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modifications on wrong residue #3748

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ValWood opened this issue Sep 25, 2024 · 8 comments
Open

modifications on wrong residue #3748

ValWood opened this issue Sep 25, 2024 · 8 comments
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@kimrutherford

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@ValWood
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ValWood commented Sep 25, 2024

I didn't think we have many of these, but this log file

https://curation.pombase.org/dumps/latest_build/logs/log.2024-09-24-21-52-42.chado_checks.modification_on_wrong_residue
now has 2302, mainly from 640df135c586fdb8

https://www.pombase.org/reference/PMID:18257517

(or are these from the Uniprot import?)
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kimrutherford added a commit to pombase/pombase-chado-json that referenced this issue Sep 25, 2024
@kimrutherford
Add "T" or "S" to mod positions, where needed
b762f88 
This is for the data from UniProt.

Refs pombase/curation#3748
Refs pombase/pombase-chado#1216
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@kimrutherford
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i thought there would be a few that we couldn't fix? maybe

I think all the UniProt modification positions should be correct.

We're ignoring data from UniProt where their sequence doesn't match ours.

kimrutherford added a commit to pombase/pombase-chado-json that referenced this issue Sep 27, 2024
@kimrutherford
Use match instead of nested if
f52c7fb 
Refs pombase/curation#3748
Refs pombase/pombase-chado#1216
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ValWood commented Oct 1, 2024

These are the PomBase ones to fix
https://github.com/pombase/allele_qc/blob/master/results/protein_modification_cannot_fix_sequence_errors.tsv

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