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Obtain dataset for pretraining ProteinBERT #12

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duongvtt96 opened this issue Mar 8, 2022 · 1 comment
Closed

Obtain dataset for pretraining ProteinBERT #12

duongvtt96 opened this issue Mar 8, 2022 · 1 comment

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@duongvtt96
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Hi, I would like to pretrain the ProteinBERT model with a smaller dataset, such as human proteins in UniRef90. I have searched in between UniProtKB and UniRef90 website but could not find out how the obtain the .xml.gz file containing GO annotations similar to your uniref90.xml.gz file.
Could you explain how to get that kind of input file?

Thank you!
@ddofer
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ddofer commented Mar 8, 2022

The easiest alternative would be to download just Swissprot (most, but not all human proteins are there), or Uniref50:
https://www.uniprot.org/downloads
https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz

@ddofer ddofer closed this as completed Mar 8, 2022
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@ddofer @duongvtt96