docs(BagIt): update community contribution and submission guides to a…

docs/submission-guides/community-contribution.md

@@ -107,6 +107,62 @@ After processing and publication, submitted community samples appear as public r
 <img src="/img/submission-process/community-contribution/8.png" width="1000"/>
 </p>
 
+Each published sample also receives a downloadable [BagIt](https://tools.ietf.org/id/draft-kunze-bagit-16.html) archive that bundles its raw data, the spectra metadata produced during processing, and checksums for every file.
+
+## Downloading the BagIt Archive
+
+The archive is built in the background, so it is not ready the moment a sample becomes public. Generation usually takes a few minutes, depending on how much data the sample contains. nmrXiv emails you once the archive is available.
+
+To download it, open the public sample page and use the **Download** menu in the top right corner. It offers two options:
+
+-   **Project Data** - the complete project data as a plain ZIP file.
+-   **Bagit Archive for this sample** - the BagIt package for the sample as described below.
+
+<p align="center">
+<img src="/img/submission-process/community-contribution/9.png" width="1000"/>
+</p>
+
+While generation is still running, the **Bagit Archive for this sample** option stays greyed out. Once the archive is ready the option becomes clickable.
+
+## What the BagIt Archive Contains
+
+The archive follows the BagIt structure: a `data/` folder holding the payload, plus tag files that describe and verify it.
+
+```
+S1020.zip
+├── bagit.txt                     BagIt version and character encoding
+├── bag-info.txt                  payload size, file count, bagging date
+├── manifest-sha256.txt           SHA-256 checksum of every file under data/
+├── tagmanifest-sha256.txt        SHA-256 checksum of the three files above
+└── data/
+    └── Perlatolic acid/          the published sample
+        ├── Perlatolic acid.mol   the assigned chemical structure
+        ├── 1_proton/             one folder per spectra dataset, as uploaded
+        │   ├── acqu, acqus       acquisition parameters
+        │   ├── fid               raw acquisition data
+        │   ├── pulseprogram      pulse sequence used
+        │   └── pdata/1/          processed spectra (1r, 1i, procs, title)
+        ├── 13_c13/
+        ├── 2_tocsy/
+        ├── 3_hsqc/
+        ├── 4_hmbc/
+        └── nmrxiv-meta/          metadata generated by nmrXiv
+            ├── S1020.nmrium      processed spectra metadata
+            ├── bio-schema.json   Bioschemas description of the sample
+            └── images/           rendered spectrum previews (PNG)
+```
+
+-   **Raw data** - every spectra dataset you uploaded is preserved unchanged under `data/<sample name>/`, including acquisition parameters, FIDs, pulse programs, and processed spectra in `pdata/`.
+-   **Structure** - the `.mol` file for the structure assigned to the sample.
+-   **nmrXiv metadata** - the `nmrxiv-meta/` folder adds the `.nmrium` file with the processed spectra metadata, a `bio-schema.json` description of the sample, and PNG previews of each spectrum.
+-   **Checksums** - `manifest-sha256.txt` lists a SHA-256 hash for every payload file, so you can confirm the download is complete and unmodified using any BagIt-compatible tool.
+
+BagIt makes each published sample a self-describing and portable data package. It keeps the raw data, processed metadata, structure information, previews, and verification files together, allowing the package to be shared, preserved, or moved between storage systems without relying on the nmrXiv website to interpret the files.
+
+-   **Integrity and preservation** - SHA-256 manifests help detect incomplete, damaged, or changed files when data is downloaded, copied, backed up, or restored.
+-   **Reproducibility and reuse** - raw acquisition files and processed spectra information remain available together for independent analysis, comparison, teaching, and method development.
+-   **Interoperability** - BagIt is an open packaging convention, so other repositories and compatible tools can inspect and validate the archive without the nmrXiv web application.
+
 ## Important Notes
 
 ::: warning

docs/submission-guides/data-lifecycle.md

@@ -5,7 +5,7 @@ Research data passes through many processes from creation to (voluntary or accid
 **Deposition:** User(s) can submit their datasets to the repository using our easy-to-use interface, or an electronic lab notebook such as Chemotion ELN. Using smart lab notebooks enables easy integration with commonly used software. We ensure that the submitted data sets are in accordance with minimum information standards and additional requirements set by the domain experts and funders. The submitter can then enrich their dataset with additional information (taxonomic and genomic information, related publication) according to standards defined by the community, with some metadata and acquisition parameters being pre-populated.
 
 **Processing/Archiving/Distribution:**
-nmrXiv infrastructure will convert the data into the standard formats using workflows over distributed infrastructure. Data and associated metadata will be processed, stored, and archived following the RDM best practises such as [BagIt](https://tools.ietf.org/id/draft-kunze-bagit-16.html).
+nmrXiv infrastructure will convert the data into the standard formats using workflows over distributed infrastructure. Data and associated metadata will be processed, stored, and archived following the RDM best practises such as [BagIt](https://tools.ietf.org/id/draft-kunze-bagit-16.html). For each publicly released sample, nmrXiv automatically generates a downloadable BagIt archive containing the raw data, processed spectra metadata, and checksums, accessible directly from the sample's public page once generation completes.
 
 **Archiving:**
 Once deposited, the users receive a stable identifier, typically a [DOI](https://www.doi.org/) hyperlink that remains unchanged for the resource's lifetime. As nmrXiv will issue [DOI](https://www.doi.org/)s, any deposited data will immediately have a stable identifier that can point to the dataset and allow its re-use or repurposing. This fully accommodates manuscript submission, peer review, and post-acceptance needs. nmrXiv will also develop restricted access models that allow only authorized reviewers to access the author's original NMR data. Upon acceptance, the [DOI](https://www.doi.org/)-labeled datasets will become publicly accessible.

docs/submission-guides/publication-deposition.md

@@ -324,6 +324,7 @@ Public records include:
 -   sample and molecule metadata,
 -   dataset-level spectra records,
 -   raw file downloads,
+-   a downloadable **BagIt archive**,
 -   license and citation information,
 -   nmrXiv identifiers and DOI metadata.
 
@@ -334,6 +335,66 @@ Public records include:
 </video>
 </p>
 
+<p align="center">
+<img src="/img/submission-process/community-contribution/8.png" width="1000"/>
+</p>
+
+Each published sample also receives a downloadable [BagIt](https://tools.ietf.org/id/draft-kunze-bagit-16.html) archive that bundles its raw data, the spectra metadata produced during processing, and checksums for every file.
+
+## Downloading the BagIt Archive
+
+The archive is built in the background, so it is not ready the moment a sample becomes public. Generation usually takes a few minutes, depending on how much data the sample contains. nmrXiv emails you once the archive is available.
+
+To download it, open the public sample page and use the **Download** menu in the top right corner. It offers two options:
+
+-   **Project Data** - the complete project data as a plain ZIP file.
+-   **Bagit Archive for this sample** - the BagIt package for the sample as described below.
+
+<p align="center">
+<img src="/img/submission-process/community-contribution/9.png" width="1000"/>
+</p>
+
+While generation is still running, the **Bagit Archive for this sample** option stays greyed out. Once the archive is ready the option becomes clickable.
+
+## What the BagIt Archive Contains
+
+The archive follows the BagIt structure: a `data/` folder holding the payload, plus tag files that describe and verify it.
+
+```
+S1020.zip
+├── bagit.txt                     BagIt version and character encoding
+├── bag-info.txt                  payload size, file count, bagging date
+├── manifest-sha256.txt           SHA-256 checksum of every file under data/
+├── tagmanifest-sha256.txt        SHA-256 checksum of the three files above
+└── data/
+    └── Perlatolic acid/          the published sample
+        ├── Perlatolic acid.mol   the assigned chemical structure
+        ├── 1_proton/             one folder per spectra dataset, as uploaded
+        │   ├── acqu, acqus       acquisition parameters
+        │   ├── fid               raw acquisition data
+        │   ├── pulseprogram      pulse sequence used
+        │   └── pdata/1/          processed spectra (1r, 1i, procs, title)
+        ├── 13_c13/
+        ├── 2_tocsy/
+        ├── 3_hsqc/
+        ├── 4_hmbc/
+        └── nmrxiv-meta/          metadata generated by nmrXiv
+            ├── S1020.nmrium      processed spectra metadata
+            ├── bio-schema.json   Bioschemas description of the sample
+            └── images/           rendered spectrum previews (PNG)
+```
+
+-   **Raw data** - every spectra dataset you uploaded is preserved unchanged under `data/<sample name>/`, including acquisition parameters, FIDs, pulse programs, and processed spectra in `pdata/`.
+-   **Structure** - the `.mol` file for the structure assigned to the sample.
+-   **nmrXiv metadata** - the `nmrxiv-meta/` folder adds the `.nmrium` file with the processed spectra metadata, a `bio-schema.json` description of the sample, and PNG previews of each spectrum.
+-   **Checksums** - `manifest-sha256.txt` lists a SHA-256 hash for every payload file, so you can confirm the download is complete and unmodified using any BagIt-compatible tool.
+
+BagIt makes each published sample a self-describing and portable data package. It keeps the raw data, processed metadata, structure information, previews, and verification files together, allowing the package to be shared, preserved, or moved between storage systems without relying on the nmrXiv website to interpret the files.
+
+-   **Integrity and preservation** - SHA-256 manifests help detect incomplete, damaged, or changed files when data is downloaded, copied, backed up, or restored.
+-   **Reproducibility and reuse** - raw acquisition files and processed spectra information remain available together for independent analysis, comparison, teaching, and method development.
+-   **Interoperability** - BagIt is an open packaging convention, so other repositories and compatible tools can inspect and validate the archive without the nmrXiv web application.
+
 ::: danger
 Once a project or sample is public, it cannot be reverted to a private draft. Review files, metadata, authors, license, and release date carefully before publishing.
 :::