Simplify case submissions and add collection-level manifest

DIRECTORY_STRUCTURE.md

@@ -1,40 +1,51 @@
 # Directory structure
 
-## Repository layout
-
 ```text
 open-science-cases/
 ├── README.md
 ├── SUBMISSION_TEMPLATE.md
 ├── DIRECTORY_STRUCTURE.md
+├── LICENSE
+├── manifest.json                 # Collection-level manifest, outside case folders
 └── cases/
-    ├── template/                  # Worked example with a .science export
+    ├── template/                 # Worked submission example
     │   ├── README.md
-    │   ├── PROMPT.md
     │   └── session.science
-    └── case-title-as-lowercase-words/
-        ├── README.md          # Completed submission template
-        ├── PROMPT.md          # Original request and user follow-ups
-        ├── session.science    # Open-Science research package, if applicable
-        ├── inputs/            # Original inputs, prompts, documents, data
-        ├── expected/          # Reference answers or target artifacts
-        ├── outputs/           # Results produced by the product
-        │   └── <run-id>/       # Example: 20260924T083000Z-v1
-        └── attachments/       # Screenshots and supporting evidence
+    └── <case-name>/
+        ├── README.md             # Research goal, credits, package, sharing scope
+        └── session.science       # Export of the actual research session
 ```
 
-The `template/` folder is a worked example. Other case paths show the intended layout. Git does not track empty directories; create a directory when adding its first file.
+The template and new case folders contain only `README.md` and `session.science`. The collection-level `manifest.json` stays at the repository root; do not add a separate manifest or `PROMPT.md` to a case folder.
+
+Use a stable, descriptive case folder name with lowercase words joined by hyphens. Existing folder IDs are retained. Link files using paths relative to the case README.
+
+## Collection-level manifest
+
+The root [manifest.json](manifest.json) has one entry per published `.science` package. It indexes the whole package; the manifest inside `.science` describes the package's internal contents.
+
+| Field | Meaning |
+|---|---|
+| `schema_version` | Version of this collection index schema; currently `1`. |
+| `repository` | Hugging Face dataset repository ID. |
+| `source_revision` | Repository commit used to obtain the published package metadata. |
+| `cases[].case_id` | Stable case folder ID. |
+| `cases[].readme_path` | Repository-relative path to the case description. |
+| `cases[].package.path` | Repository-relative path to the published `.science` file. |
+| `cases[].package.size_bytes` | Size of that file in bytes. |
+| `cases[].package.sha256` | SHA-256 digest of that file's complete contents. |
+| `cases[].is_template` | Optional flag set to `true` for the worked example. |
 
-## Naming and organization
+Research goals, credits, sharing scope, and optional research notes remain in the case README, avoiding duplicate metadata in the manifest.
 
-- Derive folder names from case titles, using lowercase ASCII letters, numbers, and hyphens. Keep names unique and stable; add a short suffix if necessary.
-- Do not group cases by year, status, or product, so review decisions and product renames do not change paths.
-- Keep product, case type, status, and tags in each case's README.
-- Use descriptive file names such as `source-paper.pdf`, `prompt.txt`, and `expected-summary.md`.
-- Reference files with relative Markdown links, for example `[Source](inputs/source-paper.pdf)`.
-- Keep each run in its own folder under `outputs/`; record its date, version, settings, and result in the case README. Use UTC timestamps with a `Z` suffix for run IDs.
-- Add only the folders relevant to a case. The completed case README is always required. An Open-Science case also needs `PROMPT.md` and `session.science`.
+### Update convention
 
-## As the library grows
+Maintainers regenerate the manifest from the published package metadata after adding or replacing a package. For files stored through Hugging Face LFS/Xet, use the LFS content SHA-256 and file size; these can be obtained from the Hub repository tree without downloading the packages. Use a computed SHA-256 for files without LFS metadata. Do not use the Git blob ID or Xet storage identifier as the package SHA-256.
+
+Record the exact commit used as `source_revision`, then commit the generated manifest. This source commit can precede the manifest's own commit; it identifies the indexed package snapshot. README descriptions can be updated independently. For an exact package download, use:
+
+```text
+https://huggingface.co/datasets/AIPOCH-AI/open-science-cases/resolve/<source_revision>/<package.path>
+```
 
-Avoid duplicating large attachments between cases; link to an existing repository file or a stable source when appropriate. Keep individual directories small. An index or a structured JSONL/Parquet export can be added later when search or automated evaluation requires it.
+If a public package is a redacted derivative, index the published derivative's bytes, size, and digest. File hashes support integrity checking and version identification; importability, reproduction, and scientific quality require separate inspection.

README.md

@@ -3,45 +3,48 @@ license: apache-2.0
 pretty_name: Open Science Cases
 tags:
   - product-cases
-  - evaluation
+  - research-workflows
 ---
 
 # Open Science Cases
 
-Private case library for AIPOCH product development, evaluation, and reproducible demonstrations. Store each case's task, source inputs, expected results, and observed outputs together.
+Public collection of research cases run with [AIPOCH Open-Science](https://github.com/aipoch/open-science). Cases document actual research workflows and the evidence retained in exported `.science` session packages.
 
-This is the **dataset repository**: `datasets/AIPOCH-AI/open-science-cases`. Use this destination for case submissions.
+The template and new case folders contain only a short **README.md** and a **session.science** file. The repository-level [manifest.json](manifest.json) stays outside the case folders and indexes the published packages with their paths, file sizes, and SHA-256 digests. Research goals, author or team credits, and sharing scope belong in each case's README.
 
-## Submit a case
+## Prepare and submit a case
 
-1. Name the case folder after its case title, using lowercase words joined by hyphens (for example, `smoking-and-depressive-symptoms-in-nhanes-2015-2016`). Check that the name does not already exist; add a short suffix if needed.
-2. Create `cases/<case-name>/`. The [worked example](./cases/template/README.md) is in `cases/template/`.
-3. Copy [SUBMISSION_TEMPLATE.md](./SUBMISSION_TEMPLATE.md) to that folder as `README.md`. Replace placeholders; use `N/A` where a section does not apply.
-4. If the case comes from Open-Science, export its session as `session.science` and add `PROMPT.md` with the original user request and meaningful user-authored follow-ups. Keep the full research history in the package.
-5. Add inputs and supporting files following [DIRECTORY_STRUCTURE.md](./DIRECTORY_STRUCTURE.md). Create only the directories needed for that case.
-6. Upload the whole case folder together. Use a commit message such as `Add case: <case-name>`.
-7. Start with status `draft`. When complete, set `ready-for-review`; a reviewer records their findings and marks it `accepted` or `needs-work`.
+1. Choose a research task relevant to your work and run it in Open-Science using your usual research workflow. Approve or revise plans, inspect results, and request corrections as appropriate; these interactions form part of the case history.
+2. Export the actual session as `session.science`. The package is the submitted record of the conversation, execution, and retained artifacts; its contents depend on the export selection.
+3. Create `cases/<case-name>/README.md` from [SUBMISSION_TEMPLATE.md](SUBMISSION_TEMPLATE.md). Briefly describe the research goal, identify the author or team and preferred attribution, link the package, and state the sharing scope. See [cases/template/README.md](cases/template/README.md) for a worked example.
+4. Submit the README and package together. This repository is public, so upload only material cleared for public distribution. Cases intended only for internal inspection should be handed to the AIPOCH team through an agreed private channel.
 
-These statuses are documentation conventions, not automated approval gates. Keep the same folder name when revising a case; Git commits record its history.
+Submit only `README.md` and `session.science` in the case folder, without a separate prompt file, poster, or case-level manifest. Maintainers update the root collection manifest when a package is added or replaced; contributors do not need to create a manifest entry.
 
-## Upload from the CLI
+### Before submission
 
-After logging in with a token that has write access to this organization:
+- Confirm that the README states the research goal, author or team, `.science` filename, and sharing scope.
+- Confirm that the exported package opens in a compatible Open-Science version and contains the session and artifacts you intend to share. Briefly note any known omissions or access requirements in the README.
+- Check the exported content against the agreed sharing scope, including third-party data and confidential material.
 
-```sh
+### Upload a public case
+
+Use a stable folder name with lowercase words joined by hyphens, for example `nhanes-smoking-depressive-symptoms`. Existing case IDs remain valid.
+
+```bash
 hf upload AIPOCH-AI/open-science-cases ./cases/<case-name> cases/<case-name> --repo-type dataset
 ```
 
-Replace `<case-name>` before running. For browser submissions, use **Files → Add file → Upload files**, preserving the case directory paths.
+You can also upload through the repository's **Files** tab, preserving the same folder paths. The destination is the dataset repository `datasets/AIPOCH-AI/open-science-cases`.
+
+## Inspect a case
 
-## What belongs here
+Start with the case README, use [manifest.json](manifest.json) to identify and check the published package, then import the `.science` file in a compatible Open-Science version to inspect the retained history and artifacts. Any re-execution is a separate step and may require dependencies, external data, or access described in the case.
 
-- Product scenarios, prompts, source documents, reproducible steps, and expected outcomes.
-- Actual outputs and evaluation notes tied to a product/model version.
-- Supporting images, PDFs, tables, or other files referenced by a case.
+The manifest describes file identity; it does not establish scientific correctness or successful reproduction. This is a folder-based case collection rather than a standardized `load_dataset()` table or Dataset Viewer dataset.
 
-Record source URLs and usage restrictions for third-party materials. Repository privacy does not grant rights to redistribute source material. Repository content is licensed under the [Apache License 2.0](./LICENSE), except where third-party materials have their own licenses or usage restrictions.
+## Sharing and maintenance
 
-## Reading cases
+The repository-level manifest is separate from the manifest inside each `.science` package. Its minimal schema and update convention are described in [DIRECTORY_STRUCTURE.md](DIRECTORY_STRUCTURE.md).
 
-Browse the `cases/` directory and open a case's `README.md`. This is a folder-based case archive, not yet a standardized table for `load_dataset()` or the Dataset Viewer. For Open-Science cases, open `PROMPT.md` for a concise request history and import `session.science` into a compatible version of Open-Science to inspect the complete package.
+The repository declares the [Apache-2.0 license](LICENSE). Third-party data and other materials may have separate terms; record relevant sources and restrictions in the case README. Public availability does not expand those permissions. Permission to reuse a case description or its figures in a preprint should also be stated in the case README or confirmed with its authors.

SUBMISSION_TEMPLATE.md

@@ -1,68 +1,33 @@
 # [Case title]
 
-Copy this file to `cases/<case-name>/README.md` and replace all placeholders. Derive `<case-name>` from the case title using lowercase words joined by hyphens.
+Copy this template to `cases/<case-name>/README.md`, replace the bracketed text, and submit it with `session.science`. Use the language most suitable for your case. The collection manifest is maintained by the repository team.
 
-## Case details
+## Research goal and case description
 
-| Field | Value |
-|---|---|
-| Case folder | cases/<case-name>/ |
-| Product / feature | [name] |
-| Author | [person or team that created the case] |
-| Submitter | [person or team that submitted this case] |
-| Created / updated | YYYY-MM-DD / YYYY-MM-DD |
-| Status | draft |
-| Case type | [demo / evaluation / regression / bug / feature-request] |
-| Tags | [topic, workflow, modality] |
-| Product / model version | [version or commit; N/A if not run] |
-
-## Goal and context
-
-What is the user trying to accomplish? Why does this case matter to the product? State the intended audience and relevant background.
-
-## Inputs and sources
-
-For Open-Science cases, link `PROMPT.md` and `session.science` here. In `PROMPT.md`, preserve the original user request and meaningful user-authored follow-ups in order. Check the export's file selection before submission.
-
-| File or URL | Purpose | Source / usage restrictions |
-|---|---|---|
-| inputs/[filename] | [what this contains] | [origin and permissions] |
+[Briefly describe the research question, relevant context or data, and what was done in this session. A short paragraph is sufficient; detailed methods and execution history can remain in the `.science` package.]
 
-List any prerequisites, settings, dependencies, and source access dates. Use relative links for files stored with this case.
+## Authors and attribution
 
-## Reproduction steps
+- Author(s) / team: [Names or team name; include affiliation if appropriate.]
+- Preferred attribution: [How the author(s) or team should be credited when describing this case.]
+- Submitted by: [Name or handle, if different from the research author(s); otherwise omit.]
 
-1. [Set up the product and relevant settings.]
-2. [Provide the exact input, prompt, or user action.]
-3. [Describe how to inspect the result.]
+## Session package
 
-### Exact prompt or request
+- [`session.science`](session.science): [Briefly state which session or stage this export covers.]
 
-```text
-[Paste the full prompt or request, or link a file in inputs/.]
-```
+[Optional: known omissions, external data or access requirements, or the Open-Science version used, if known. No separate transcript, prompt file, execution log, or output directory is required.]
 
-## Expected result and acceptance criteria
+## Sharing scope
 
-Describe a successful result. Link reference outputs in `expected/`, if available.
-
-| Criterion | How to check | Pass condition |
-|---|---|---|
-| [criterion] | [manual check or metric] | [specific expected behavior or threshold] |
-
-## Actual result
-
-Write `Not run` if this is a proposed case. Otherwise record the run date, product/model version, settings, and links to outputs under `outputs/<run-id>/`.
-
-| Criterion | Result (pass / fail / not-run) | Evidence |
-|---|---|---|
-| [criterion] | not-run | [relative file link or observation] |
+| Use | Permission / conditions |
+|---|---|
+| AIPOCH team inspection and reproduction | [Allowed / requires confirmation / not allowed; conditions if any.] |
+| Case description or selected figures in the preprint | [Allowed / requires confirmation / not allowed; attribution or review conditions if any.] |
+| Public distribution of the `.science` package and README | [Allowed / requires confirmation / not allowed; applicable license or data restrictions.] |
 
-Describe deviations, limitations, and relevant screenshots. Keep observed results separate from expected results.
+[Mention relevant third-party sources or terms where applicable. If public distribution is not approved, submit through an agreed private channel rather than this public repository.]
 
-## Review
+## Additional notes (optional)
 
-- Reviewer: [unassigned]
-- Review date: [pending]
-- Decision: [pending / accepted / needs-work]
-- Notes and next actions: [notes]
+[Any result caveats, unfinished work, or context helpful to a reviewer. Omit this section if unnecessary.]

cases/template/PROMPT.md

@@ -1,18 +0,0 @@
-# Prompts: NHANES smoking and depressive symptoms case
-
-These are the user-authored requests in the exported Open-Science session, in order. The wording is preserved. Automated auditor messages are omitted from this summary and remain in `session.science`.
-
-## Initial request
-
-> I'd like to conduct a retrospective analysis of existing NHANES 2015–2016 survey data to investigate how cigarette smoking relates to depressive symptoms. My aim is to understand the observed pattern and explore factors that might help explain it, to inform a future study. Could you explore what these cross-sectional data can support and help me decide on a useful first analysis?
-
-## Follow-up requests
-
-1. > add visualization and sensitive analysis
-2. > make a one-to-one verification for values in tables and figures comparing with those in report
-3. > tell me the position for the 6 failed in source results and report
-4. > i see the part of your fixed of the first 4 position is "on symptom-score scale" at the start of the paragraph, should it be from linear or logistic model result?
-5. > can you find why the agent cause this inconsistent values. where does it get the wrong valuew?
-6. > add strobe flowchart for research
-
-For the full conversation, artifacts, and review trail, inspect [`session.science`](session.science) in Open-Science.

cases/template/README.md

@@ -1,40 +1,30 @@
 # NHANES 2015–2016: Smoking and depressive symptoms
 
-## Case details
+This folder is a worked submission example. Future cases can use [SUBMISSION_TEMPLATE.md](../../SUBMISSION_TEMPLATE.md) and a descriptive folder name.
 
-| Field | Value |
-|---|---|
-| Folder | `cases/template/` |
-| Product / feature | AIPOCH Open-Science research workflow and `.science` export |
-| Author | Not recorded in the export |
-| Submitter | `bobo-xxx` |
-| Session created | 2026-09-23 |
-| Status | ready-for-review |
-| Case type | evaluation / research workflow |
-| Tags | NHANES, epidemiology, reproducibility, report verification |
+## Research goal and case description
 
-This folder is a worked example for future case submissions. Name future case folders after their case titles.
+Explore what a cross-sectional analysis of NHANES 2015–2016 can support about the association between cigarette smoking and depressive symptoms. The session includes requests for visualizations, sensitivity analysis, checks of report values against source tables and figures, investigation of inconsistent values, and a STROBE flowchart.
 
-## Goal
+This README describes the recorded research task and does not certify its scientific results.
 
-Explore what a cross-sectional analysis of NHANES 2015–2016 can support about the association between cigarette smoking and depressive symptoms. The session later requested visualizations, sensitivity analysis, a check of report values against source tables and figures, an investigation of inconsistent values, and a STROBE flowchart.
+## Authors and attribution
 
-## Files
+- Author / team: Not recorded in the existing export metadata.
+- Preferred attribution: Not recorded; confirm with the research author or team before attributing research authorship.
+- Submitted by: `bobo-xxx`.
 
-- [`session.science`](session.science): exported Open-Science session package. Its manifest identifies the session as “Smoking and depressive symptoms in NHANES 2015-2016.” The export was created on 2026-09-24 at 07:51 UTC. SHA-256: `40b1d4c7d81932bf8c89d34d7668fc558328a20c4aff8130801fa575de39f6ad`.
-- [`PROMPT.md`](PROMPT.md): the initial user request and subsequent user-authored follow-ups, in session order. Automated auditor messages are not copied into this prompt file; they remain in the package history.
+## Session package
 
-## Review focus
+- [`session.science`](session.science): exported Open-Science session titled “Smoking and depressive symptoms in NHANES 2015-2016.” The session was created on 2026-09-23 and the export on 2026-09-24 at 07:51 UTC.
+- Published package size and SHA-256: see the `template` entry in the collection-level [manifest.json](../../manifest.json).
 
-1. Can another reviewer import and inspect the `.science` package in a compatible version of Open-Science?
-2. Do reported numbers in text, tables, and figures agree with the underlying results and the correct model scale?
-3. Are the selection flowchart labels and counts supported by the data?
-4. Are conclusions framed as associations rather than causal effects from cross-sectional data?
+The `.science` file retains the exported conversation, execution records, and artifacts. Its contents depend on the export selection. Import the file in a compatible Open-Science version to inspect the retained history; re-execution is a separate step.
 
-Record findings and product version when reviewing. This README describes the case; it does not certify the scientific results.
+## Sharing scope
 
-## Package notes
+This package and README are currently distributed in the public case repository. Additional case-specific permissions for manuscript descriptions, selected figures, or further reuse were not recorded in the existing metadata; confirm them with the research author or team when needed. NHANES data and other third-party material remain subject to their source terms. The repository license is described in the [root README](../../README.md).
 
-Open-Science imports `.science` packages as read-only research history. The package may include conversation history, selected file versions, Notebook records, and verification evidence. File inclusion depends on the export selection. The package manifest says account credentials, permission grants, and provider continuation identities are excluded. Review content before wider sharing; keep this dataset private.
+## Additional notes
 
-The `.science` format comes from [aipoch/open-science](https://github.com/aipoch/open-science).
+When inspecting this case, useful checks include agreement between report values and underlying results, support for selection flowchart counts, and appropriate interpretation of a cross-sectional association. Record any findings separately from the original session history.

manifest.json

@@ -0,0 +1,260 @@
+{
+  "schema_version": 1,
+  "repository": "AIPOCH-AI/open-science-cases",
+  "source_revision": "2bfe1c8ec5af3c2ead842810489949c9d26b32cf",
+  "cases": [
+    {
+      "case_id": "case1",
+      "readme_path": "cases/case1/README.md",
+      "package": {
+        "path": "cases/case1/session.science",
+        "size_bytes": 4422601,
+        "sha256": "b2e680e213f2eda4c903491ed1069e25117a020b84627384d8a630dbd82bf16d"
+      }
+    },
+    {
+      "case_id": "case2",
+      "readme_path": "cases/case2/README.md",
+      "package": {
+        "path": "cases/case2/session.science",
+        "size_bytes": 147092867,
+        "sha256": "91df8f326eb4b3c10add6216ed85de9e78b93cfa0c309342f732a00108ddf420"
+      }
+    },
+    {
+      "case_id": "case3",
+      "readme_path": "cases/case3/README.md",
+      "package": {
+        "path": "cases/case3/session.science",
+        "size_bytes": 200891766,
+        "sha256": "77f2479441a56685ba8985e9e0b8ed9c1138460063a6d439b9120c28fde52c3f"
+      }
+    },
+    {
+      "case_id": "case4",
+      "readme_path": "cases/case4/README.md",
+      "package": {
+        "path": "cases/case4/session.science",
+        "size_bytes": 264317535,
+        "sha256": "120d442fb6b20a01cbcddb3f02cd764f537c1182d20cf679c27710aa958ff6ba"
+      }
+    },
+    {
+      "case_id": "case5",
+      "readme_path": "cases/case5/README.md",
+      "package": {
+        "path": "cases/case5/session.science",
+        "size_bytes": 2733119,
+        "sha256": "ec183c501a0f9138152e0af519174698423fd62cadf64734a2841cce957a9b67"
+      }
+    },
+    {
+      "case_id": "case6",
+      "readme_path": "cases/case6/README.md",
+      "package": {
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+        "size_bytes": 76283248,
+        "sha256": "fe3db6a7ddd54e15db365935c49db16093693c87d92106a2efe758cbcd99f198"
+      }
+    },
+    {
+      "case_id": "case7",
+      "readme_path": "cases/case7/README.md",
+      "package": {
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+        "size_bytes": 991179045,
+        "sha256": "b2ca04d9c95766d798809f0d61d8c7a431e48679cb83e77fd481c60622c53a1f"
+      }
+    },
+    {
+      "case_id": "case8",
+      "readme_path": "cases/case8/README.md",
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+        "path": "cases/case8/session.science",
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+        "sha256": "72d6f7df93991c438d3ec211fa3f6afd18d5089910dff40a9ab8a1d4811da11a"
+      }
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+    {
+      "case_id": "case9",
+      "readme_path": "cases/case9/README.md",
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+        "path": "cases/case9/session.science",
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+        "sha256": "044e6a003401f5aa887bb1ad5b2fa470ee845feab662129a56d07bbc26834610"
+      }
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+    {
+      "case_id": "case10",
+      "readme_path": "cases/case10/README.md",
+      "package": {
+        "path": "cases/case10/session.science",
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+        "sha256": "631098baf785781b7fa2ac41c03fb70b73505f3e214c4cbf4bc67b3a6db39d7d"
+      }
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+    {
+      "case_id": "case11",
+      "readme_path": "cases/case11/README.md",
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+        "path": "cases/case11/session.science",
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+      }
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+    {
+      "case_id": "case12",
+      "readme_path": "cases/case12/README.md",
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+        "path": "cases/case12/session.science",
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+        "sha256": "96b6a074fb9e6aedae667b9d87c72112e1f6bf03e067356e7f9398e76b3bd542"
+      }
+    },
+    {
+      "case_id": "case13",
+      "readme_path": "cases/case13/README.md",
+      "package": {
+        "path": "cases/case13/session.science",
+        "size_bytes": 14506784,
+        "sha256": "2197426d15e62434ae145e196a364b16eeef5c2bd89aac078a45482a6d8bb5ca"
+      }
+    },
+    {
+      "case_id": "case14",
+      "readme_path": "cases/case14/README.md",
+      "package": {
+        "path": "cases/case14/session.science",
+        "size_bytes": 14002784,
+        "sha256": "20c3e4777b398ca0bae0c574ce887c40868fd02f02d57fd7ec6e2c3335f92412"
+      }
+    },
+    {
+      "case_id": "case15",
+      "readme_path": "cases/case15/README.md",
+      "package": {
+        "path": "cases/case15/session.science",
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+        "sha256": "7ff908b1c8fb1478ec8bebd5598875975a9ead6ef5b73c1e3918a23982fe81fe"
+      }
+    },
+    {
+      "case_id": "case16",
+      "readme_path": "cases/case16/README.md",
+      "package": {
+        "path": "cases/case16/session.science",
+        "size_bytes": 3061611,
+        "sha256": "fb3366cfa1759d364303d40c18f7a55d2fa99b8e2d9d517380f45ac74d78bca0"
+      }
+    },
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