new residue=x on RNA methytransferase

[ValWood]

I put the residue=X on this publication in Canto https://www.pombase.org/reference/PMID:37403782 and now the original annotation has disappeared from the website

[kimrutherford]

There are some new warnings in the log that prevent the annotations loading: https://curation.pombase.org/dumps/builds/pombase-build-2023-07-20/logs/log.2023-07-19-22-13-48.curation-tool-data-load-output

Probably the Chado loader needs fixing.

warning in eec0954c4a56c293: in annotation extension for SPNCRNA.530.1, can't parse identifier in "modified_residue(A64)"
warning in eec0954c4a56c293: in annotation extension for SPSNORNA.25.1, can't parse identifier in "modified_residue(A41)"

[kimrutherford]

Transferred to the Chado tracker. I'll fix it today.

[ValWood]

It might be my fault. This is actually a "methylation guide" and I can't remember if I asked for the "residue=" on guide activities (although I was able to add it in Canto, which I wasn't for methyltransferases, so I am assuming that isn't the problem)

[kimrutherford]

I've fixed the Chado loader to accept modified_residue() in extensions. The change went in after the load so I'll check on Saturday.

[kimrutherford]

I've fixed the Chado loader to accept modified_residue() in extensions.

That worked but last night's load has a different error:

warning in eec0954c4a56c293: modified_residue() not allowed for molecular_function, annotation: SPNCRNA.530.1 <-> snRNA 2'-O-ribose methylation guide activity
warning in eec0954c4a56c293: modified_residue() not allowed for molecular_function, annotation: SPSNORNA.25.1 <-> snRNA 2'-O-ribose methylation guide activity

I've fixed the configuration in load-pombase-chado.yaml and I'll check again tomorrow.

[kimrutherford]

New day, new error. "modified_residue" isn't isn't a relation in any of the CVs we have configured for extension relations:

warning in eec0954c4a56c293: can't find relation cvterm for: modified_residue in these CVs: relationship go/extensions/gorel fypo_extension_relations PSI-MOD_extension_relations external fission_yeast_phenotype
warning in eec0954c4a56c293: can't find relation cvterm for: modified_residue in these CVs: relationship go/extensions/gorel fypo_extension_relations PSI-MOD_extension_relations external fission_yeast_phenotype

I'll add modified_residue to go/extensions/gorel which we get from SVN these days:

pombe-embl/mini-ontologies/gene_ex_extension_relations.obo

I'll also change the GAF exporter to remove that relation from the extension while exporting for GO.

[kimrutherford]

Still not fixed. This time because I made a typo in the code that checks the modified_residue extension when loading into Chado. Fixed now and I'll have a look at the logs on Tuesday morning.

[kimrutherford]

Finally working!

https://www.pombase.org/reference/PMID:37403782

[ValWood]

Thanks!