search-sop

name	Search SOP
description	Standard operating procedure for academic literature search. Covers local library search, 18 academic database APIs (L1), web_fetch direct access (L1.5), browser RPA for CNKI/Google Scholar (L2), and optional API services (L3). Includes domain routing, recency protocol, search iteration protocol (evaluate → refine → re-search up to 3 rounds), and Zotero/EndNote import bridges.

Search SOP — 文献搜索标准操作规程

适用场景

Read this skill when the user's request involves any of:

• Searching for academic papers, preprints, or datasets
• Importing references from Zotero, EndNote, BibTeX, or RIS
• Importing a local PDF into the library
• Asking for "最新/latest/recent" papers (recency search)
• Requesting literature from a specific database (CNKI, Google Scholar, WoS, etc.)
• Multi-concept intersection queries (e.g., "PFAS + machine learning")
• Understanding which API tool to use for a specific academic domain

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1. Three-Layer Search Architecture

Literature search uses a priority fallback model. Start from Layer 0 for local imports; Layer 1 for search; escalate to Layer 2/3 when the previous layer cannot satisfy the request.

Layer 0 — Local Reference Manager Import (not search)

One-time or periodic import from user's existing reference manager. These are NOT search tools — they read local databases directly.

Source	Detect → Import	Mechanism	Env
Zotero	library_zotero_detect → library_zotero_import	~/Zotero/zotero.sqlite (read-only)	Native
EndNote	library_endnote_detect → library_endnote_import	~/Documents/*.enl (read-only)	Native
BibTeX/RIS	library_import_bibtex / library_import_ris	Parse content string	All

Zotero fallback chain (try in order):

1. SQLite direct — fastest, works offline, Zotero need not be running
2. Local API (localhost:23119) — Zotero must be running, read-only
3. Web API v3 (api.zotero.org) — needs API Key + User ID, full CRUD
4. Format export — library_export_bibtex/ris → guide user to import manually

EndNote fallback chain: SQLite direct → Format export (no API available).

Docker environment: SQLite and Local API unavailable (host filesystem isolated). Explain to user: use BibTeX/RIS export from source app, or mount host Zotero directory as Docker volume.

Reverse path (RC → Zotero/EndNote): If Zotero Web API Key configured → library_zotero_web_create (requires approval_card). Otherwise → library_export_bibtex + guide user to File > Import in their reference manager.

Other reference managers (Mendeley, ReadCube, JabRef, Citavi, etc.): No direct bridge. Guide user to export BibTeX/RIS → library_import_bibtex/library_import_ris.

Key behaviors: detect → available: false in Docker → explain host isolation, suggest BibTeX/RIS. Reverse write via Web API → approval_card (risk_level: medium). First detection → record in MEMORY.md ## Global > ### Environment.

Layer 1 — Built-in API Tools (free, no auth, structured data)

Always available, require NO API keys. Use as primary search method.

Tool	Coverage	Best for
search_crossref / resolve_doi	150M+ DOIs	Default first choice — broadest DOI coverage
search_openalex / get_work / get_author_openalex	250M+ works	All disciplines, institutions, topics
search_europe_pmc	33M+ biomedical	Biomedical + full text + OA + citations
search_doaj	9M+ verified OA	Guaranteed open access
search_openaire	170M+ records	EU-funded research
search_arxiv / get_arxiv_paper	2M+ preprints	CS, physics, math
search_dblp / search_dblp_author	7M+ CS records	CS conferences + journals
search_pubmed / get_article	36M+ citations	Medicine, biology
search_biorxiv / search_medrxiv / get_preprint_by_doi	400K+ preprints	Biology / medical preprints
get_citations_open / get_references_open / get_citation_count	2B+ links	Citation tracking (all disciplines)
get_epmc_citations / get_epmc_references	Europe PMC	Biomedical citation tracking
find_oa_version (Unpaywall)	20M+ OA	Finding free PDFs by DOI
search_zenodo / get_zenodo_record	3M+ records	Datasets, software, supplementary
search_orcid / get_orcid_works	18M+ scholars	Author disambiguation
search_inspire / get_inspire_paper	1.5M+ HEP	High-energy physics
search_hal	4M+ French OA	French/European research
search_osf_preprints	30+ preprint servers	SocArXiv, PsyArXiv, EarthArXiv, etc.
search_datacite / resolve_datacite_doi	50M+ dataset DOIs	Dataset DOI resolution
search_ror	100K+ institutions	Institution disambiguation

Layer 1.5 — web_fetch Direct Access (relaxed — any public academic URL)

Between L1 API tools and L2 browser, use web_fetch to directly access any publicly accessible academic URL (not limited to known URLs).

Allowed targets (non-exhaustive):

• arXiv RSS (latest by category): https://rss.arxiv.org/rss/{category} (e.g. cs.CV)
• arXiv API (structured): https://export.arxiv.org/api/query?search_query=ti:transformer&sortBy=submittedDate&sortOrder=descending&max_results=20
• Semantic Scholar API: https://api.semanticscholar.org/graph/v1/paper/search
• CORE API: https://api.core.ac.uk/v3/search/works
• OA full-text links — URLs returned by find_oa_version (Unpaywall)
• Author/lab homepages — publication lists, preprint links
• Conference proceedings pages — NeurIPS, ICML, ACL, AAAI proceedings
• Preprint servers — bioRxiv, medRxiv, SSRN landing pages
• PubMed RSS: subscribe URLs from PubMed search results
• Repository metadata — GitHub/GitLab README for research software

RESTRICTIONS (do NOT web_fetch):

• Pages requiring login/authentication
• Paywalled full-text (use find_oa_version first)
• Pages with anti-scraping measures that return empty content

When to use web_fetch: Any public academic URL; page is static HTML or API endpoint; extracting content from a specific page. When to use browser instead: Form interaction needed; JavaScript rendering required; multi-page navigation.

Layer 2 — Browser RPA (databases without public APIs)

When Layer 1 tools cannot reach the required database, use the browser tool.

Target databases: Google Scholar, CNKI / 万方 / 维普, Web of Science / Scopus, IEEE Xplore, ACM DL, SpringerLink, any user-specified database.

IMPORTANT: Never pass profile parameter — omit it to use the default managed browser.

Workflow: open url → snapshot mode=efficient (note targetId) → act kind=type (query) → act kind=click (submit) → snapshot mode=efficient (extract results) → library_add_paper or report → close.

Critical: Always use mode=efficient (~10K chars vs 80K default). Always pass targetId from snapshot into act calls.

Error recovery: "Element not found" → one fresh snapshot, retry once. "Tab not found" → browser action=tabs for active targetIds. Context overflow → extract from last snapshot and close.

Operational limits (revised):

• Max 8 browser snapshots per search session
• Pagination: allowed up to 3 pages of results
• Click into paper detail pages: allowed for extracting abstract, citation count, and metadata
• STILL FORBIDDEN: downloading PDFs, submitting forms, creating accounts, entering personal data (standard GDPR/cookie consent banners may be dismissed with a single click)
• MUST always close browser after search is complete

Layer 3 — API Key Required (optional, user configures)

Do NOT prompt users to register. Only use when the user has already configured.

Service	Tools	Best for
Wentor API (wentor.ai account)	wentor_qa, wentor_search	Chinese literature, semantic search
OpenAlex (optional key)	search_openalex etc.	Higher rate limits (works without key at L1)

Third-party keys (Serper, Tavily, etc.): user installs skill/MCP themselves. Never ask users to register for third-party API keys.

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2. Domain → Tool Routing

Domain routing below is a STARTING POINT, not a hard constraint. If primary tools return insufficient results, expand to other tools (see §15 Search Iteration Protocol). Do NOT send queries to the wrong domain's tool.

Domain	Primary Tools	NEVER use	Notes
CS / AI / ML	search_dblp + search_arxiv	—	dblp = conferences; arXiv = preprints
Biomedical / Clinical	search_pubmed + search_europe_pmc	search_arxiv	bioRxiv/medRxiv for preprints only
Physics / Math	search_arxiv + search_inspire	—	INSPIRE for high-energy physics
Economics	search_crossref(journal=...)	search_arxiv	Top-5: AER, QJE, JPE, Econometrica, REStud
Social Sciences	search_osf_preprints(socarxiv) + search_crossref	search_arxiv	SocArXiv for preprints
Psychology	search_osf_preprints(psyarxiv) + search_pubmed	—	PsyArXiv + PubMed
Environmental Sci	search_crossref + search_openalex	search_arxiv	search_pubmed for health-effects angle
Chemistry	search_crossref	—	ChemRxiv blocked; CrossRef + browser
Engineering	search_osf_preprints(engrxiv) + search_crossref	—
Earth Sciences	search_osf_preprints(eartharxiv) + search_crossref	—
French/European	search_hal + search_openaire	—	HAL for French; OpenAIRE for EU-funded
Datasets / Software	search_zenodo + search_datacite	—
Chinese Literature	Layer 2 Browser → CNKI	All L1 tools	No free API covers Chinese journals
HEP / Astrophysics	search_inspire + search_arxiv	—	INSPIRE is authoritative for HEP

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3. Tool Filter Capability Matrix

What each tool CAN filter — determines routing decisions.

Tool	Journal	Year	Author	OA	Sort
search_crossref	✅ journal/issn	✅ from_year/until_year	❌	❌	relevance, published, cited-by
search_openalex	❌	✅ from_year/to_year	❌	✅	relevance_score, publication_date, cited_by_count
search_europe_pmc	✅ JOURNAL: in query	❌	✅ AUTH:	❌	RELEVANCE, DATE_DESC, CITED
search_pubmed	✅ [Journal] in query	✅ min_date/max_date	✅ [Author]	❌	relevance, pub_date
search_arxiv	✅ cat:	❌	✅ au:	all OA	relevance, date
search_dblp	❌	❌	❌	❌	relevance only
search_doaj	✅ field	✅ field	✅ field	all OA	custom field
search_openaire	❌	✅ from_date/to_date	✅ author	✅ oa_only	N/A
search_biorxiv/medrxiv	N/A	✅ date interval	❌	all OA	by date
search_inspire	✅ SPIRES j	❌	✅ SPIRES a	❌	mostrecent, mostcited
search_hal	❌	✅ sort	❌	all OA	producedDate
search_osf_preprints	✅ provider	❌	❌	all OA	N/A
search_zenodo	N/A	❌	❌	✅	bestmatch, mostrecent
search_datacite	N/A	✅ from_year	❌	❌	relevance

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4. Sort Parameters Quick Reference

When the user asks for "latest/最新" papers, you MUST pass date-based sort params.

Tool	Sort parameter	Recency value	Date filter params
search_arxiv	sort_by	'submittedDate'	—
search_crossref	sort	'published'	from_year, until_year
search_openalex	sort_by	'publication_date'	from_year, to_year
search_pubmed	sort	'pub_date'	min_date, max_date
search_biorxiv	—	(date-ordered by default)	interval: 'YYYY-MM-DD/YYYY-MM-DD'
search_europe_pmc	sort	'DATE_DESC'	—
search_inspire	sort	'mostrecent'	—
search_zenodo	sort	'mostrecent'	—
search_hal	sort	'producedDate_s desc'	—

Default sort is relevance for most tools. Never rely on the default when the user wants recent papers.

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5. Trigger Word Table

Trigger (zh/en)	Primary tool	Fallback
搜论文 / search papers	search_arxiv, search_crossref	search_openalex, browse skills/literature/search/
最新论文 / latest papers	search_arxiv (按时间排序), search_crossref (按时间排序)	search_openalex, browser
入库 / add paper	library_add_paper	library_batch_add
标签 / tag	library_tag_paper	library_manage_collection
导入 / 添加PDF / import PDF	library_add_paper	Read (built-in) + search_arxiv
Zotero 导入 / import Zotero	library_zotero_detect → import	Layer 0 fallback chain
同步到 Zotero / sync to Zotero	library_export_bibtex → guide import	With API Key: library_zotero_web_*
EndNote 导入 / import EndNote	library_endnote_detect → import	BibTeX/RIS fallback
RIS 导入 / import RIS	library_import_ris	library_import_bibtex

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6. Recency Search Protocol

When the user asks for "最新", "latest", "recent", or "past N months/weeks" papers, you MUST override default relevance sorting with date-based sorting.

Recency search workflow:

1. Determine time range: "最新" = last 3 months; "近期" = last 6 months; explicit range if stated.
2. Select 2+ sources by domain (see §2 Domain→Tool Routing).
3. Pass date-based sort and date filter where both are supported (see §4).
4. If API results are insufficient, escalate:
   • web_fetch arXiv RSS feed: https://rss.arxiv.org/rss/{category}
   • browser → Google Scholar with date filter (Tools → Custom range)
5. Never cite web_search / Brave Search unavailability as a reason to stop.

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7. Selection Logic Decision Tree

0. "latest/最新/recent"? → §6 Recency Protocol. MUST pass date sort.
1. Database NOT in L1 (CNKI, WoS, Scopus, GScholar)? → Layer 2 Browser.
2. Journal name specified? → search_crossref(journal=...) + search_europe_pmc(JOURNAL:...).
   Returns 0? → Layer 2 Browser.
3. Complex multi-filter? → Combine broadest tool + local filtering.
   Still insufficient? → Layer 2 Browser.
4. Simple keyword? → Route by domain (§2). Use 2+ sources for targeted/exhaustive.
5. L1 returns 0? → Suggest broadening keywords + offer L2/web_fetch.
   Do NOT retry same source. Do NOT cite "web_search not configured."
6. Multi-concept intersection? → §8 Decomposition.

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8. Multi-Concept Query Decomposition

When the user's topic spans multiple distinct concepts (e.g., "PFAS / microplastics / EDCs + machine learning"), a single combined query returns noisy results because text-based search engines match ANY keyword, not the intersection.

Decomposition strategy:

1. Identify the anchor concept — the methodological or thematic constant (e.g., "machine learning").
2. Split domain-specific concepts into separate sub-queries, each paired with the anchor.
3. Run each sub-query independently on the appropriate L1 tool(s) for the domain.
4. Merge and deduplicate results by DOI / title before presenting.
5. Use filters (from_year, has_abstract: true, sort: "published") on each sub-query.

Anti-patterns:

• Concatenating all keywords into one query string
• Using arXiv for non-CS/physics/math domains just because "machine learning" appears
• Reporting noisy results without filtering — always rate relevance before presenting

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9. L1 → L2 Escalation Rules

Use L2 when: user asks for CNKI/WoS/Scopus/Google Scholar, L1 returns 0 for journal query, need paywall fulltext, need faceted search or conference proceedings.

Do NOT use L2 for: simple keyword search (L1 faster), DOI resolution (resolve_doi), citation tracking (get_citations_open).

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10. Source Health Awareness

Tool responses include _source_health: { source, latency_ms }.

• Within session: 2+ errors (429/503/timeout) from a source → stop using it, switch to alternative (§2).
• Across sessions: 3+ consecutive sessions with failures → record in MEMORY.md: Source {name} unreliable since {date}: {pattern}. Prefer {alt}.
• Always use at least two sources for targeted/exhaustive scopes.

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11. Dynamic Tool Priority

User-configured API keys override defaults by elevating that service to L1:

• Record in MEMORY.md ## Global > ### Environment: "Wentor API: configured", etc.
• MUST-USE rule: User-configured API → call FIRST, then supplement with standard L1. Example: Wentor API configured → wentor_search FIRST, then arXiv/CrossRef.
• Brave API Key → web_search at L1. Zotero API Key → library_zotero_web_*.
• Never store actual API key values — only "configured" status.

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12. PDF Import Protocol

"导入PDF / import PDF" workflow:

1. Read the PDF (extract metadata: title, authors, DOI, abstract).
2. Verify via resolve_doi / search_arxiv (match title or DOI).
3. Dedup with library_search (check if already in library).
4. library_add_paper with source: "local_import" + pdf_path.
5. Never fabricate metadata — if extraction fails, ask the user.

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13. Post-Search Processing

1. Deduplicate — check DOI / arXiv ID against local library before adding.
2. Rate relevance — high / medium / low. Only add high + medium to library.
3. Batch import — use library_batch_add for 3+ papers.
4. Tag immediately — apply topic tags at import time for future retrieval.

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14. Paper Evaluation Criteria

Rate each paper high / medium / low based on: venue quality, citation count (adjusted for age), methodology soundness, reproducibility, and relevance to the user's question. Only add high + medium papers to the library unless user requests otherwise.

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15. Search Iteration Protocol

After every search execution, you MUST evaluate results before presenting them to the user. Do NOT treat one-shot search as final.

Evaluation Checklist (执行完每次搜索后必须评估)

1. Quantity: ≥5 relevant papers? If NO → broaden keywords OR switch source
2. Recency: Includes papers from last 2 years? If NO → add date filter
3. Coverage: Different methodologies/schools covered? If NO → cross-source search
4. Key papers: High-citation papers included? If NO → re-search with search_openalex(sort_by='cited_by_count') or search_crossref(sort='cited-by')

Iteration Rules

• Maximum 3 search iterations per topic
• Each iteration: use a different tool OR different keywords (NEVER repeat the same query)
• After each iteration, report a brief summary to the user (what was found, what is still missing)
• If 3 iterations exhausted and still insufficient → inform user and suggest web_fetch (L1.5), Layer 2 browser, or Layer 3 APIs

Cross-Source Search (supplements §2 domain routing)

§2 domain routing is a starting point. When primary results are insufficient:

1. Primary search: Use 1–2 tools from §2 domain routing
2. Supplementary search: If primary results fail the Evaluation Checklist → expand to other L1 tools or web_fetch
3. Merge & dedup: Deduplicate by DOI / title across all sources before presenting

Iteration Decision Flow

Search executed
  → Run Evaluation Checklist (4 criteria above)
  → ALL pass? → Present results, DONE
  → ANY fail?
      → Iteration count < 3?
          YES → Refine (different tool / keywords / filters) → re-search → re-evaluate
          NO  → Present best results + inform user of gaps + suggest next steps

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RC Local Tools Reference

library_* Call Patterns

Scenario	Tool chain
Single paper found via API	library_search (dedup check) → library_add_paper → library_tag_paper
Batch import (3+ papers)	library_batch_add (auto-dedup by DOI) → library_tag_paper per paper
Zotero import	library_zotero_detect → library_zotero_import (auto-dedup)
EndNote import	library_endnote_detect → library_endnote_import (auto-dedup)
BibTeX file import	library_import_bibtex (parse content)
RIS file import	library_import_ris (parse content)
PDF file import	Read (metadata) → resolve_doi (verify) → library_search (dedup) → library_add_paper
Citation tracking	get_citations_open / get_references_open → filter → library_batch_add
Dedup before adding	library_search with DOI or exact title — if found, skip
Export to Zotero	Without API key: library_export_bibtex → guide import. With key: library_zotero_web_create

search_* → library_* Integration

After search: present paper_card per result → user selects → library_add_paper or library_batch_add → auto task_link if active project → tag with search topic.

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Related Research-Plugins Skills

Browse these subcategory indexes for fine-grained methodology skills:

• literature/search/ — Boolean search, arXiv API, Semantic Scholar, citation chains
• literature/metadata/ — DOI resolution, OpenCitations, impact factors
• literature/fulltext/ — Unpaywall, OA strategies, preprint access
• literature/discovery/ — paper recommendation, trend monitoring
• tools/knowledge-graph/ — citation networks, knowledge graph construction
• tools/scraping/ — web scraping for academic sources
• tools/ocr-translate/ — OCR for scanned PDFs, multilingual translation
• domains/ — 16 discipline-specific subcategories (ai-ml, biomedical, chemistry, cs, ecology, economics, education, finance, geoscience, humanities, law, math, pharma, physics, social-science, business). Browse domains/{discipline}/ for domain-specific search strategies and database guides