How to download PDB and Alphafold data

[katewarner]

Can you please provide instructions on how to download PDB and Alpafold data for each release? I will then document the process in our data downloads file.

[rykahsay]

@katewarner @jeet-vora @ubhuiyan I guess I have to keep doing this since datasets _protein_pdb_map.csv and _protein_xref_alphafolddb.csv must be created first (which depend on EBI nt downloads).

Instead, during every release, make sure to create a ticket for me on updating the following downloads I do on my end:

• medline
• pubchem
• pdb
• alphafold

[katewarner]

@rykahsay

Okay no problem. At which point in the release would you like the ticket? When we've started the downloading or when we've completed our downloads and they're ready for processing?

[ubhuiyan]

@rykahsay @katewarner Just a heads up, I believe I write a ticket for Robel to download the Medline files as per the Glycan Download Instructions, would we prefer to consolidate all these resources into a single ticket? I typically write the ticket while I am downloading Nathan's exports.

[katewarner]

@ubhuiyan sounds like a good idea. You would have to wait until I've downloaded and QC'd the protein datasets to make the ticket, but I don't see that as a problem as long as the downloads have no issues since I've usually finished the downloads when you're preparing the files for Nathan

[rykahsay]

Yea, one ticket is good idea --- the ticket should be created at the beginning of the release

[ubhuiyan]

Sure thing. I can add this to the documentation.

[ubhuiyan]

I have added this to the documentation. Closing the ticket now.