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Friday, 15 February 2013

Latest activities on the Activities table in ChEMBL_15


For the recent ChEMBL_15 release, a considerable part of our efforts was focussed on the standardisation and harmonisation of the data in the Activities table. The latter holds all the quantitative and qualitative experimental measurements across compounds, assays and targets; needless to say that without it there's no ChEMBL!

This is a summary of what we've incorporated so far:

  1. Flag missing data: Records with null published values and null activity comments were flagged as missing.
  2. Standardise activity types and units: Conversion of heterogenous published activity type descriptions and units to a standard_type and set of standard_units (e.g., for IC50 convert mM/uM/pM measurements to nM).
  3. Flag unusual units: Records with unusual published units for their respective activity types were flagged as 'non standard'. For example, a hypothetical record with IC50 type and units in kg would be flagged!
  4. Convert the log values: The records with activity types such as pKi and logIC50 were appropriately converted to their non-log equivalents (by considering the units and sign of course as well). This updated a whopping 25% of the activities table - this means that significantly more data will become more comparable for subsequent analyses.
  5. Round values: For records with a standard activity value above 10, the rounding was done to the second decimal place. Otherwise, rounding was performed after the first three significant digits. For example 0.00023666666 would become a more concise 0.000237
  6. Check activity ranges: Records with a standard activity value outside the range specified by our expert biological curators, given the standard unit and type, were appropriately flagged.
  7. Detect duplicated values: For this one, we were inspired by a recent publicationWhat we did is we detected and flagged duplicated activity entries and potential transcription errors in activity records that come from publications. The former are records with identical compound, target, activity, type and unit values that were most likely reported as citations of measurements from previous papers, even when these measurements were subsequently rounded. The latter cases consist of otherwise identical entries whose activity values differ by exactly 3 or 6 orders of magnitude indicating a likely error in the units (e.g. uM instead of nM).

As a result of our efforts, we added 2 new columns in the Activities table, namely Data_validity_comment and Potential_duplicate. The former takes one out of 5 possible values: NULL, 'Potential missing data' (see point 1), 'Non standard unit for type' (see point 3), 'Outside typical range' (see point 6) and 'Potential transcription error' (see point 7). The latter column contains a binary (0,1) flag to indicate whether we think the specific activity record is a duplicate, as per point 7 above.

Stay tuned for more posts on the changes/improvements introduced by the new ChEMBL_15 release. Meanwhile, if you have any comments/feedback on the curation process or on the activity types we should prioritise, please let us know

George

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