📥
ChEMBL Data Deposition Guide
  • Introduction
  • Overview
    • Source Identifier
    • Depositor-Defined Identifiers
      • AIDX
      • RIDX
      • CIDX
    • File types and names
  • File structure
    • File hierarchy
    • Simplified input data schema
    • Deposition file list
    • Field names and data types - basic submission
      • The CONTACT field
      • ACTION_TYPE valid names
      • TARGET_TYPE list
      • Adding context using the ACTIVITY_PROPERTIES file
    • The ASSAY_DESCRIPTION field
  • Complex results sets
    • Linking files through depositor defined IDs
    • Linking multiple result types using TEOID
    • Supplementary data in the ACTIVITY_SUPP file
    • Flexible SAMID mapping
    • Field names and data types - more complex data types
  • Example dataset
  • Common data issues
  • Advanced features and documentation
  • Depositing activities against other depositors entities
  • Creating a COMPOUND_CTAB file from a file containing SMILES strings
  • FAQs
  • Glossary
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  1. File structure

Deposition file list

Files that may be included in a CHEMBL deposition

Filenames

Level

Depositor defined identifier (DDI) defined by this file

Records in this file can be 'Foreign-Keyed' to...

REFERENCE.tsv

primary

RIDX

-

COMPOUND_RECORD.tsv

primary

CIDX

RIDX

COMPOUND_CTAB.sdf

secondary

-

CIDX

ASSAY.tsv

primary

AIDX

-

ASSAY_PARAM.tsv

secondary

-

AIDX

ACTIVITY.tsv

tertiary

ACT_ID

CIDX, AIDX, RIDX

ACTIVITY_PROPERTIES.tsv

tertiary

-

ACT_ID

ACTIVITY_SUPP.tsv

tertiary

SAMID, REGID

ACT_ID

ACTIVITY_SUPP_MAP.tsv

tertiary

-

ACT_ID, SAMID

INFO.txt

tertiary

-

-

File: All filenames must have the appropriate 3 letter extension, '.tsv', '.sdf' or '.txt'.

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