getHumanOrthologs error

[marlisese]

Dear David, I am running some templates from biokitr and found out an issue with mouse <-> human orthologs. My dataset is mouse but not all of genes were being annotated with the human ortholog, despite they being well known (e.g. Cxcl11 = CXCL11). I went to the code, and it uses ribiosAnnotation function:

orths <- data.table(getHumanOrthologs(organism, useRibios = TRUE))

This function can have 2 routes if we have ribiosAnnotation credentials (which I have now in my home as specified) However, the function fails because of the following error:

Error in rjson::fromJSON(file = file) : not all data was parsed (570 chars were parsed out of a total of 950 chars)

Have you encounter this before? I have tested with R4.1.2 and R4.2.0 (sHPC). Thanks, Martha

[marlisese]

Hi David, My quest has changed. I found an error in my credentials file and now the function runs as expected. However, when looking at the orths result, I can not find the human ortholog for the mouse geneID 56066 (GeneSymbol Cxcl11). I have checked at the MongoDB collection behind "ncbi_gene_orthologs", and indeed these gene associations do not exist, but the "ensembl_orthologs" does find the association.

[Accio]

Hi Martha, thanks. The example is helpful, I will check.

Best regards David

Martha Serrano @.***> schrieb am Do. 30. März 2023 um 14:51:

Hi David, My quest has changed. I found an error in my credentials file and now the function runs as expected. However, when looking at the orths result, I can not find the human ortholog for the mouse geneID 56066 (GeneSymbol Cxcl11). I have checked at the MongoDB collection behind "ncbi_gene_orthologs", and indeed these gene associations do not exist, but the "ensembl_orthologs" does find the association.

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[Accio]

Dear @marlisese, thanks for reporting the issue. I confirm your findings.

The notes below are for me: biokitr::getHumanOrthologs wraps ribiosAnnotation::humanOrthologsByTaxID, which looks up in "ncbi_gene_orthologs". Apparently human orthologue (CXCL11) is not annotated for the mouse gene Cxcl11 by NCBI, but "ensembl_orthologs" does report so.