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Sunday, March 04, 2012

ChEMBL 13 as RDF

Update: this work is now described in this paper.
Last week, ChEMBL 13 was released, with even more data, data fixes, etc. Since my RDF for ChEMBL 09 my workflow has become more solid and uses more common ontologies, started using more common ontologies and ontologies I just like, such as CHEMINF and CiTO. Below is an overview of the resource types present in the RDF: activities (almost 7M now), chemical entities, assays, targets, and documents. 


The data on Kasabi will be updated soon, and the SPARQL end point hosted by Uppsala University was updated yesterday, including the SNORQL frontend:


The new data is not fully backwards compatible. The changes to the RDF include the use of cito:citesAsDataSource, more typing using existing ontologies, e.g. with cheminf:CHEMINF_000000 and pro:PR_000000001 from the PRotein Ontology.

A paper dedicated to the ChEMBL-RDF is in preparation. Existing use cases can be found here.