Template talk:Infobox genome

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Molecular Biology: Genetics

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taxId no longer works

If you click on a "NCBI genome ID" link, it redirects to just https://www.ncbi.nlm.nih.gov/datasets/genome/ and the old website says "Effective June 2024, NCBI's Assembly resource will no longer be available. NCBI Assembly data can now be found on the NCBI Datasets genome pages." Akeosnhaoe (talk) 05:49, 28 May 2024 (UTC)[reply]

Hi - I found this from WikiUser70176's question at the Teahouse regarding a broken genome link for Tomato. It appears the use of the taxonomy ID to reference genome pages is now selectively broken.

The error in the Template code arises from its use of this URL to point to genomes: https://www.ncbi.nlm.nih.gov/genome/?term={{{taxId}}}. According to this NCBI update, the Genome & Assembly services are being replaced with the Datasets service.

Here's an example of how this is affecting us:

The NCBI taxonomy ID for Solanum lycopersicum (Tomato) is 4081.
When the Infobox genome template is used with taxId=4081 it produces this URL: https://www.ncbi.nlm.nih.gov/genome/?term=4081. NCBI redirects the request to https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=905054 (I don't know where 905054 comes from).
905054 is the taxonomy ID for Tobacco leaf curl Pusa virus; thus, genomes matching this virus are shown instead of Tomato genomes.

Not every page is affected the same way. As WikiUser70176 pointed out, Cucumber still works properly. Infobox genome with taxId=1639 produces https://www.ncbi.nlm.nih.gov/genome/?term=1639; NCBI redirects this to https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=3659. 3679 is the correct taxonomy ID for Cucumber (Cucumis sativus), so it appears NCBI can sometimes correctly map an old genome ID to a new taxonomy ID. Chimpanzee, Clostridium botulinum, and Picea sitchensis are all examples of entities with taxonomy IDs that the NCBI doesn't redirect properly when used as genome IDs. I haven't looked at all the pages using this infobox but I'm sure there are many more examples.

Unfortunately, I don't think there's a way to fix this without modifying this template and updating the taxId for each page. This template should instead use https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=<taxId> as the URL for the genome lookup, and each page should be updated to use the entity's taxonomy ID as the taxId for the infobox. — nmael ^talk 13:01, 8 August 2024 (UTC)[reply]