Error in biomaRt useMart and useDataset accessing ovis aries genome

Question

[Michael]

Hi all, I am having an issue accessing the Ovis Aries gene annotation data. For years, I have used the following code without issue:

ensembl <- useDataset(dataset = "oaries_gene_ensembl", mart = useEnsembl(biomart = "genes"))

Now I am receiving the following error message:

Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: oaries_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.

When I search using listDatasets() as suggested, the ovis aries genome indeed isn't listed, but the sheep genome is still an option to query on the Ensembl website. I have sorted out a workaround with the following:

ensembl <- useMart(biomart="ensembl", dataset="oaries_gene_ensembl", host = "https://may2024.archive.ensembl.org")

But curious if anyone has any idea why I can no longer access the ovis aries genome without querying an archived ensembl.org

Thanks

Answer 1

[Louisse_Ensembl]

Hi Michael

Thank you for your question and my sincere apologies for the errors you are having accessing the BioMart sheep data. We are aware of this issue and are aiming to have it fixed by the end of this week. In the meantime, please continue accessing the archive.

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All the best, Louisse (Ensembl Helpdesk)

[Michael]

Hi Louisse, Do you mind updating on this thread when the issue has been addressed? Thanks!

[Raquel]

Hi, I have the same problem with Scophthalmus maximus and Sparus aurata species. The problem with the last update was that when using useMart or getBM, these species did not appear to exist, but in previous versions they did.

I hope this will be fixed soon.

Thanks

Answer 2

[Louisse_Ensembl]

Hi Michael and Raquel

Just an update on the BioMart issue - I'm afraid that resolving the missing species is taking longer than expected, but please know that we are working on it. I suggest you continue using the Ensembl 112 archive for now. My sincere apologies for this inconvenience.

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All the best, Louisse (Ensembl Helpdesk)