141 lines
4.9 KiB
Markdown
141 lines
4.9 KiB
Markdown
# QQsci
|
|
|
|
QQsci is a Codex workflow skill for scientific manuscript projects. It acts as
|
|
the top-level orchestrator for materials-science writing, literature-grounded
|
|
revision, submission-package audit, Word DOI-only citation comments, and future
|
|
specialized modules such as QQwrite, QQfigure, and QQppt.
|
|
|
|
It is designed for workflows that combine:
|
|
|
|
- manuscript and Supporting Information `.docx` files
|
|
- main figures, SI figures, and TOC `.pptx` files
|
|
- Zotero literature items and AI-generated Zotero child notes
|
|
- QQnote-generated literature summaries or comparison tables
|
|
- target-journal positioning and reviewer-style pre-submission audit
|
|
- AFM Word article template assets
|
|
|
|
## Workflow Role
|
|
|
|
QQsci is the research-writing workflow controller, not a single-purpose writing
|
|
tool. It should decide which module to call, pass structured inputs between
|
|
modules, and perform final package-level quality control.
|
|
|
|
Planned module ecosystem:
|
|
|
|
| Module | Role |
|
|
|---|---|
|
|
| QQnote | Zotero child-note summaries and paper comparison tables |
|
|
| QQwrite | Long-form manuscript drafting, section rewriting, and Word template use |
|
|
| QQfigure | Materials figures, mechanism diagrams, TOC graphics, and figure QA |
|
|
| QQppt | Group meeting, journal club, submission, and defense slides |
|
|
| nature-citation | High-quality DOI candidates and claim-reference support |
|
|
| nature-data | Data availability, source data, repository, and FAIR checks |
|
|
| nature-response | Reviewer-response and revision-letter workflows |
|
|
| academic-humanizer | Academic de-AI wording, style naturalization, and consistency checks |
|
|
|
|
QQsci's built-in modules remain the quality-control layer until specialized
|
|
QQ* modules are developed.
|
|
|
|
## Current Scope
|
|
|
|
QQsci owns the manuscript-facing reasoning:
|
|
|
|
- extract manuscript keywords from topic, draft, figures, SI, or cover material
|
|
- classify strongly and weakly related papers
|
|
- compare the manuscript with strongly related papers
|
|
- audit missing experiments, controls, mechanisms, benchmarks, and statistics
|
|
- check figures, captions, SI consistency, formatting, spelling, and terminology
|
|
- produce Markdown reviewer reports
|
|
- add Word native citation comments containing DOI strings only
|
|
- route work to QQnote and future QQwrite/QQfigure/QQppt modules
|
|
- manage project-level DeepSeek, Zotero, Obsidian, and template configuration
|
|
|
|
QQsci does not directly insert Zotero Word fields. For Word manuscripts, citation
|
|
suggestions are added as native comments with one DOI per line.
|
|
|
|
## QQnote Relationship
|
|
|
|
QQnote is used only as the literature-note input tool.
|
|
|
|
QQnote may:
|
|
|
|
- generate or refresh Zotero child-note summaries
|
|
- summarize selected Zotero papers into Markdown comparison tables
|
|
|
|
QQsci then consumes those notes/tables and makes the manuscript decisions. QQnote
|
|
should not decide whether a paper is strongly related, weakly related, necessary
|
|
for citation, or sufficient as reviewer evidence.
|
|
|
|
QQnote must remain usable by itself. When QQsci calls QQnote, QQsci can inject
|
|
its own DeepSeek and Zotero configuration through
|
|
`scripts/run_qqnote_with_qqsci_config.py`.
|
|
|
|
When QQsci calls QQnote, use:
|
|
|
|
```powershell
|
|
py "$env:USERPROFILE\.codex\skills\qqsci\scripts\run_qqnote_with_qqsci_config.py" --script summarize_zotero_table -- --vault "C:\Users\qyh15\Documents\Obsidian Vault" --item-keys "SXAIQUJT X7GJZ627"
|
|
```
|
|
|
|
## Configuration
|
|
|
|
Use `config/config.template.json` as the public template and create a private
|
|
local file:
|
|
|
|
```text
|
|
config/config.local.json
|
|
```
|
|
|
|
Do not commit `config/config.local.json`.
|
|
|
|
QQsci is the top-level configuration owner for manuscript workflows. It maps its
|
|
DeepSeek and Zotero settings into QQnote-compatible environment variables when
|
|
calling QQnote:
|
|
|
|
- `deepseek.api_key` -> `AWESOMEGPT_API_KEY`
|
|
- `deepseek.base_url` -> `AWESOMEGPT_BASE_URL`
|
|
- `deepseek.model` -> `AWESOMEGPT_MODEL`
|
|
- `zotero.web_api_key` -> `ZOTERO_API_KEY`
|
|
- `zotero.user_id` -> `ZOTERO_USER_ID`
|
|
|
|
QQnote remains independently usable through its own environment variables, vault
|
|
`.env`, or AwesomeGPT/Zotero preferences.
|
|
|
|
## Submission Package Audit
|
|
|
|
For a full submission package, QQsci checks files in this order:
|
|
|
|
1. `Manuscript.docx`
|
|
2. `Figures.pptx`
|
|
3. `Supplementary Information.docx`
|
|
4. `Supplementary Information.pptx`
|
|
5. `Highlights.docx`
|
|
6. `CoverLetter.docx`
|
|
7. `TOC.pptx`
|
|
|
|
The manuscript and main figures define the story. SI, highlights, cover letter,
|
|
and TOC must stay consistent with that story.
|
|
|
|
## Writing Templates
|
|
|
|
Bundled template:
|
|
|
|
```text
|
|
assets/templates/afm/article-template.docx
|
|
```
|
|
|
|
This is stored as an asset. Do not edit it in place. Copy it to a manuscript
|
|
output path before use.
|
|
|
|
QQsci can keep journal templates and evidence/audit logic. A future QQwrite
|
|
skill can reuse these templates for long-form manuscript drafting and formatting.
|
|
|
|
## Installed Location
|
|
|
|
For Codex discovery, install under:
|
|
|
|
```text
|
|
C:\Users\qyh15\.codex\skills\qqsci
|
|
```
|
|
|
|
The source repository is maintained separately and can be pushed to Gitea.
|