Obsoletion: [ GO:0030433 | ubiquitin-dependent ERAD pathway ]

[ValWood]

• GO term ID and label for which you request a new superclass

I have annotated to GO:0030433 | ubiquitin-dependent ERAD pathway | ISO with S000002284

but I am picking up a mapping to GO:0071712 | ER-associated misfolded protein catabolic process

but GO:0030433 | ubiquitin-dependent ERAD pathway IS_A ER-associated misfolded protein catabolic process
based on its definition:
The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.

so it seems to be missing a superclass?

• New superclass (parent) suggested

[ValWood]

Actually, I think these terms are describing the same pathway. Although I'm not sure that the pathway distinguishes between "misfolded" and other Protein Quality Control issues.

[ValWood]

the refs for
ER-associated misfolded protein catabolic process (GO:0071712)
both refer to ERAD

[pgaudet]

Merge?

[ValWood]

I think so. The children of
GO:0036503 ERAD pathway
are a bit confusing.

[ValWood]

GO:0030433 | ubiquitin-dependent ERAD pathway
and GO:0036503 ERAD pathway
are also the same thing

[ValWood]

Also the child

GO:1904379    protein localization to cytosolic proteasome complex involved in ERAD pathway
GO:1904379 protein localization to cytosolic proteasome complex involved in ERAD pathway

This is a phenotype (single EXP)

[ValWood]

• obsoletion notice
• GO friends e-mail
• annotation tracker tickets

[pfey03]

we had 4 ISS which I replaced with other terms; there are still quite some IBA with the above term

[ValWood]

Moved ubiquitin-dependent glycoprotein ERAD pathway
directly under
ERAD pathway
(we can decide what to do with this later, suspect it is unnecessary but is isn't included in this ticket)

2. deprecated
   GO:0030433 ubiquitin-dependent ERAD pathway
   GO:0071712 ER-associated misfolded protein catabolic process

3. deprecated
   GO:1903069 regulation of ER-associated ubiquitin-dependent protein catabolic process
   GO:1903070 negative regulation of ER-associated ubiquitin-dependent protein catabolic process
   GO:1903071 positive regulation of ER-associated ubiquitin-dependent protein catabolic process (+ 39 TG definitions!)
   Note that these are the regulation children for GO:0030433 ubiquitin-dependent ERAD pathway
   even though the labels are different

in fact, the Equivalent to is for GO:1903070 is
'biological regulation' and ('negatively regulates' some 'ERAD pathway')
which is identical to

GO:0036503 ERAD pathway
'biological regulation' and ('negatively regulates' some 'ERAD pathway')

How can that happen? @pgaudet @balhoff

5. deprecated
   GO:1904379 protein localization to cytosolic proteasome complex involved in ERAD pathway

[ValWood]

How can that happen? @pgaudet @balhoff

Ignore, it is presumably because I deprecated GO:0071712 first?