FAQs

FAQs are listed below.

Who Can Deposit Data in ChEMBL ?

Deposition of bioactivity data to ChEMBL is largely by invitation. However, if you have data sets that you think will add value to ChEMBL, then please contact us by email: [e-mail]

Who are the main depositors ?

The current list of ChEMBL sources can be found on the ChEMBL Interface Documentation.

Why can't we accept V3000 molfiles?

The InChI binaries we use currently do not accept V3000 molfiles, and so we cannot accept V3000 molfiles as we need an InChI Key for ChEMBL.

When should I use ACTIVITY_PROPERTIES and ACTIVITY_SUPP? What is the difference?

The ACTIVITY_PROPERTY file is utilised where there is an experimental result in the ACTIVITY file which can or should be qualified with another parameter. Such additional information is often useful in assessing the mechanism behind the result, or the quality or reliability of the reported main value.

Examples include:

• Independent variables in the assay which may have been systematically changed in order to assess their influence on the ACTIVITY VALUE (e.g. dose of test substance).

• Calculated values relating to the ACTIVITY VALUE if considered particularly useful in assessing the quality of the ACTIVITY VALUE (e.g. the slope of an IC50 curve).

ACTIVITY_SUPP is utilised for bulk storage of raw data relating to ACTIVITY values, including both data used directly to calculate the ACTIVITY value, and also miscellaneous data from the same experiment, not used in this calculation, but which may be of interest to the specialist user.

Examples include:

• Individual percentage inhibition points on a curve where an IC50 value has been quoted in the ACTIVITY file.

• Additional observations on the experimental animals from which data was assessed (e.g. Kidney cyst formation).

When should I use the ASSAY_PARAMETERS?

The ASSAY_PARAMETERS table can be used to add structured, supplementary data about assay level variables.

There are a large number of metadata fields in the ASSAYS table which support the deposition of diverse data. These fields contain specific information about, for example, the protein target, assay tissue or assay cell type used. In addition to these fields the assay description is a free text field which can be used to summarise the method, overall assay aim, target plus isoform/mutation details and any other biological entities present in the assay.

Where depositors want to include more structured metadata which is not regularly captured in the ASSAYS table, the ASSAY_PARAMETERS can be used to capture additional information. This could concentration of compound used, the pH of the buffer, the instrument used for data collection or the timepoints of the experiment.