QQsci-skill/README.md

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:

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:

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:

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:

C:\Users\qyh15\.codex\skills\qqsci

The source repository is maintained separately and can be pushed to Gitea.