zmahnoor14 · zmahnoor14 · Mar 18, 2026 · Mar 18, 2026 · Mar 18, 2026 · Mar 18, 2026
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 ![Contributors](https://img.shields.io/github/contributors/zmahnoor14/BioXend)
 
 # BioXend 
-BioXend is a new computational framework for submitting Microbial Biotransformation of Xenobiotics data. 
+BioXend is a new computational framework for submitting Microbial Biotransformation of Xenobiotics data. You can checkout the webpage for BioXend project here: https://zmahnoor14.github.io/BioXend/
 - WP1: is to develop minimum reporting standards based on community consensus
 - WP2: is to automate the metadata collection
 - WP3: is to develop a submission workflow to [ChEMBL](https://www.ebi.ac.uk/chembl/)

diff --git a/Standards/MIXMB_Biotransformation.md b/Standards/MIXMB_Biotransformation.md
@@ -59,7 +59,6 @@ This document identifies Minimum Information (MI) required to report the biotran
 - [11. Data Quality Tiers](#11-data-quality-tiers)
 - [12. Example Complete Record](#12-example-complete-record)
 - [13. Integration with Other Standards](#13-integration-with-other-standards)
-- [15. Version History](#15-version-history)
 - [16. References](#16-references)
 - [17. Contact and Contributions](#17-contact-and-contributions)
 
@@ -1571,15 +1570,152 @@ cross_references:
 
 ---
 
-## 15. Version History
+## 14. Data Access and Repository Guidance
+
+### 14.1 Repository and Standard Documents
+
+The MIX-MB standard documents, submission template, and BioXend pipeline are openly available:
+
+- **Standard documents:** [GitHub — zmahnoor14/BioXend](https://github.com/zmahnoor14/BioXend), under `Standards/`
+- **Submission template:** `Standards/Templates/Template.xlsx` — the **Activity** sheet covers MIX-MB(B)
+- **BioXend pipeline:** Nextflow workflow (`main.nf`) in the repository root
+
+### 14.2 Files Generated by This Standard
+
+MIX-MB(B) experimental data feed the activity and assay parameter files required for ChEMBL deposition. The BioXend pipeline produces:
+
+| Output File | Generator Script | Content |
+|-------------|-----------------|---------|
+| `ASSAY.tsv` | `generate_assay.R` | Assay descriptions per organism × condition |
+| `ASSAY_PARAM.tsv` | `generate_assay.R` | Quantitative experimental parameters |
+| `ACTIVITY.tsv` | `write_activity_tsv.R` | Compound–assay activity links with measurements |
+
+These files are joined to compound records via CIDX (MIX-MB(X)) and organism records via AIDX (MIX-MB(M)).
+
+### 14.3 Submitting to ChEMBL
+
+MIX-MB(B) activity files are deposited to [ChEMBL](https://www.ebi.ac.uk/chembl/) as part of the complete six-file MIX-MB submission package. For deposition enquiries, contact **chembl-help@ebi.ac.uk**.
+
+**Pre-submission checklist for activity data:**
+- Every `ACTIVITY.tsv` row has a valid CIDX, AIDX, and RIDX
+- `ACTION_TYPE` uses only controlled vocabulary terms (Section 8.3)
+- `ACTIVITY_COMMENT` is non-empty for every row
+- All controls (Section 9) are documented in `ASSAY_PARAM.tsv` or `ASSAY_DESCRIPTION`
+
+### 14.4 Raw Data Repositories
+
+Raw analytical data accompanying a MIX-MB(B) submission should be deposited alongside the ChEMBL files:
+
+| Repository | URL | Data type |
+|------------|-----|-----------|
+| MetaboLights | https://www.ebi.ac.uk/metabolights/ | LC-MS raw data (.mzML), processed peak tables |
+| GNPS | https://gnps.ucsd.edu/ | MS/MS spectral data, molecular networks |
+| MassIVE | https://massive.ucsd.edu/ | Raw MS data (alternative to MetaboLights) |
+
+Record the repository accession in `ACTIVITY_COMMENT` and in the Bioschemas Dataset `@id` field (Section 2.3).
+
+---
+
+## 15. Licence and Reuse
+
+### 15.1 Standard Documents
+
+The MIX-MB standard documents are released under the **Creative Commons Attribution 4.0 International (CC BY 4.0)** licence ([https://creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/)).
+
+You are free to share, adapt, and build upon this standard for any purpose, provided you give appropriate credit:
+
+> Zulfiqar M. *et al.* MIX-MB: Minimum Information about Xenobiotics-Microbiome Biotransformation (v0.1.0). GitHub: https://github.com/zmahnoor14/BioXend
+
+### 15.2 Pipeline and Code
+
+The BioXend Nextflow pipeline and associated scripts are released under the **MIT Licence**. See `LICENSE` in the repository root for full terms.
+
+### 15.3 Submitted Data
+
+Data deposited using MIX-MB formats in public repositories are subject to that repository's terms:
+
+| Repository | Licence |
+|------------|---------|
+| ChEMBL | CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/) |
+| MetaboLights | CC0 1.0 or CC BY 4.0 (depositor's choice at submission) |
+| GNPS / MassIVE | CC0 (public domain) |
+
+When reusing MIX-MB-formatted datasets, cite both the original study (via its RIDX/DOI) and the MIX-MB standard.
+
+---
+
+## 16. Provenance
+
+Provenance records the origin, history, and chain of custody of biotransformation experimental data reported under MIX-MB(B). Complete provenance supports the **Reusable** principle of FAIR and enables independent reproducibility assessment.
+
+### 16.1 Study-Level Provenance
+
+Every activity record is anchored to a **Reference record** (RIDX) in `REFERENCE.tsv`:
+
+| Field | Description |
+|-------|-------------|
+| `RIDX` | Study-local identifier linking all six submission files |
+| `DOI` | Digital Object Identifier of the source publication |
+| `TITLE`, `AUTHORS`, `YEAR` | Full bibliographic metadata |
+
+The RIDX appears in every row of `ACTIVITY.tsv`, `ASSAY.tsv`, and `COMPOUND_RECORD.tsv`, making the publication the root provenance node for the entire data package.
+
+### 16.2 Experimental Provenance
+
+MIX-MB(B) traceability runs from raw measurement back to the study:
+
+```
+REFERENCE.tsv  (RIDX)
+       │
+       ├── COMPOUND_RECORD.tsv  (CIDX) ← chemical identity and source (MIX-MB(X))
+       ├── ASSAY.tsv            (AIDX) ← organism, strain, and conditions (MIX-MB(M))
+       └── ACTIVITY.tsv   (CIDX × AIDX × RIDX) ← measured outcome
+```
+
+Each activity row therefore carries the full experimental context via its three index keys.
+
+### 16.3 Protocol and Method Provenance
+
+Document the analytical and experimental methods in:
+
+| Location | What to record |
+|----------|----------------|
+| Bioschemas LabProtocol record (Section 2.2) | Step-by-step protocol with reagents and instruments |
+| `ASSAY_PARAM.tsv` | Quantitative parameters (temperature, duration, cell density, pH) |
+| `ASSAY_DESCRIPTION` in `ASSAY.tsv` | Free-text assay description including key conditions |
+| `ACTIVITY_COMMENT` | Analytical method details, processing software, mass accuracy |
+
+**Minimum method provenance for Gold-tier submissions (Tier 1):**
+- Instrument model and manufacturer
+- Software versions used for data acquisition and processing (e.g., MZmine 2.53, Xcalibur 4.1)
+- Spectral library used for metabolite annotation (e.g., MassBank, HMDB)
+
+### 16.4 Raw Data Provenance
+
+For each study, record:
+
+- **MetaboLights / GNPS accession** — in `ACTIVITY_COMMENT` and in the Dataset Bioschemas `@id` (Section 2.3)
+- **Raw data format** — mzML (preferred) or vendor format with conversion notes
+- **Processing pipeline** — version and parameters used (e.g., MZmine feature detection settings)
+
+### 16.5 Pipeline Provenance
+
+When generating submission files with BioXend, record in `REFERENCE.tsv` or `ASSAY_DESCRIPTION`:
+
+- **BioXend pipeline version** — from `versions/pipeline.txt`
+- **Date of file generation** — ISO 8601 format (YYYY-MM-DD)
+
+---
+
+## 17. Version History
 
 | Version | Date | Changes |
 |---------|------|---------|
 | 0.1.0 | 2026-02-05 | Initial draft: Core biotransformation standards |
 
 ---
 
-## 16. References
+## 18. References
 
 1. ChEMBL Bioactivity Database: https://www.ebi.ac.uk/chembl/
 2. BioAssay Ontology (BAO): http://www.bioassayontology.org/
@@ -1594,7 +1730,7 @@ cross_references:
 
 ---
 
-## 17. Contact and Contributions
+## 19. Contact and Contributions
 
 For questions, suggestions, or contributions to this standard, please contact:
 - **Maintainer:** Mahnoor Zulfiqar

diff --git a/Standards/MIXMB_Microbes.md b/Standards/MIXMB_Microbes.md
@@ -40,10 +40,11 @@ This document identifies Minimum Information (MI) required to report microbial o
   - [7.4 Growth Phases](#74-growth-phases)
 - [4. Data Validation Rules](#4-data-validation-rules)
 - [5. Data Quality Tiers](#5-data-quality-tiers)
-- [6. How to use the Template](#6-how-to-use-the-template)
-- [7. Version History](#7-version-history)
-- [8. References](#8-references)
-- [9. Contact and Contributions](#9-contact-and-contributions)
+- [8. Data Access and Repository Guidance](#8-data-access-and-repository-guidance)
+- [9. Licence and Reuse](#9-licence-and-reuse)
+- [10. Provenance](#10-provenance)
+- [11. References](#11-references)
+- [12. Contact and Contributions](#12-contact-and-contributions)
 
 ---
 
@@ -679,7 +680,131 @@ The MIX-MB submission template is provided as [Templates/Template.xlsx](Template
 
 ---
 
-## 8. References
+## 8. Data Access and Repository Guidance
+
+### 8.1 Repository and Standard Documents
+
+The MIX-MB standard documents, submission template, and BioXend pipeline are openly available:
+
+- **Standard documents:** [GitHub — zmahnoor14/BioXend](https://github.com/zmahnoor14/BioXend), under `Standards/`
+- **Submission template:** `Standards/Templates/Template.xlsx` (see Section 6)
+- **BioXend pipeline:** Nextflow workflow (`main.nf`) in the repository root
+
+### 8.2 Files Generated by This Standard
+
+MIX-MB(M) organism data feed the assay files required for ChEMBL deposition. The BioXend pipeline (`generate_assay.R`) produces:
+
+| Output File | Content |
+|-------------|---------|
+| `ASSAY.tsv` | Assay descriptions per organism × condition, indexed by AIDX |
+| `ASSAY_PARAM.tsv` | Quantitative experimental parameters (temperature, pH, incubation time, cell density) |
+
+These files are linked to compound and activity records via AIDX (see MIX-MB(B)).
+
+### 8.3 Submitting to ChEMBL
+
+MIX-MB(M) assay files are deposited to [ChEMBL](https://www.ebi.ac.uk/chembl/) as part of a full MIX-MB submission package. For deposition enquiries, contact **chembl-help@ebi.ac.uk** or use the ChEMBL deposition portal.
+
+**Pre-submission checklist for organism data:**
+- All assay rows pass Section 4 validation rules
+- Every `ASSAY_TAX_ID` is a valid, numeric NCBI TaxID
+- Scientific name matches the registered NCBI name for that TaxID
+- At least one `sameAs` URL to NCBI Taxonomy (Gold tier)
+
+### 8.4 Supplementary Sequence Data Repositories
+
+Sequencing data linked to strains used in a MIX-MB study should be deposited in:
+
+| Repository | URL | Data type |
+|------------|-----|-----------|
+| NCBI SRA | https://www.ncbi.nlm.nih.gov/sra | Short-read and long-read sequencing |
+| ENA | https://www.ebi.ac.uk/ena | Alternative / European submission |
+| NCBI Assembly | https://www.ncbi.nlm.nih.gov/assembly | Genome assemblies (GCA/GCF accessions) |
+
+Record the assembly accession in `additionalProperty` → `genome_assembly` (Section 2.3) and include it in the `sameAs` field of the Taxon record.
+
+---
+
+## 9. Licence and Reuse
+
+### 9.1 Standard Documents
+
+The MIX-MB standard documents are released under the **Creative Commons Attribution 4.0 International (CC BY 4.0)** licence ([https://creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/)).
+
+You are free to share, adapt, and build upon this standard for any purpose, provided you give appropriate credit:
+
+> Zulfiqar M. *et al.* MIX-MB: Minimum Information about Xenobiotics-Microbiome Biotransformation (v0.1.0). GitHub: https://github.com/zmahnoor14/BioXend
+
+### 9.2 Pipeline and Code
+
+The BioXend Nextflow pipeline and associated scripts are released under the **MIT Licence**. See `LICENSE` in the repository root for full terms.
+
+### 9.3 Submitted Data
+
+Data deposited using MIX-MB formats in public repositories are subject to that repository's terms:
+
+| Repository | Licence |
+|------------|---------|
+| ChEMBL | CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/) |
+| NCBI SRA / Assembly | NCBI data use policies (https://www.ncbi.nlm.nih.gov/home/about/policies/) |
+| ENA | EMBL-EBI data access policies |
+
+When reusing MIX-MB-formatted datasets, cite both the original study (via its RIDX/DOI) and the MIX-MB standard.
+
+---
+
+## 10. Provenance
+
+Provenance records the origin, history, and chain of custody of microbial organism data reported under MIX-MB(M). Complete provenance supports the **Reusable** principle of FAIR and enables reproducibility of biotransformation experiments.
+
+### 10.1 Study-Level Provenance
+
+Every assay record is anchored to a **Reference record** (RIDX) in `REFERENCE.tsv`:
+
+| Field | Description |
+|-------|-------------|
+| `RIDX` | Study-local identifier linking all submission files |
+| `DOI` | Digital Object Identifier of the source publication |
+| `TITLE`, `AUTHORS`, `YEAR` | Full bibliographic metadata |
+
+The RIDX appears in every row of `ASSAY.tsv`, making the publication the root provenance node for all organism data.
+
+### 10.2 Strain Identity Provenance
+
+The organism identifiers documented in Section 1.4 serve as provenance anchors for strain identity:
+
+| Identifier | Provenance Source |
+|------------|------------------|
+| **NCBI TaxID** | Verified against NCBI Taxonomy; links to authoritative taxonomy record |
+| **LPSN name** | Valid scientific name from the List of Prokaryotic Names (https://lpsn.dsmz.de/) |
+| **Culture collection ID** | Physical strain held at a registered biobank (ATCC, DSMZ, CGSC, etc.) |
+| **Genome assembly accession** | Sequenced genome lodged in NCBI Assembly or ENA |
+| `sameAs` URLs | Direct links to NCBI Taxonomy, LPSN, BacDive, or other authoritative records |
+
+For novel isolates without a registered TaxID, the closest assigned TaxID plus a note in `ACTIVITY_COMMENT` constitutes the strain's provenance record until formal registration.
+
+### 10.3 Environmental and Isolation Provenance
+
+For strains isolated from environmental or clinical samples, document the following MIxS-compliant fields (Section 3.3) as part of strain provenance:
+
+| Field | Provenance Aspect |
+|-------|------------------|
+| `isolation_source` | Biological or environmental matrix from which the strain was obtained |
+| `collection_date` | ISO 8601 date of sample collection |
+| `geo_loc_name` | Geographic origin of the sample |
+| `env_broad_scale` / `env_local_scale` | ENVO-annotated habitat classification |
+
+### 10.4 Pipeline Provenance
+
+When generating submission files with BioXend, record in `REFERENCE.tsv` or `ASSAY_PARAM.tsv`:
+
+- **BioXend pipeline version** — from `versions/pipeline.txt`
+- **`generate_assay.R` version** — from the script header
+- **Date of generation** — ISO 8601 format (YYYY-MM-DD)
+
+---
+
+## 11. References
 
 1. NCBI Taxonomy Database: https://www.ncbi.nlm.nih.gov/taxonomy
 2. Genomic Standards Consortium (GSC): https://www.gensc.org/
@@ -693,7 +818,7 @@ The MIX-MB submission template is provided as [Templates/Template.xlsx](Template
 
 ---
 
-## 9. Contact and Contributions
+## 12. Contact and Contributions
 
 For questions, suggestions, or contributions to this standard, please contact:
 - **Maintainer:** Mahnoor Zulfiqar

diff --git a/Standards/MIXMB_Standards_main.md b/Standards/MIXMB_Standards_main.md
@@ -4,11 +4,17 @@
 **Version:** 0.1.1  
 **Release Date:** March 16, 2026 (Draft)  
 **Status:** Draft Standard  
-**DOI:** XXXXXXX (to be assigned upon stable release)
 
 
 ---
 
+## Document structure overview
+
+<p align="center">
+  <img src="standards-main.png" />
+</p>
+
+
 ## Table of Contents
 
 - [Abstract](#abstract)
@@ -25,7 +31,7 @@
     - [How are assay/microbe data files integrated into the Template.xlsx](#how-are-assaymicrobe-data-files-are-integrated-into-the-templatexlsx)
   - [4. Biotransformation Metadata File(s)](#4-biotransformation-metadata-files)
     - [How are biotransformation data files integrated into the Template.xlsx](#how-are-biotransformation-data-files-are-integrated-into-the-templatexlsx)
-- [Identifiers and Cross-Referencing](#identifiers-and-cross-referencing)
+- [Identifiers and Cross-Referencing](#naming-convention-for-identifiers-and-cross-referencing-in-ChEMBL)
   - [Minting Scheme for Unknowns](#minting-scheme-for-unknowns)
 - [ChEMBL Links and FAQs](#chembl-links-and-faqs)
 
@@ -70,7 +76,7 @@ MIX-MB does not currently cover:
 
 ## Component Standards
 
-This standard comprises three interconnected sub-standards:
+This standard comprises three interconnected sub-standards: (individual components under construction)
 
 | Component | Description | Version | Last Updated (YYYY-MM-DD) | Document |
 |-----------|-------------|---------|--------------------------|----------|