# MIX-MB Standards

**Minimum Information about Xenobiotics-Microbiome Biotransformation**

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**Version:** 0.1.1 · **Status:** Draft Standard · **Last updated:** March 2026\
**Maintainers:** Mahnoor Zulfiqar & Eleonora Mastrorilli (EMBL, Molecular Systems Biology Unit)\
**Funding:** NFDI4Microbiota FlexFund 2026
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MIX-MB defines the minimum metadata and data elements required to describe, share, and deposit xenobiotic microbial biotransformation experiments in a FAIR-compliant and reproducible way. It covers three interconnected aspects of every study:

* **MIX-MB(X)** — the chemical substrate (xenobiotic, drug, pesticide, dietary compound)
* **MIX-MB(M)** — the microbial organism or community
* **MIX-MB(B)** — the biotransformation assay, experimental conditions, and measured outcomes

Together these components ensure data can be directly deposited into community databases such as [ChEMBL](https://www.ebi.ac.uk/chembl/).

***

## Component Standards

| Component                                                                                  | Description                                                            | Version |
| ------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------- | ------- |
| [MIX-MB(X) — Xenobiotics](/embl-docs/component-standards/mixmb_xenobiotics.md)             | Chemical substrate identity, structure, and physicochemical properties | 0.1.1   |
| [MIX-MB(M) — Microbes](/embl-docs/component-standards/mixmb_microbes.md)                   | Microbial organism taxonomy, strain, and culture conditions            | 0.1.1   |
| [MIX-MB(B) — Biotransformation](/embl-docs/component-standards/mixmb_biotransformation.md) | Assay design, experimental conditions, and activity outcomes           | 0.1.1   |

For the full top-level overview including scope, ChEMBL file structure, and identifier conventions, see [MIX-MB Overview](/embl-docs/component-standards/mixmb_standards_main.md).

***

## How to Use These Standards

### If you are reporting data from a new study

1. **Assign identifiers first** — mint a RIDX (study), CIDXs (compounds), and AIDXs (assays) before entering any data. See the identifier conventions in [MIX-MB Overview](/embl-docs/component-standards/mixmb_standards_main.md).
2. **Fill in the submission template** — download the template from [Templates & Downloads](/embl-docs/submission-template/templates.md) and complete the relevant sheets.
3. **Run BioXend** — the Nextflow pipeline converts your template into six ChEMBL-ready files (`REFERENCE.tsv`, `COMPOUND_RECORD.tsv`, `COMPOUND_CTAB.sdf`, `ASSAY.tsv`, `ASSAY_PARAM.tsv`, `ACTIVITY.tsv`).
4. **Deposit to ChEMBL** — contact <chembl-help@ebi.ac.uk> or use the ChEMBL deposition portal.

### Data quality tiers

Each component standard defines three compliance tiers:

| Tier | Label                    | Suitable for                              |
| ---- | ------------------------ | ----------------------------------------- |
| 1    | Gold — Publication-Ready | ChEMBL submission, FAIR data publications |
| 2    | Silver — Research-Grade  | Internal data sharing, preprints          |
| 3    | Bronze — Preliminary     | Large-scale screening, initial deposits   |

{% hint style="warning" %}
The **submission template** (`Template_open.ods`) is the primary user-facing file. Do not modify its column structure — changes must go through the community review process described in [Versioning Policy](/embl-docs/governance/versioning.md).
{% endhint %}

***

## Scope

MIX-MB applies to experimental studies that measure the biotransformation of xenobiotic compounds by microbial organisms or microbial-derived systems. This includes in vitro single-strain assays, purified enzyme reactions, mixed microbial communities, time-course experiments, and product identification studies.

MIX-MB does **not** cover purely computational predictions of biotransformation, or metabolomics / genomics data (which have their own established standards).

***

## Licence and Citation

Standard documents are released under **CC BY 4.0**. The BioXend pipeline is released under the **MIT Licence**.

> Zulfiqar M. *et al.* MIX-MB: Minimum Information about Xenobiotics-Microbiome Biotransformation (v0.1.1). GitHub: <https://github.com/zmahnoor14/BioXend>

For questions, contributions, or endorsements: <zmahnoor14@gmail.com> · [GitHub Issues](https://github.com/zmahnoor14/BioXend/issues)


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