Obsoletion request: GO:0039668 viral entry into host cell via pilus basal pore and GO:0039669 viral entry into host cell via pilus retraction and membrane fusion

[pgaudet]

GO:0039667 viral entry into host cell via pilus retraction, GO:0039668 viral entry into host cell via pilus basal pore > 4 annotations CAFA, will be remapped GO:0039669 viral entry into host cell via pilus retraction and membrane fusion > 0 annotations

are more granular than the ViralZone term. Replace by
virion attachment to host cell pilus which corresponds to the VZ term, https://viralzone.expasy.org/981

[pgaudet]

Obsolete GO:0035635 entry of bacterium into host cell >> 10 manual annotations >> replace by symbiont entry into host cell Obsolete GO:0039707 virus-mediated pore formation in host cell membrane > 2 EXP; replace by symbiont entry into host cell via pore formation in plasma membrane

[pgaudet]

Dear all,

The proposal has been made to obsolete the following 'entry into host cell' terms: GO:0039667 viral entry into host cell via pilus retraction > Replace by GO:0039666 virion attachment to host cell pilus GO:0039668 viral entry into host cell via pilus basal pore > Replace by GO:0039666 virion attachment to host cell pilus GO:0039669 viral entry into host cell via pilus retraction and membrane fusion > Replace by GO:0039666 virion attachment to host cell pilus GO:0035635 entry of bacterium into host cell > replace by GO:0046718 symbiont entry into host cell GO:0039707 virus-mediated pore formation in host cell membrane > replace by GO:0044694 symbiont entry into host cell via pore formation in plasma membrane

There are 16 EXP annotations, 2 Reactome mappings, 6 InterPro and 1 HAMAP mapping, see https://github.com/geneontology/go-annotation/issues/4882

Impacted groups:	Database	Count
AgBase	4
CACAO	1
GO_Central	1
MGI	2
CAFA	4
UniProt	2
Reactome	2
InterPro	6
HAMAP	1

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/26669

Thanks, Pascale

[deustp01]

GO:0035635 entry of bacterium into host cell > replace by GO:0046718 symbiont entry into host cell

This line seems wrong. GO:0046718 is "viral entry into host cell", and I can't find a term with the name "symbiont entry into host cell" nor any plausible children of GO:0044409 "entry into host".

Help!

[deustp01]

Obsolete GO:0035635 entry of bacterium into host cell >> 10 manual annotations >> replace by symbiont entry into host cell

Same discrepancy in immediately preceding comment, above. The text says "symbiont" but the link points to a term for "virus"

[pgaudet]

Hi @deustp01 I have renamed the terms, but I agree for now this is confusing.

[deustp01]

Hi @deustp01 I have renamed the terms, but I agree for now this is confusing.

I'm OK with being confused. So I should use GO:0046718 to replace the existing terms and the "viral" name will get corrected the next time we update our local copy of GO against the central one?

[pgaudet]

That's right. GO:0046718 is now 'symbiont entry into host cell'; this will show up with the next snapshot.

Pascale

[suzialeksander]

Just noting that GO:0035635 entry of bacterium into host cell is still a valid term.