Linkset files for ChEMBL are provided directly by the ChEMBL curators and available for download along with the standard ChEMBL RDF datasets. The following Linkset files are provided for ChEMBL version 22.1:

  • chembl_22.1_complextarget_targetcmpt_ls.ttl.gz
  • chembl_22.1_grouptarget_targetcmpt_ls.ttl.gz
  • chembl_22.1_molecule_chebi_ls.ttl.gz
    • chembl compound -> chebi
  • chembl_22.1_singletarget_targetcmpt_ls.ttl.gz
    • chembl target -> chembl target component
  • chembl_22.1_targetcmpt_uniprot_ls.ttl.gz
    • chembl target component -> uniprot TrEMBL


The GitHub project ‘ops-uniprot-linksets’ contains 13 *.sparql query files to create Linkset files from UniProt data. The ‘data’ directory appears to contain 12 *.ttl.gz files resulting from executing the 13 *.sparql queries. The load.xml contains the 12 files in the ‘data’ directory. The one *.sparql file that does not seem to be included in the data is called ‘uniprot_ipi.sparql’.

Q: What about that “uniprot_ipi.sparql’ file that is created but does not appear to be loaded into IMS?


New Linksets related to WikiPathways will be created by Egon W. and the folks at Maastricht.

They will also be creating some (or all?) of the linksets for the following:

  • chebi
  • goa
  • hgnc
  • Ensembl


ocrs (Chemistry)




Ensembl linksets for Human and Mouse, Sept, 2015.