How to get ontologies from a PDB IDs list?

Yasser Almeida Hernandez @Yasser_Almeida_Hernandez

12 December 2012 1 9K Report

I have a list of PDB IDs list and I need to get ontology data to verify any enrichment of protein family, function, cellular localization, etc. Which tool is the more suitable?

René Dreos

Hi, I would use biomart. If you are not familiar with it, go to Biomart website (link below) and select the dataset you want to query. Then, in the "Filter" area choose "Gene" and for "IDs limits" select PDB IDs. Copy and paste your ID in the window or upload a file with them.

From the attributes (this are the fields in the output) choose the "External" group and all the GO terms you want

Hope this help

http://www.ensembl.org/biomart/martview/

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