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Fix UniProt SPARQL query example 49 #7

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merged 3 commits into from
May 23, 2024
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@vemonet vemonet commented May 23, 2024

It was broken due to an outdated Bgee SPARQL endpoint URL used for the SERVICE call, and mismatching ensembl URI used to map the gene in Bgee

We need to use a regex to convert the ensembl URI that includes the version at the end http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000165029.17 (in UniProt) to http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000165029 (in Bgee)

The regex is quite costly (makes the query goes from ~8s to ~35s), but that is the only way I found to make the query work at the moment, because http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000165029.17 cannot be resolved as subject in UniProt (so we cannot quickly get the actual ensembl ID without version)

Not sure what would be the ideal solution to handle those new ensembl URIs with version included

Also note that resolution of ensembl URIs using the namespace http://rdf.ebi.ac.uk/resource/ensembl/ is broken, it seems like the new namespace to use is https://www.ensembl.org/id/ according to https://bioregistry.io/reference/ensembl:/ENSG00000165029.17

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JervenBolleman commented May 23, 2024

@vemonet the EBI RDF platform is now truly gone and broken. However, changing all these IRIs is not a great idea at this point in time.

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vemonet commented May 23, 2024

Yes of course, I just wanted to note it since I just realized

@JervenBolleman JervenBolleman merged commit 1c9820c into master May 23, 2024
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@JervenBolleman JervenBolleman deleted the fix-uniprot-example-49 branch October 30, 2024 09:59
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