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Ensembl / VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)
Apache License 2.0
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Link for DisGenet Input data not working anymore #739

Closed pietrojulia closed 1 month ago

pietrojulia commented 2 months ago

According to DisGenet documentation, you can download the input vcf file from: https://www.disgenet.org/downloads.

But now, disgenet is a private site, that you need to create an account and hire a plan to have access to the data.

I want now if there's any other known and reliable datasets for variant disease pmid associations to run with DisGenet plugin.

olaaustine commented 2 months ago

Hi @pietrojulia, Thank you very much for your patience. Following discussions within the team, we are going to deprecate the DisGenet plugin due to the recent changes to the data availability. For other reliable datasets for variant disease pmid associations to run, you can use the Mastermind CLI plugin, it returns the Mastermind search URI for articles/journals associated with the variant. You can also use our Phenotypes CLI plugin , it returns the Phenotypes informations from different sources and the source id which you can then search on different sources for publication information. Please let us know if this helps. Thank you Ola.