Review annotations to GO:0072321 chaperone-mediated protein transport & children

[pgaudet]

Hello,

The proposal has been made to obsolete GO:0072321 chaperone-mediated protein transport & children, see https://github.com/geneontology/go-ontology/issues/20850

There are 27 annotations to review:

https://docs.google.com/spreadsheets/d/18cumXK6_Iim-kkq5krL-kYsbAUq4mDVi929p0w1INPk/edit#gid=0

Contributor (Assigned by) -- AgBase | 1 - Done BHF-UCL | 10 CACAO | 2 ComplexPortal | 3 EcoCyc | 5 FlyBase | 1 - Done MGI | 1 PseudoCAP | 1 UniProt | 3

Thanks, Pascale

[pgaudet]

Note that suggestions have been made for reaannotation, but a new term has just been created, needed for many reannotations, so it may not be immediately available in annotation tools.

[hattrill]

Hi @pgaudet the proteins that I am looking at are descibed as transporters/chaperones. So, they probably keep the membrane protein in a state (in ER, poss co-translational) that is capable of being transported and accompany that protein to the membrane. So for activity, I am kind of somewhere between 'protein folding chaperone' and 'protein transporter activity' or both. Will the new term 'protein carrier activity' cover this?

[pgaudet]

FlyBase had a single protein, right ? FB:FBgn0038749 - or did you find others ?

The carrier activity is described as something that binds and moves together with its substrate, so it's inconsistent with 'transporter activity', which allows the solutes to move through.

Which is it ?

[hattrill]

There is another that acts like it: an Xport-A and an Xport-B. So trying to be consistent and give these samwe MF. In that case it is a 'carrier'.

I think that the comment for 'transporter activity' should be merged with the description in part, as description does not explictly say 'move through' gp and 'protein transporter activity' has this 'Directly binding to a specific protein and delivering it to a specific cellular location' then mentions carriers in comment as an example of transporters.

[hdrabkin]

@pgaudet, I am having a bit of trouble locating the annotation you list in the spreadsheet. I see we have an iso to GO:0061741 to a rat protein, UniProtKB:P63018; Is this the one you mean? Based on PMID:18644871; RGD would then take this to make an annotation based on what we supply. So is the ISO MGI annotation the one you mean here?

[pgaudet]

https://docs.google.com/spreadsheets/d/18cumXK6_Iim-kkq5krL-kYsbAUq4mDVi929p0w1INPk/edit#gid=0

[bmeldal]

ComplexPortal:CPX-6125 hasn't got an annotation in question but is already annotated to GO:0045039 protein insertion into mitochondrial inner membrane.

I will wait for the new term for BAT3 complex.

[hdrabkin]

Hi @pgaudet The 'new ' GO:0140597 ; not present in daily snapshot go-basic download (so not available for us yet). It's in go-edit.obo

[hdrabkin]

It appears the most recent snapshot of go-basic is dated 2-8-21, two days before the term was made. @kltm ?

[kltm]

@hdrabkin It appears that a new snapshot has cleared. Is the term now available?

[hdrabkin]

Hi @kltm Not loaded into MGI yet (still pointing to 2/8/2021 snapshot from last night’s load; we must pick it up just before it changed to 2/16/2021). Tonight’s load should get it.

Harold

[pgarmiri]

Hi, the SWIE annotations have been updated. Thanks, Penelope

[pgarmiri]

Hello again,

I just noticed that the NEW GO:0140597 'protein carrier activity' comes with a suggestions for additional (inferable) annotation to:

GO ID | Category | Name

GO:0015671 | Process | oxygen transport |  

Is that right?

Thanks,

Penelope

[hdrabkin]

@kltm,j the new term GO:0140597 is now in MGI to use. Thanks.

[bmeldal]

BAT3 complexes updated.

PS: The def for the yeast ortholog of BAT3, GO:0072380 TRC complex, is misleading; it sounds like the def for GO:0043529 GET complex, which is next in the process ;-) I'm opening a new ticket but have to read a bit first as the existing entries are rather old.

[pgaudet]

Hi @pgarmiri

I just saw your question - I just noticed that the NEW GO:0140597 'protein carrier activity' comes with a suggestions for additional (inferable) annotation to: GO:0015671 | Process | oxygen transport |

You mean in P2GO ? this sounds wrong. I dont see that inference in Protégé.

[pgarmiri]

Hi @pgaudet , Yes, indeed. I tried it again just now and I got the same message.

[ukemi]

I think this is due to the transports-o-has_part issue we talked about on the ontology developers' call last week. @balhoff was going to remove that property chain.

protein has_part some protein polypeptide chain protein polypeptide chain has_part some oxygen atom

protein carrier activity = 'molecular carrier activity' and ('transports or maintains localization of' some protein)

[ukemi]

I just checked the reasoner explanation for this inference. It is because of that property chain.

[RLovering]

as Penelope says the ontology has a 'part_of' link to oxygen carrier activity. I will delay my revisions until this relationship is removed (see below) Thanks Ruth

[pgaudet]

This problem is coming from RO. Hopefully this will be merged today and the incorrect inference removed (see https://github.com/geneontology/go-ontology/issues/20624 - I know it seems completely unrelated but I think the same inference chain causes both problems).

Annotations should be safe, the inference will be removed.

[pgaudet]

The bad inference is now removed.

[hdrabkin]

mgi done

[RLovering]

ucl - done

[keseler]

EcoCyc done