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Multiple updates supporting ROs 4542, 4552, 4553, & 4555 #17

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@brindakv brindakv commented Feb 3, 2025

This PR addresses the following:

  • Load database_2 to support extended PDB IDs
  • Update PDBx/mmCIF dictionary to the latest version 5.410
  • Add search metadata for data items in pdbx_vrpt_summary_geometry
  • Update description for rcsb_polymer_instance_feature_summary.coverage

@brindakv brindakv requested a review from valasatava February 3, 2025 23:21
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Thank you, @brindakv! One comment

"type": "array",
"items": {
"type": "object",
"properties": {
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It seems that the pdbx_database_accession is missing

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Thanks for picking this up @valasatava.

This has been addressed in the latest commit. Please review.

@brindakv brindakv requested a review from valasatava February 4, 2025 22:26
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Thanks, @brindakv. Just one doubt about bringing in DOIs

}
]
},
"pdbx_DOI": {
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Do we want to load the DOI as well? I think we're currently building DOIs on the fly in frontend

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Good point @valasatava.

It is an attribute in the public database_2 category. Is it ok to have it in the data warehouse for external users?

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@valasatava do you recommend that we suppress pdbx_DOI explicitly? Or can it be included as is?

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There is no issue with including this item, but I am being cautious about what we expose in the public API. @josemduarte what's your opinion?

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I think it can't hurt to include it. So that we offer the data out to users. But let's not add to search.

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Thanks @josemduarte. There is no search metadata for pdbx_DOI.

@brindakv brindakv requested a review from valasatava February 5, 2025 02:12
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3 participants