Introduction to the ChEMBL Loader Gateway
The ChEMBL Gateway aims to satisfy a number of requirements for loading and storing data in ChEMBL
Although loading data to ChEMBL will remain by invitation only, and will remain in the complete control of ChEMBL administrators, the external facing 'Gateway' aims to stimulate external requests, and assist depositors in correctly formatting depositions before submission to ChEMBL.
Below are listed some of the basic key concepts used in the new ChEMBL loader. Other documentation pages go into many of these concepts in more detail, and some complex aspects are dealt with by examples (see 'Examples' above).


A depositor is equivalent to a src_id. In practice, multiple individuals within and organization may be recognized as individuals permitted to deposit data on behalf of a src_id. The management of multiple depositors for a single src_id is not dealt with by ChEMBL, but is the responsibility of the ChEMBL administrators.
Every src_id is also assigned a 'default RIDX' which is used as the RIDX if the load files do not specify an alternative RIDX.

Load files

Load files must be ascii or UTF-8 encoded, and named and formatted as described in the 'Requirements' section. Within these files, column headers such as 'CIDX', 'AIDX' and 'RIDX' are used to indicate the column position of the Depositor defined IDs. Depositor defined IDs may consist of a string of up to 200 UniCode characters
  • For each of these three key entities a single ('primary') file is used to define (or redefine) them, as shown in the 'Requirements' section.
  • Other (secondary) files may define or redefine properties of existing Depositor defined IDs (ie: which either exist in the corresponding primary file in the same deposition job, or already exist in the database).
  • Activity files must also cite only existing Depositor defined IDs.
Currently, ChEMBL only accepts data formatted into tsv (tab-separated variable) files, but alternative formats will be available in the future..

Advanced features and documentation

These are necessary reading for the majority of contributors. The documentation explains more complex results sets and options for the handling, normalization and release of the data.
Activity data that is more complicated than a simple 'cpdX has affinity Y nM against target Z' can now be accommodated in ChEMBL.
A Compound Normalization procedure is run separately from loading processes, and now includes an assessment of the quality of the drawn structures.


Embargoing is managed by administrators by appending a '-E date' option when loading a job.
Tagging and Freezing of 'sets' of deposition job_id is achieved with the loader, but the process is dealt with separately from the loading process itself.