diff --git a/README.md b/README.md index 71ab872..9ae7a6f 100644 --- 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 index 7aef2cb..67769f3 100644 --- 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) @@ -1571,7 +1570,144 @@ 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 | |---------|------|---------| @@ -1579,7 +1715,7 @@ cross_references: --- -## 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 index c83299e..b483539 100644 --- 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 index 17ab50f..ed961a2 100644 --- 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 + +

+ +

+ + ## 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 | |-----------|-------------|---------|--------------------------|----------| diff --git a/Standards/MIXMB_Xenobiotics.md b/Standards/MIXMB_Xenobiotics.md index 17b0941..1ad4a2d 100644 --- a/Standards/MIXMB_Xenobiotics.md +++ b/Standards/MIXMB_Xenobiotics.md @@ -30,10 +30,11 @@ This document identifies the Minimum Information (MI) required to report xenobio - [3.5 MIX-MB Controlled Vocabularies](#35-mix-mb-controlled-vocabularies) - [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) --- @@ -541,7 +542,132 @@ 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(X) compound data feed the chemical structure files required for ChEMBL deposition. The BioXend pipeline (`generate_compound_files.py`) produces: + +| Output File | Content | +|-------------|---------| +| `COMPOUND_RECORD.tsv` | Compound metadata indexed by CIDX | +| `COMPOUND_CTAB.sdf` | 2D chemical structures with embedded CIDX, InChI, and InChIKey | +| `chembl_mapping.tsv` | CIDX–ChEMBL ID cross-reference for known compounds | + +These files are linked to assay and activity records via CIDX (see MIX-MB(B)). + +### 8.3 Submitting to ChEMBL + +MIX-MB(X) compound 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 compound data:** +- All compounds pass Section 4 validation rules +- SMILES–InChIKey consistency verified (`generate_compound_files.py` performs this automatically) +- At least one external database ID present (Gold tier) or SMILES + name (Bronze minimum) +- `COMPOUND_CTAB.sdf` contains a valid molblock for every compound + +### 8.4 Supplementary Spectral Data Repositories + +Raw spectral data for detected biotransformation products (Section 2.2) should be deposited alongside the ChEMBL submission: + +| Repository | URL | Data type | +|------------|-----|-----------| +| MetaboLights | https://www.ebi.ac.uk/metabolights/ | LC-MS raw data, processed peak tables | +| GNPS | https://gnps.ucsd.edu/ | MS/MS spectral libraries, molecular networks | +| MassIVE | https://massive.ucsd.edu/ | Raw MS data (alternative to MetaboLights) | + +Record the repository accession in `ACTIVITY_COMMENT` for every row that cites an externally deposited spectrum. + +--- + +## 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/) | +| 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. + +--- + +## 10. Provenance + +Provenance records the origin, history, and chain of custody of chemical data reported under MIX-MB(X). Complete provenance supports the **Reusable** principle of FAIR and enables independent verification of compound identities and analytical assignments. + +### 10.1 Study-Level Provenance + +Every compound record is anchored to a **Reference record** (RIDX) in `REFERENCE.tsv`, which provides the top-level provenance anchor for the entire submission: + +| 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 `COMPOUND_RECORD.tsv`, `ASSAY.tsv`, and `ACTIVITY.tsv`, making the publication the root provenance node for all data. + +### 10.2 Compound Identity Provenance + +The external identifiers documented in Section 1.4 serve as compound provenance anchors: + +| Identifier | Provenance Source | +|------------|------------------| +| **InChIKey** | Derived computationally from the SMILES; validated against a reference database | +| **ChEMBL ID** | Structure matched in ChEMBL via API query (`generate_compound_files.py`) | +| **PubChem CID** | Structure registered in PubChem | +| **ChEBI ID** | Classification from ChEBI Ontology | +| `sameAs` URLs | Direct links to the authoritative source records | + +For compounds not found in any external database (novel metabolites, unknowns), the SMILES string and MSI identification level (Section 2.2) together constitute the compound's provenance record. + +### 10.3 Analytical Evidence Provenance + +For biotransformation products, the MSI level (Section 2.2) encodes the evidence chain supporting each structural assignment: + +| MSI Level | Required Provenance Evidence | +|-----------|------------------------------| +| Level 1 | Authentic reference standard; `reference_standard` (supplier, catalog no.), `retention_time_match`, `ms2_similarity_score` | +| Level 2 | Spectral library accession (`library_match_id`), `spectral_library`, match score ≥ 0.7 | +| Level 3 | `structural_hypothesis`, `fragment_pattern`, `chemont_class` | +| Level 4–5 | Observed m/z and `detection_consistency` only | + +### 10.4 Pipeline Provenance + +When generating submission files with BioXend, record in `REFERENCE.tsv` or `ACTIVITY_COMMENT`: + +- **BioXend pipeline version** — from `versions/pipeline.txt` +- **`generate_compound_files.py` version** — from the script header +- **Date of generation** — ISO 8601 format (YYYY-MM-DD) + +--- + +## 11. References 1. ChEMBL Database Guidelines: https://www.ebi.ac.uk/chembl/ 2. Metabolomics Standards Initiative: https://metabolomicssociety.org/resources/metabolomics-standards-initiative 3. Bioschemas Specifications: https://bioschemas.org/ @@ -554,7 +680,7 @@ 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/docs/assets/logo_bioxend.png b/docs/assets/logo_bioxend.png index 557cfa0..b2e6bbb 100644 Binary files a/docs/assets/logo_bioxend.png and b/docs/assets/logo_bioxend.png differ diff --git a/docs/index.html b/docs/index.html index 460a061..1981738 100644 --- a/docs/index.html +++ b/docs/index.html @@ -10,12 +10,13 @@