Review annotations to GO:0061077 chaperone-mediated protein folding / GO:0051086 chaperone mediated protein folding independent of cofactor/ GO:0051085 chaperone cofactor-dependent protein refolding/ & regulation children

[ValWood]

Dear all,

The proposal has been made to obsolete

GO:0061077 chaperone-mediated protein folding
GO:0051085 chaperone cofactor-dependent protein refolding
GO:0051086 chaperone mediated protein folding independent of cofactor
plus regulation terms

see geneontology/go-ontology#21869

Experimental annotations that need to be reviewed are here:
https://docs.google.com/spreadsheets/d/1H8Holc3fuL5tw7tB_jv-UgHPv8oRui1wnU_jBeT5Gb8/edit?gid=0#gid=0

Impacted groups:
2 ARUK-UCL @RLovering direct replacement - done
18 BHF-UCL @RLovering direct replacement - done
5 CAFA @Antonialock direct replacement
2 CGD @jlewsmith direct replacement
14 FlyBase @hattrill direct replacement
3 RGD @gthayman direct replacement
7 SGD @edwong57 direct replacement
1 ParkinsonsUK-UCL @RLovering direct replacement - done
3 RGD @gthayman direct replacement
7 SGD @edwong57 direct replacement
29 MGI @LiNiMGI direct replacement
56 UniProt @Antonialock direct replacement
3 WB @vanaukenk direct replacement
3 dictyBase @pfey03 direct replacement

Need fixing
22 ComplexPortal @sandraorchard
56 EcoCyc @amandamackie
2 GeneDB @uliboehme
1 PomBase @ValWood fixed
14 SynGO ? @ftwkoopmans
11 TAIR @lreiser

---

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule)

@pedruzzi
@sarach06
@deustp01

GO:0051085 | unirule2go | UniRule:UR000667787 > GO:chaperone cofactor-dependent protein refolding ; GO:0051085
3 | GO:0051085 | interpro2go | InterPro:IPR017378 Torsin 1/2 > GO:chaperone cofactor-dependent protein refolding ; GO:0051085
4 | GO:0051086 | reactome2go | Reactome:R-HSA-390450 > GO:chaperone mediated protein folding independent of cofactor ; GO:0051086
5 | GO:0061077 | unirule2go | UniRule:UR000165448 > GO:chaperone-mediated protein folding ; GO:0061077
6 | GO:0061077 | interpro2go | InterPro:IPR001829 Pili assembly chaperone, bacterial > GO:chaperone-mediated protein folding ; GO:0061077
7 | GO:0061077 | interpro2go | InterPro:IPR030873 Beta-barrel assembly-enhancing protease > GO:chaperone-mediated protein folding ; GO:0061077
8 | GO:0061077 | interpro2go | InterPro:IPR043183 DnaJ homolog subfamily B member 2/6-like > GO:chaperone-mediated protein folding ; GO:0061077
9 | GO:0061077 | interpro2go | InterPro:IPR044609 Peptidyl-prolyl cis-trans isomerase FKBP2/11 > GO:chaperone-mediated protein folding ; GO:0061077
10 | GO:0061077 | hamap2go | HAMAP:MF_00940 > GO:chaperone-mediated protein folding ; GO:0061077

Thanks.

[ValWood]

Plus extensiosn for

@RLovering
@hattrill
@ValWood
@edwong57

BHF-UCL | UniProtKB:P48643 | CCT5 | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   |
3 | BHF-UCL | UniProtKB:P49368 | CCT3 | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   | UniProtKB:P49368 | PANTHER:PTHR11353 | 20240710 | UniProtKB:Q9BUR4|GO:0032212|GO:0051086 | NCBITaxon:9606
4 | BHF-UCL | UniProtKB:P50990 | CCT8 | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   | UniProtKB:P50990 | PANTHER:PTHR11353 | 20240710 | UniProtKB:Q9BUR4|GO:0032212|GO:0051086 | NCBITaxon:9606
5 | BHF-UCL | UniProtKB:P50991 | CCT4 | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   | UniProtKB:P50991 | PANTHER:PTHR11353 | 20240710 | UniProtKB:Q9BUR4|GO:0032212|GO:0051086 | NCBITaxon:9606
6 | BHF-UCL | UniProtKB:P78371 | CCT2 | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   | UniProtKB:P78371 | PANTHER:PTHR11353 | 20240710 | UniProtKB:Q9BUR4|GO:0032212|GO:0051086 | NCBITaxon:9606
7 | BHF-UCL | UniProtKB:P17987 | TCP1 | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   | UniProtKB:P17987 | PANTHER:PTHR11353 | 20240710 | UniProtKB:Q9BUR4|GO:0032212|GO:0051086 | NCBITaxon:9606
8 | BHF-UCL | UniProtKB:P40227 | CCT6A | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   | UniProtKB:P40227 | PANTHER:PTHR11353 | 20240710 | UniProtKB:Q9BUR4|GO:0032212|GO:0051086 | NCBITaxon:9606
9 | BHF-UCL | UniProtKB:Q9BUR4 | WRAP53 | PMID:25467444 |   | GO:0051087 | protein-folding chaperone binding | IPI | UniProtKB:P78371 | UniProtKB:Q9BUR4 | PANTHER:PTHR13211 | 20151211 | GO:0034504|GO:0007004|GO:0051086 | NCBITaxon:9606
10 | BHF-UCL | UniProtKB:Q99832 | CCT7 | PMID:25467444 |   | GO:0044183 | protein folding chaperone | IDA |   | UniProtKB:Q99832 | PANTHER:PTHR11353 | 20240710 | UniProtKB:Q9BUR4|GO:0032212|GO:0051086 | NCBITaxon:9606
11 | FlyBase | FB:FBgn0030344 | Nrd1 | PMID:28017472|FB:FBrf0234411 |   | GO:0044183 | protein folding chaperone | IDA |   |   | PANTHER:PTHR43690 | 20231220 | FB:FBgn0010352|GO:0061077|GO:0005739 | NCBITaxon:7227
12 | PomBase | PomBase:SPCC338.06c | hsp20 | PMID:18543332 |   | GO:0044183 | protein folding chaperone | EXP |   |   |   | 20230702 | GO:0034605|GO:0061077 | NCBITaxon:4896
13 | SGD | SGD:S000003682 | IDS2 | PMID:30516470 |   | GO:0051087 | protein-folding chaperone binding | IDA |   | UniProtKB:P46958 | PANTHER:PTHR11183 | 20211130 | SGD:S000004798|GO:0061077 | NCBITaxon:559292

[ValWood]

Not that there will be a direct replacement "protein folding"
but you might want o check that the MF chaperone term is annotated

[deustp01]

Reactome instance fixed.

[hattrill]

FB done

[jlewsmith]

CGD done

[amandamackie]

EcoCyc done

[lreiser]

tair done

[vanaukenk]

Reviewed WB annotations - done.

[ftwkoopmans]

SynGO done. Replaced respective GO IDs with "protein folding" and uploaded the updated dataset via the syngo2lego_data_conversion repository