Tutorial on model upload to QSPR-THESAURUS web using JRC models

Tutorial on model upload to QSPR-THESAURUS web using JRC models

  1. Find a model in JRC

  2. Download data

    • Go to '9.3 Supporting information' section in QRMF form
    • Download both training and test sets (two sdf files)
    • If something does not work, download Training and Test set files.
  3. Verify or add the article

    • Go to http://www.qspr-thesaurus.eu
    • Login by clicking 'BCF tutorial' link
    • Go to 'Article/Books' section and search for Paola Gramatica article 'An Update of the BCF QSAR Model Based on Theoretical Molecular Descriptors', article A5794
    • The article is there. You can start with next step now.
  4. Data upload

    • Go to 'Batch data upload'
    • Select upload one of the sdf files that you downloaded before
    • Inspect preview: select and remap required columns
    • CAS to CASRN (Known column)
    • LogBCF experimental to BCF (Property)
    • add also ARTICLEID by selecting the aforementioned article
    • Start data upload and wait until records are uploaded
    • You will see that records are already in the database (duplicates)
    • (optional) Repeat the same procedure with the Test set
    • If something does not work, upload Excel file with re-mapped columns. Download Excel file
  5. Create the training and test sets

    • Go to 'Article/Books' section
    • Select article A5794
    • Select all molecules from the article
    • Create Training set using sort by time
    • Do the same for the Test set
    • If something does not work you can use public sets 'BCF tutorial train' and 'BCF tutorial test' (check 'Show public sets' in browser of sets)
  6. Model upload

    • Select the training and test sets
    • Select correct units
    • Select pre-processing steps
    • Select descriptors and 3D pre-procesing (according to your list)
    • Create Excel file with model coefficients as indicated on the tutorial page or download it here
    • Use information from QRMF
    • Upload model
    • Confirm descriptors
    • Wait until descriptors will be shown
    • Correct name of the descriptor
      vIMD,Deg to IDDM
      and repeat all previous steps with model upload again
    • Check AD calculation (leverage)
    • Start calculation of the model
    • Explore the model
    • You can also explore this public model here
  7. Add QRMF

    • Go to http://cadaster.eu/QMRF/
    • Select the option 'Upload from an XML file' and click 'Enter the selection'
    • Select the previously downloaded XML file and click 'submit
    • Check the chapters to make sure, everything was parsed in a correct way
    • Click to submit and your QMRF will be stored in the database
    • Use ID on the model page to add QMRF description
    • You can also download the XML file here.