Name conflict (fixed), add GO annotation, infer to PomBase

[snezhkaoliferenko]

While curating this paper - PMID:32243490 - I noticed that they named SJAG_03891 as Alx1, but the database name is Rim20. What should we do about it? Thanks! S.

[ValWood]

Rim20 comes from S. cerevisiae, but as this is not a published name in fission yeast, I can change the pombe entry to Alx1 and make Rim20 a synonym. This way SJAG_03891 will become Alx1 automagically.

In other situations we have a method to diverge the pombe and japonicus names if required (there is a configuration file somewhere to override the pombe names)

@kimrutherford

[ValWood]

I updated this at pombase so we can check tomorrow if it all gets updated OK.

@snezhkaoliferenko if you have a better product line than "BRO1 domain protein' I can also update that. I use functions >> complex membership > domains

[ValWood]

Also sorry I only just saw this. I wasn't monitoring the tracker !

[ValWood]

ESCRT-III regulator?

[ValWood]

ESCRT-III adaptor I see from human it is an adaptor for ESCRT-III proteins? https://www.uniprot.org/uniprot/Q8WUM4

Multifunctional protein involved in endocytosis, multivesicular body biogenesis, membrane repair,

Adapter for a subset of ESCRT-III proteins, such as CHMP4, to function at distinct membranes. Required for completion of cytokinesis (PubMed:17853893, PubMed:17556548, PubMed:18641129).

[ValWood]

Also maybe these phenotypes are specific enough to annotate to the GO biological process term

GO:0031468 nuclear membrane reassembly

Then I can make an inference from japonicus to pombe for "nuclear membrane organization" (the first!) I think that since this is likely involved in membrane repair it is a better inference than the current PomBase one to "vesicle-mediated transport"

[kimrutherford]

there is a configuration file somewhere to override the pombe names

It's here: https://github.com/japonicusdb/japonicus-curation/blob/main/names_and_products.tsv

[ValWood]

New name and product now propagated from fission yeast. http://japonicusdb.kmr.nz/gene/SJAG_03891

~I'll transfer this ticket to the curation tracker.~ this is the curation tracker. To do: Decide if some GO processes can be made (we can also use these for PomBase)

[snezhkaoliferenko]

@ValWood thank you! Re: annotating Alx1, I think 'ESCRT-III regulator' is good, although it is possible that it might have ESCRT-III-unrelated functions, as per the genetics part of this paper. But let's go with ESCRT-III regulator.

This is correct: GO:0031468 nuclear membrane reassembly

Now to this part: "Then I can make an inference from japonicus to pombe for "nuclear membrane organization" (the first!) I think that since this is likely involved in membrane repair it is a better inference than the current PomBase one to "vesicle-mediated transport" - I would scrap 'vesicle-mediated transport'. Its functions though are not necessarily limited to 'nuclear membrane organization' - just not enough data to exclude other possible functions. Perhaps add 'membrane remodeling'?

[ValWood]

I annotated to

from this paper.

This will annotate to all of these terms indirectly:

I'll keep the vesicle-mediated transport inference for alx1 from SGD for now also.

I can also use the "mitotic nuclear membrane reassembly" for pombe because we defined this to cover open and closed mitosis:

The mitotic cell cycle process involving ESCRTIII that results in reformation of the nuclear envelope after mitotic nuclear division. In organisms undergoing closed mitosis this involves resealing or 'repair' of the nuclear envelope in the nuclear bridge. PMID:26040712 PMID:28242692 PMID:32109380 PMID:3284825

[ValWood]

For GO, making the most specific annotation possible is best, because the ancestors are inferred in the queries. Other more specific roles can be added later but this annotation will also automatically annotate all to more general terms like "endomembrane system organization"

v

[ValWood]

See for example query on endomembrane system organization http://japonicusdb.kmr.nz/term/GO:0010256

[ValWood]

Although this will change the numbers and bring a lot more into this query: https://github.com/geneontology/go-ontology/issues/21846