# ChEMBL Data Deposition Guide

## ChEMBL Data Deposition Guide

- [Introduction](https://chembl.gitbook.io/chembl-data-deposition-guide/master.md)
- [Overview](https://chembl.gitbook.io/chembl-data-deposition-guide/deposition-overview.md)
- [Source Identifier](https://chembl.gitbook.io/chembl-data-deposition-guide/deposition-overview/source-identifier.md)
- [Depositor Defined Identifiers](https://chembl.gitbook.io/chembl-data-deposition-guide/deposition-overview/depositor-defined-identifiers.md)
- [RIDX](https://chembl.gitbook.io/chembl-data-deposition-guide/deposition-overview/depositor-defined-identifiers/ridx.md): Depositor-defined Reference IDs
- [AIDX](https://chembl.gitbook.io/chembl-data-deposition-guide/deposition-overview/depositor-defined-identifiers/aidx.md): Depositor-defined Assay IDs
- [CIDX](https://chembl.gitbook.io/chembl-data-deposition-guide/deposition-overview/depositor-defined-identifiers/cidx.md): Depositor-defined Compound IDs
- [File Types, Naming, and Deposition](https://chembl.gitbook.io/chembl-data-deposition-guide/file-types-naming-and-deposition.md): How to structure your deposition files and folder, and send it to us
- [File structure](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure.md)
- [File hierarchy](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/loader-files.md)
- [Simplified input data schema](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/loader-model.md)
- [Deposition file list](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/deposition-file-list.md)
- [Field names and data types - minimal data submission](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission.md)
- [README.toml](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/readme.toml.md): The README file that explains your dataset
- [REFERENCE.tsv](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/reference.tsv.md)
- [COMPOUND\_RECORD.tsv](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/compound_record.tsv.md)
- [COMPOUND\_CTAB.sdf](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/compound_ctab.sdf.md): The chemical structure file
- [Creating a COMPOUND\_CTAB file from a file containing SMILES strings](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/compound_ctab.sdf/creating-a-compound_ctab-file-from-a-file-containing-smiles-strings.md): If you need to create the file but you only have your compound structures as SMILES strings.
- [ASSAY.tsv](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/assay.tsv.md)
- [ACTIVITY.tsv](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/activity.tsv.md)
- [When to use VALUE and TEXT\_VALUE](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/activity.tsv/when-to-use-value-and-text_value.md)
- [Linking multiple result types from the same experiment, using TEOID](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/activity.tsv/linking-multiple-result-types-from-the-same-experiment-using-teoid.md)
- [Controlled vocabularies](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/controlled-vocabularies.md)
- [TARGET\_TYPE list](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/controlled-vocabularies/target_type-list.md): Specifies the type of target the experiment is assessing in the ASSAYS file.
- [ACTION\_TYPE valid names](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/field-names-and-data-types-minimal-data-submission/controlled-vocabularies/action_type-valid-names.md): Specifies the effect of the drug on its target for protein-based assays in the ACTIVITIES file.
- [Supplementary data files](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files.md)
- [ASSAY\_PARAM.tsv - Adding additional assay information.](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/assay_param.tsv-adding-additional-assay-information..md)
- [ACTIVITY\_PROPERTIES.tsv - Adding context to experimental results](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/activity_properties.tsv-adding-context-to-experimental-results.md)
- [ACTIVITY\_SUPP.tsv - Multiplex assays, supporting data, and complex results sets](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/complex-results.md)
- [ACTIVITY\_SUPP.tsv and ACTIVITY\_SUPP\_MAP.tsv](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/complex-results/activity_supp.tsv-and-activity_supp_map.tsv.md)
- [Linking supplementary data through SAMID and REGID](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/complex-results/linking-supplementary-data-through-samid-and-regid.md)
- [Flexible SAMID mapping](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/complex-results/linking-supplementary-data-through-samid-and-regid/flexible-samid-mapping.md)
- [Graphical representations of complex data linking](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/complex-results/graphical-representations-of-complex-data-linking.md)
- [Supporting data - Submission to BioStudies / BioImage Archive](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/supporting-data-submission-to-biostudies-bioimage-archive.md)
- ['INFO' files - Other context](https://chembl.gitbook.io/chembl-data-deposition-guide/file-structure/supplementary-data-files/info-files-other-context.md)
- [Example dataset](https://chembl.gitbook.io/chembl-data-deposition-guide/example.md): An example dataset, showing the structure of all required files and advice on avoiding common issues.
- [Common data issues](https://chembl.gitbook.io/chembl-data-deposition-guide/common-data-issues.md)
- [FAQs](https://chembl.gitbook.io/chembl-data-deposition-guide/faq.md)
- [Glossary](https://chembl.gitbook.io/chembl-data-deposition-guide/untitled-2.md)