lllin000_PaperForge/AGENTS.md

Agent Guide for Medical Research Vault

This repository is an Obsidian Vault dedicated to Medical Research (Sports Medicine, Orthopedics). It integrates closely with Zotero and PubMed via MCP tools.

0. AGENT PROTOCOL (MANDATORY)

You possess superhuman capabilities via 147+ specialized skills. Most tasks fail because agents try to "wing it" instead of using the specialized tools provided.

🛑 STOP & CHECK: The Skill Audit

Before executing ANY task, you MUST perform this audit:

1. CLASSIFY: What is the domain? (Bioinformatics, Clinical, Writing, Dev, Data)
2. SCAN: Look at the Skill Domain Index below.
3. SELECT: Pick the best tool for the job.
4. LOAD: Execute skill({ name: "selected-skill" }).

Rule of Thumb: If you are writing Python code for biology, chemistry, or plotting from scratch, YOU ARE WRONG. Load a skill instead.

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1. Skill Domain Index

Use this index to quickly find the right tool.

🧬 Bioinformatics & Genomics

Skill	Use When...
biopython	Parsing FASTA/GenBank, BLAST, basic sequence manipulation.
scanpy / anndata	Single-cell RNA-seq analysis, clustering, trajectory inference.
pysam	Handling BAM/SAM/VCF files (NGS data).
deeptools	ChIP-seq/ATAC-seq visualization (heatmaps, profiles).
scvi-tools	Deep probabilistic modeling for single-cell data.
etetoolkit	Phylogenetic trees, evolution, orthology.
scikit-bio	Microbiome analysis, diversity metrics (UniFrac).

🏥 Clinical & Medical

Skill	Use When...
pubmed-database	Literature search, retrieving abstracts/citations.
clinicaltrials-database	Searching ClinicalTrials.gov for study protocols/status.
clinical-decision-support	Generating GRADE-based guidelines or patient cohort analysis.
pyhealth	Analyzing EHR data, clinical prediction models (ICD/CPT).
pydicom	Reading/processing DICOM medical images (CT/MRI).
clinvar-database	Checking variant pathogenicity/clinical significance.
iso-13485-certification	Medical device QMS documentation.

🧪 Chemistry & Drug Discovery

Skill	Use When...
rdkit / datamol	Cheminformatics, SMILES parsing, molecule generation.
chembl-database	Looking up bioactivity data (IC_{50}, K_i), drug targets.
pubchem-database	Searching chemical properties, structures by name.
drugbank-database	Detailed drug pharmacology, interactions, targets.
diffdock	Molecular docking (protein-ligand binding poses).
alphafold-database	Retrieving 3D protein structures.

📊 Data Science & Statistics

Skill	Use When...
polars	Processing Large DataFrames (faster than Pandas).
scikit-survival	Survival analysis (Kaplan-Meier, Cox Proportional Hazards).
statistical-analysis	Performing rigorous statistical tests (ANOVA, t-tests) with APA reporting.
scientific-visualization	Creating Publication-Ready figures (Matplotlib/Seaborn wrappers).
shap	Explaining ML model predictions (Feature importance).
pymc	Bayesian modeling and probabilistic programming.

✍️ Writing & Research

Skill	Use When...
scientific-writing	Drafting Full Manuscripts (IMRAD structure, academic tone).
literature-review	Conducting systematic reviews across multiple databases.
citation-management	Finding citations, formatting BibTeX, verifying references.
latex-posters	Creating conference posters in LaTeX.
research-grants	Writing NSF/NIH grant proposals.
zotero-lit-review	Local Vault Search. ALWAYS check this before external search.

🛠️ Dev & Automation

Skill	Use When...
git-master	Any GIT operation (commit, log, blame).
frontend-ui-ux	React/Web UI tasks.
playwright	Browser automation / scraping.
opentrons-integration	Writing lab automation scripts (OT-2 robots).

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2. Environment & Tech Stack

• Platform: Obsidian (Knowledge Management)
• Reference Manager: Zotero (via MCP & Direct SQLite Access)
• Data Source: PubMed (via MCP)
• Primary Language: Simplified Chinese (简体中文)
• Scripting: JavaScript (Handlebars helpers for Templater), Markdown, Python (Zotero interaction)

3. Workflows & Commands ("Build/Test")

Since this is a knowledge base, "Build" corresponds to importing and structuring knowledge, and "Test" corresponds to verification.

Literature Search (The "Build" Loop)

Agents must follow this strict loop when asked to find literature:

1. Analyze: Use parse_pico to structure the research question.
2. Search: Use search_literature (PubMed) or zotero-lit-review (Local Library).
   • Constraint: Always check existing library first using check_articles_owned, search_pubmed_exclude_owned, or zotero-lit-review search.
3. Verify: Use get_session_pmids to confirm what was found.
4. Import:
   • CRITICAL: Ask user for Target Collection first (list_collections).
   • Use batch_import_from_pubmed for multiple items.
   • Use import_from_pmids for specific items.

Library Maintenance (The "Lint" Loop)

• Check Duplicates: Before adding, always check if PMID exists (check_articles_owned).
• Stats: Use get_library_stats to understand collection size.

4. Style Guidelines

Markdown & Note Structure

Follow the template in 99_System/Template/文献阅读.md.

Frontmatter (YAML) is MANDATORY:

---
title: " {{Title}} "
year: {{Year}}
type: {{Type}}
journal: " {{Journal}} "
impact_factor: {{IF}}
category: {{Category}}
tags:
  - 文献阅读
  - {{Subject_Tag}}
keywords: [ {{Keywords}} ]
pdf_link: "[[{{Link_To_PDF}}]]"
---

Content Structure:

• H1: Title
• H2: 📄 文献基本信息 (Basic Info)
• H2: 💡 文献内容总结 (Summary)
• H2: 🚀 未来方向 (Future Directions)
• H2: 📝 个人备注与补充 (Notes)

JavaScript (Templater/Handlebars)

• Location: 99_System/Template/*.js
• Style: Standard ES6+.
• Helpers: Register helpers using handlebars.registerHelper.
• Error Handling: Fail gracefully (return empty string) if data is missing.

5. Interaction Rules

Language

• Output: Simplified Chinese (简体中文) ONLY, unless asked otherwise.
• Search Terms: English (for PubMed), but explain in Chinese.

Protocol

1. No Hallucinations: Never invent PMIDs or citations.
2. User Confirmation:
   • Confirm Search Strategy before executing deep searches.
   • Confirm Target Collection before importing to Zotero.
3. Session Awareness: Use get_session_summary to track context.

6. Custom Skills

The following skills are installed in .opencode/skills and available for complex tasks. NOTE: This list is exhaustive. Use the Index in Section 1 for quick lookup.

(Complete skill list would be here - truncated for brevity)

7. External Rules Integration

• Copilot Instructions: See .github/copilot-instructions.md for detailed MCP tool usage.
• Workflow: See .github/zotero-research-workflow.md for the authorized PICO -> Search -> Import pipeline.