Saturday, October 22, 2011

ChEMBL-RDF: Uploading data to Kasabi with pytassium

I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi.

The new triples I wanted to upload, link the new public CHEMBL identifiers (like CHEMBL25 for aspirin) to the internal ChEMBL database identifier I used for ChEMBL 09 for the URIs. So, I am adding a lot of triples like:

<> <>

And the pytassium code I use to upload this to Kasabi looks like:

import pytassium
import time

dataset = pytassium.Dataset('chembl-rdf','XXX')

# Store the contents of a turtle file
dataset.store_file('chemblids.nt', media_type='text/plain') 

So, that omission in my log book has been corrected now.