# Templates & Downloads

The MIX-MB submission template is the primary entry point for researchers who want to deposit biotransformation data. It captures all mandatory, recommended, and optional fields across the three MIX-MB components in a single structured spreadsheet.

{% hint style="success" %}
**Download the submission template below.** Open it in LibreOffice Calc, Excel, or any spreadsheet application that supports the ODS format.
{% endhint %}

> **Can't open ODS?** Use [LibreOffice](https://www.libreoffice.org/) (free, cross-platform) or import directly into Google Sheets via File → Import.

***

## Template Structure

The template has four sheets, one per MIX-MB component plus a study reference sheet:

| Sheet                     | Maps to                                     | Covered by                                                             |
| ------------------------- | ------------------------------------------- | ---------------------------------------------------------------------- |
| **Reference**             | `REFERENCE.tsv`                             | Study / publication metadata                                           |
| **Chemicals**             | `COMPOUND_RECORD.tsv` + `COMPOUND_CTAB.sdf` | [MIX-MB(X)](/embl-docs/component-standards/mixmb_xenobiotics.md)       |
| **Microbes / Experiment** | `ASSAY.tsv` + `ASSAY_PARAM.tsv`             | [MIX-MB(M)](/embl-docs/component-standards/mixmb_microbes.md)          |
| **Biotransformation**     | `ACTIVITY.tsv`                              | [MIX-MB(B)](/embl-docs/component-standards/mixmb_biotransformation.md) |

***

## Colour Coding

Each column is colour-coded to indicate its requirement level:

| Colour    | Meaning                                                                      |
| --------- | ---------------------------------------------------------------------------- |
| 🟢 Green  | **Mandatory** — must be filled for a valid submission                        |
| 🔵 Blue   | **Recommended** — strongly encouraged; required for Gold (Tier 1) compliance |
| 🟡 Yellow | **Optional** — fill if available                                             |

{% hint style="info" %}
Fields marked **Auto-filled by BioXend** can be left empty — the pipeline will populate them automatically using RDKit (chemical properties) and the NCBI Taxonomy API (organism TaxIDs).
{% endhint %}

***

## Filling the Template: Quick Steps

1. **Reference sheet** — fill one row for your study. The `Reference_identifier` (RIDX) ties all other sheets together. If left empty, BioXend will generate one.
2. **Chemicals sheet** — one row per compound. Provide at minimum: `Common_Name`, `SMILES`, and `Chemical_identifier` (CIDX). BioXend auto-fills `InChIKey`, `Molecular_formula`, and `Molecular_weight` from the SMILES.
3. **Microbes / Experiment sheet** — one row per organism × condition combination. Provide: `assay_identifier` (AIDX), `Bacteria_scientific_name`, and `ASSAY_TYPE`. BioXend looks up `NCBI_Tax_ID` automatically.
4. **Biotransformation sheet** — one row per compound–assay interaction. Fill `Chemical_identifier`, `ASSAY_identifier`, and either `TEXT_VALUE` (qualitative) or `VALUE` + `UNITS` (quantitative).

{% hint style="warning" %}
The `Chemical_identifier` (CIDX) in the Biotransformation sheet must exactly match the `Chemical_identifier` in the Chemicals sheet. The same applies to `assay_identifier` (AIDX) across the Microbes and Biotransformation sheets.
{% endhint %}

***

## Identifier Quick Reference

| Identifier                 | Format                                   | Example                                         | Defined in      |
| -------------------------- | ---------------------------------------- | ----------------------------------------------- | --------------- |
| **RIDX** — Reference Index | `[Author]_[Label]`                       | `Zimmermann_GutAtlas`                           | Reference sheet |
| **CIDX** — Compound Index  | `CIDX[nnnn]`                             | `CIDX0001`                                      | Chemicals sheet |
| **AIDX** — Assay Index     | `[Author]_[Genus]_[species]_[Condition]` | `Zimmermann_Actinomyces_graevenitzii_anaerobic` | Microbes sheet  |

All three must appear together in every row of the Biotransformation sheet.

***

## Further Reading

{% content-ref url="/pages/9BIkGKtsjN7ewEKYaB9C" %}
[MIX-MB Overview](/embl-docs/component-standards/mixmb_standards_main.md)
{% endcontent-ref %}

{% content-ref url="/pages/fqiGj62sdbATgdJKqudY" %}
[MIX-MB(X) — Xenobiotics](/embl-docs/component-standards/mixmb_xenobiotics.md)
{% endcontent-ref %}

{% content-ref url="/pages/tIoqOvtGJTfj57IPrpSc" %}
[MIX-MB(M) — Microbes](/embl-docs/component-standards/mixmb_microbes.md)
{% endcontent-ref %}

{% content-ref url="/pages/3DH04X0B9OlDmgKVndFT" %}
[MIX-MB(B) — Biotransformation](/embl-docs/component-standards/mixmb_biotransformation.md)
{% endcontent-ref %}


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