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. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKVCIE4W474YNJPWF4NSE3W6V6THANCNFSM6AAAAAAWNBGEHM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Jitao David Zhang http://jdzhang.me/ ***@***.*** Inzlingerstrasse 53 4125 Riehen, Switzerland

[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.