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PomBase curation
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rixosome complex #3674

Closed ValWood closed 3 months ago

ValWood commented 3 months ago

Annotate the other 3 rixosome complex subunits using ISS

Screenshot 2024-03-08 at 07 45 32
ValWood commented 3 months ago

comment

ValWood commented 3 months ago

We are missing some rixosome subunits. We need to annotate these with the evidence code "ISO" and a characterised protein in the "with" field. YOu will need the svn checkout for this. @kimrutherford can set you up with svn and git repositories next week, but i nthe short term you will mainly need svn

Once that is done I'll describe the legacy GO files.

ValWood commented 3 months ago

The fist task is to track down the missing orthologs.

I would usually try https://www.ebi.ac.uk/QuickGO/annotations?goUsage=descendants&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:0120330 and filter on EVIDENCE=experimental

ValWood commented 3 months ago

Actually, nobody has annotated all the subunits.

We might be able to use tracable author statement from https://europepmc.org/article/MED/32491985

@Antonialock do you know if this is annotated in UniProtKB?

ValWood commented 3 months ago

ACtually I found the original requesting ticket https://github.com/geneontology/go-ontology/issues/23192 we'll probably need to go with TAS for now.

But there is a newer paper here, so human could be annotated too, if it isn't already. Cite Share

Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation. Thoms M, Lau B, Cheng J, Fromm L, Denk T, Kellner N, Flemming D, Fischer P, Falquet L, Berninghausen O, Beckmann R, Hurt E. EMBO Rep. 2023 Dec 6;24(12):e57984. doi: 10.15252/embr.202357984. Epub 2023 Nov 3. PMID: 37921038 Free PMC article. The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. ...Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic pos …

ValWood commented 3 months ago

added PomBase SPBC16C6.12c GO:0120330 PMID:37921038 TAS X XXX protein taxon:4896 20240404 PomBase PomBase SPCC830.03 GO:0120330 PMID:37921038 TAS X XXX protein taxon:4896 20240404 PomBase

will also filter some false positive mappings