2021 à 6:51 PM, Helen Attrill ***@***.***> a écrit :

…

And, just for fun - polysome is_a GO:1990904 ribonucleoprotein complex — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#21143 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABEPWUCTA6EFLEIKKQZDDQ3TEI4SVANCNFSM4ZMJKE2A> .

[mah11]

I came across this ticket while investigating some of our annotation warnings. A couple of them trace to the ancestry of GO:0042788 ! polysomal ribosome.

Can't [ribosome] be both an intracellular non-membrane-bounded organelle and a complex?

I don't think this is consitent with our rules.

... for protein-containing complex the geneproduct2term relation is part_of, while for cellular anatomical strucutres, it's located_in or is_active_in

So, I dont think a term can be a is_a child of BOTH complex and cellular anatomical entity.

This reasoning looks backwards to me. Surely the links within the ontology should be determined by the actual biology that the ontology represents, and then the gp-to-term relation rules should be adapted if necessary.

Historically the ribosome has sometimes been counted as an organelle because of its size and importance; at the same time, it's unquestionably a complex of RNA and protein. So I think biologists would find ribosome is_a ribonucleoprotein complex AND ribosome is_a organelle intuitive. If this is too sloppy for ontological formality, that's a bit of a loss for biologist-friendliness, but it would be a far better reason for choosing one or the other classification within the ontology than rules about annotations that use the ontology.

Also, as @hattrill noted, ribosome (GO:0005840) and polysome (GO:1990904) aren't handled consistently at present. Although there is the mRNA present in a polysome, it's not clear why that makes a polysome count as a ribonucleoprotein complex when a "plain" ribosome doesn't. If ribosome can only be in one branch, the case for "complex" seems slightly stronger.

[ValWood]

I don't see why ribosome can't be both organell and ribonucleoprotein complex.

polysome is_a ribonucleoprotein complex seems odd to me because it's not a single complex.

[mah11]

polysome is_a ribonucleoprotein complex seems odd to me because it's not a single complex.

Maybe the idea is that the mRNA connects all the ribosomes up into one humongous complex? Anyway, I agree it's a bit odd but not as odd as ribosome not being is_a RNP ...

[ValWood]

Maybe the idea is that the mRNA connects all the ribosomes up into one humongous complex?

That seems a bit weird. They are only connected by being on the same mRNA (like beads on a string). But they are still discrete complexes.

[hattrill]

I don't see why ribosome can't be both organell and ribonucleoprotein complex.

One major problem and why it's on our radar as an issue:
Now we have gp2term relations, it can't be both - part_of a complex and located_in an organelle.

[ValWood]

Now we have gp2term relations, it can't be both - part_of a complex and located_in an organelle

But lots (most?) of complexes are located in organelles!
Maybe part_of complex takes precedence over located_in organelle?

[hattrill]

There's only one slot for the gp2term rel.
but I guess I would argue that the protein is part of a complex and the complex is located in the organelle.

[deustp01]

It does look like an edge case. For that matter, if one had the patience to list all the components, a chromosome or a nucleolus could a complex (or a series of complexes for each, with transformations between them).

[pgaudet]

I put this to discuss with GO editors on out next call, Nov 15th.

[ValWood]

So was there a decision about whether we can add "ribonucleoprotein complex" as a parent to ribosome?

[pgaudet]

@ValWood
Because of the Geneproduct2term rules, we cannot have both 'cellular anatomical entity' and 'protein-containing complex' as parents of the same term.

Another way to think about this may be, how do we want to annotate this?
two possible statements:

• protein 1 is part_of the ribosome
• protein 2 is_active_in the ribosome (as we would have 'is active_in' the nucleus, for a nuclear protein).

Is one or the other better?

Thanks, Pascale

[ValWood]

Part_of ribosome sounds more correct. is_active_in ribosome sounds weird...but I don't know the implications