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Entity "mexA Pseudomonas (PseudoCAP:PA0425)" accepted by Noctua, but cannot apply annotations? #933

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Pauldenny opened this issue Dec 3, 2024 · 4 comments
Open

Entity "mexA Pseudomonas (PseudoCAP:PA0425)" accepted by Noctua, but cannot apply annotations? #933

Pauldenny opened this issue Dec 3, 2024 · 4 comments

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@Pauldenny
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Pauldenny commented Dec 3, 2024 •
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Entity "mexA Pseudomonas (PseudoCAP:PA0425)" is accepted by Noctua, but I cannot apply annotations?
every time I try, a red symbol appears next to the GO MF identifier.
mexA Pseudomonas (PseudoCAP:PA0425) is a synonym for Swiss-Prot / UniProt:P52477. Unfortunately, Noctua appears to not recognise P52477 either.
@pgaudet
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pgaudet commented Dec 4, 2024

@kltm
PseudoCAP doesn't provide a GPI in the datasets/yaml
https://github.com/geneontology/go-site/blob/master/metadata/datasets/pseudocap.yaml

Should we get the entities from UniProt?

@Pauldenny
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Yes, please, it's UniProt:P52477

@kltm
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kltm commented Dec 4, 2024

@pgaudet Re: "PseudoCAP doesn't provide a GPI in the datasets/yaml"
In that case, it should be falling back to the GAF, which is what is indicated by the build (https://github.com/brinkmanlab/pseudomonas-genome-database/raw/master/pseudocap-annotation-files/gene_association.pseudocap.gz).

@pgaudet
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pgaudet commented Dec 5, 2024

But that means we can only annotate entities that are already annotated; I've added this as a discussion point on our next call.

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@kltm @pgaudet @Pauldenny