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PomBase website v2
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paper on website not in Canto #2139

Closed ValWood closed 8 months ago

ValWood commented 8 months ago

This paper is on the rpb1 literature list?

Screenshot 2024-02-05 at 13 37 52
ValWood commented 8 months ago

got it, PMID: 29899453

ValWood commented 8 months ago

I don't know where it's coming from though, I thought it must be in the 'legacy' gaf, but not

kimrutherford commented 8 months ago

Hi Val. I think it's because of this line in pombe-embl/supporting_files/allele_synonyms.txt:

cdk9-T212A      cdk9T212A       PMID:2989945

It shouldn't be showing on the rpb1 page though - that's a bug which I'll fix. It's showing in the literature list because cdk9-T212A is an allele in one of the genotypes on the rpb1 page and PMID:2989945 is a reference associated with cdk9-T212A.

kimrutherford commented 8 months ago

It shouldn't be showing on the rpb1 page though - that's a bug which I'll fix.

I've thought about this. It is a bug but it's a pain to fix and it's only a problem if there's a data error (probably only with the allele comments and synonyms files). I prefer to fix every bug but sometimes it's lots of effort for little gain.

So let's close this once allele_synonyms.txt is fixed.

ValWood commented 8 months ago

Agreed. Is it possible to do a diff between papers in Canto and papers in Pombase CHado. That could identify any others?

ValWood commented 8 months ago

This one is fixed btw.

kimrutherford commented 8 months ago

Agreed. Is it possible to do a diff between papers in Canto and papers in Pombase CHado. That could identify any others?

There are 175. This is the full list: non_canto_pubs.txt

The ones I've spot checked look sensible.

Here's a sample:

uniquename title
PMID:8580465 The beta 7 integrins in mucosal homing and retention.
PMID:29514954 Assembling the mitochondrial ATP synthase.
PMID:19893618 Roles for the conserved spc105p/kre28p complex in kinetochore-microtubule binding and the spindle assembly checkpoint.
PMID:29440398 Assembly of the membrane domain of ATP synthase in human mitochondria.
PMID:27903914 Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7.
PMID:35190689 Using deep learning to annotate the protein universe.
PMID:29937227 The Inner Nuclear Membrane Is a Metabolically Active Territory that Generates Nuclear Lipid Droplets.
PMID:28335716 Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor.
PMID:24823650 RNA mimicry by the fap7 adenylate kinase in ribosome biogenesis.
PMID:19933165 CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes.
PMID:35633597 UBAP2/UBAP2L regulate UV-induced ubiquitylation of RNA polymerase II and are the human orthologues of yeast Def1.
PMID:25008109 A mutation in the human CBP4 ortholog UQCC3 impairs complex III assembly, activity and cytochrome b stability.
PMID:11083870 Bovine coupling factor 6, with just 14.5% shared identity, replaces subunit h in the yeast ATP synthase.
PMID:28162953 Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.
ValWood commented 8 months ago

yep, of course, sometime I use non-pombe papers to annotate GO

ValWood commented 8 months ago

How is PMID:35190689 | Using deep learning to annotate the protein universe. used? I can't think how I could use that?

kimrutherford commented 8 months ago

How is PMID:35190689 | Using deep learning to annotate the protein universe. used? I can't think how I could use that?

Looks like an ortholog: https://www.pombase.org/reference/PMID:35190689

ValWood commented 8 months ago

i don't remember that!

kimrutherford commented 8 months ago

Can we close this?

ValWood commented 8 months ago

yep!