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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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Overview

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Last updated 19 days ago

Loading data to ChEMBL is largely by invitation. However, if you believe you have high quality bioactivity data that others would benefit from viewing in ChEMBL, then please contact us by email: chembl-help@ebi.ac.uk.

This document provides a basic introduction to how bioactivity data should be formatted in order to be loaded into ChEMBL. Many aspects of this are best explained by reference to examples (see Example Load Dataset).

Deposition Overview

There is a downloadable guide to the basics of deposition here, designed to be easy to share with your collaborators.

Video Guide

We also have a short video guide to producing these files, using an example dataset.

Checklist

There is a checklist for the deposition process here, which we recommend working through once you have created files to send to us.

Deposition Process Chart

You can see a flowchart explaining the deposition process below.