nature-academic-search

Files (47)

• README.md
• README_EN.md
• SKILL.md
• mcp-snippet.json · config/
• settings-snippet.json · config/
• triggers-academic-search.toml · config/
• install.sh
• manifest.yaml
• README.md · mcp-server/
• academic_search_server.py · mcp-server/
• config.toml · mcp-server/
• requirements.txt · mcp-server/
• __init__.py · mcp-server/sources/
• arxiv.py · mcp-server/sources/
• crossref.py · mcp-server/sources/
• elsevier_common.py · mcp-server/sources/
• pubmed.py · mcp-server/sources/
• sciencedirect.py · mcp-server/sources/
• scopus.py · mcp-server/sources/
• __init__.py · mcp-server/tests/
• test_elsevier_live.py · mcp-server/tests/
• test_mcp_tools.py · mcp-server/tests/
• test_sources.py · mcp-server/tests/
• __init__.py · mcp-server/utils/
• config.py · mcp-server/utils/
• errors.py · mcp-server/utils/
• logging.py · mcp-server/utils/
• citation-parser.md · references/
• dedup-engine.md · references/
• pubmed-28344011.bib · references/
• pubmed-28344011.nbib · references/
• pubmed-28344011.ris · references/
• ris-bibtex-format.md · references/
• search-strategy.md · references/
• source-tiers.md · references/
• wf1-multi-source-search.md · references/workflows/
• wf2-citation-verification.md · references/workflows/
• wf3-mesh-strategy.md · references/workflows/
• wf4-citation-file-mgmt.md · references/workflows/
• wf5-reference-mgmt.md · references/workflows/
• wf6-strict-other-citation-impact-audit.md · references/workflows/
• academic_search.py · scripts/
• converters.py · scripts/
• format-converter.py · scripts/
• preflight.py · scripts/
• routing-and-ops.md · static/core/
• tools.md · static/core/

SKILL.md (first lines)

# Academic Search — Router

This skill is split into two layers:

- A **static layer** under `static/` that holds versioned, reusable content fragments (the MCP tool inventory and shared modules, and source routing plus operational rules).
- A **dynamic layer** (this file plus `manifest.yaml`) that detects which workflow the user needs and loads that workflow, reaching for shared modules and scripts only when a step needs them.

Do not try to apply the search logic from memory or from this router. Always load fragments from disk as described below.

## Routing protocol

Follow these five steps every time the skill is invoked.

### 1. Load the manifest and the core layer

Read [manifest.yaml](manifest.yaml). It declares the `workflow` axis, the allowed values, and the file paths each value maps to.

Also read every file listed under `always_load`:

- `static/core/tools.md` — the MCP tool inventory (core search, extended search, PubMed utilities) and the shared-module map.
- `static/core/routing-and-ops.md` — the T1→T2→T3 source routing quick guide, environment setup, error handling, and limitations.

### 2. Detect the workflow

Map the user's need to one or more `workflow` values:

- `multi-source-search` — find literature across sources.
- `citation-verification` — verify citations extracted from a document.
- `mesh-strategy` — build a MeSH/PubMed search strategy.
- `citation-file-mgmt` — convert/manage `.nbib`/`.ris`/`.bib` files.
- `reference-mgmt` — BibTeX, related-article discovery, ID conversion.
- `strict-other-citation-impact-audit` — determine strict independent other-citations, build article-level citation metric tables, identify high-profile citers (academy members, presidents/deans, talent-award holders, fellows, field leaders), and extract how they cited the target paper.

A combined request (for example search then export) may need more than one. State the detected workflow(s) in one short line before proceeding.

### 3. Load the matching workflow fragment(s)

Read the file mapped for each detected workflow (under `references/workflows/`). Do **not** read every workflow. Each workflow file links to the shared modules it needs.

### 4. Run the workflow using the loaded material

Apply the loaded material in this order:

1. Core tools and routing (`core/tools.md`, `core/routing-and-ops.md`) — which MCP tool for which need, and the T1→T2→T3 fallback chain that is the standard execution order across all workflows.
2. The workflow fragment — its specific steps.
3. Shared modules and scripts on demand (dedup, citation parser, search strategy, RIS/BibTeX format, format converter).

Report specific tool failures and continue with remaining tools; broaden terms when there are no results; fall back to manual generation from MCP-fetched metadata if a script fails twice.

### 5. Reach for references only when needed

The files under `references/` (and `scripts/`) are deep references, not defaults. Open them on demand per the `references.on_demand` table in the manifest — for example `references/source-tiers.md` for the full reliability classification, `references/dedup-engine.md` / `references/citation-parser.md` / `references/search-strategy.md` / `references/ris-bibtex-format.md` for the shared modules, and `scripts/academic_search.py` (no-MCP fallback discovery search) / `scripts/format-converter.py` / `scripts/preflight.py` for the tooling.

## Why this split

- The static layer is versioned and reviewable; the workflow files and shared modules were already factored this way.
- The dynamic layer keeps each invocation cheap: only the workflow the user needs enters context, instead of all six plus every module.
- The router itself is short on purpose. Update fragments and references, not this file, when adding scope.
- This structure mirrors the other nature-* skills (`nature-writing`, `nature-polishing`, `nature-reader`, `nature-paper2ppt`, `nature-figure`, `nature-citation`, `nature-response`, `nature-data`).

From ypan50918-ops/Yuan1z0825-nature-skills, Apache-2.0.

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