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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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PDB IDs from gene_ids? #187

Closed tommycarstensen closed 7 years ago

tommycarstensen commented 7 years ago

Is it possible to get PDB IDs and/or Uniprot IDs from gene_ids and/or transcript_ids using PyEnsembl? Thanks.

iskandr commented 7 years ago

Hey @tommycarstensen -- theoretically it's possible but I've never looked into it. Do you know of a database mapping Ensembl IDs to PDB?

tommycarstensen commented 7 years ago

Hi @iskandr ! I asked around yesterday and it can now be achieved with BioDBNet of bioservices written by @cokelaer as per issue 86. I asked both of you after reading the question "Can I map gene symbols to PDB ids?" on biostars.org and not seeing a Python solution. Uniprot has this flat text file, which links PDB IDs to Uniprot IDs, and it seems to be updated frequently: http://www.uniprot.org/docs/pdbtosp.txt