dao-paper-search-mcp 1.0.0

MCP server for DAO-centred research: Zenon DAI, IAA Publications, ADAJ, plus a curated cross-platform paper-search surface (Crossref, OpenAlex, Semantic Scholar, arXiv, CORE, Zenodo, bioRxiv) — every hit pre-renders an inline_citation block for verbatim agent copy.

dao-paper-search-mcp

DAO-centred MCP server for academic research — Levant archaeology, biblical archaeology, Bronze/Iron Age, plus a curated cross-platform paper-search surface for the wider humanities. Started as a vertical complement to paper-search-mcp; now also reimplements the cross-platform adapters that matter for DAO/DH workflows (Crossref, OpenAlex, Semantic Scholar, arXiv, CORE, Zenodo) so every hit carries the same pre-rendered inline_citation block.

The DAO-specific sources (Zenon DAI, IAA Publications, ADAJ) are the original raison d'être and remain the strongest reason to use this server for Levantine archaeology. The horizontal adapters reduce the need to run paper-search-mcp alongside.

Sources

DAO-specific (Tier 1, original scope)

Tool	Source	Status
search_zenon	Zenon DAI (~1M records, multilingual DE/EN/FR/IT/HE/AR)	implemented
search_iaa	IAA Publications (ʿAtiqot, HA-ESI, IAA Book Series, Favissa, …)	implemented (OAI-PMH backend since v0.5.0)
search_adaj	DoA Publication Archive (ADAJ, SHAJ, Munjazat, JERD, Athar)	implemented
resolve_author	Wikidata SPARQL + local override list + GND fallback	implemented
resolve_site	iDAI.gazetteer (DAI's authoritative place register)	implemented

Cross-platform (selective paper-search-mcp substitution)

Tool	Source	Status
search_crossref	Crossref (~150M DOI-bearing scholarly works)	implemented (Sprint 1)
search_openalex	OpenAlex (~250M works, broadest open scholarly graph)	implemented (Sprint 1)
search_semantic_scholar	Semantic Scholar (citation graph, recommendations)	implemented (Sprint 2)
search_arxiv	arXiv (preprints, esp. Digital Humanities methods)	implemented (Sprint 2)
search_core	CORE (open-access full-text aggregator)	implemented (Sprint 3)
search_zenodo	Zenodo (data, software, preprints, every record gets a DOI)	implemented (Sprint 3)
search_biorxiv	bioRxiv + medRxiv preprints (via Europe PMC) — aDNA / paleogenomic currency	implemented (Sprint 4)

Tier 2 (DAO-specific)

Tool	Source	Status
search_propylaeum	PropylaeumDOK — FID Altertumswissenschaften OA repository (UB Heidelberg); classical archaeology, ancient history, Near East, Levant; multilingual DE/EN/IT/FR	implemented
search_ixtheo	IxTheo — Index Theologicus (UB Tübingen); theology, biblical studies, church history	implemented
search_openedition	OpenEdition — ~600 French SSH journals + books incl. Syria, Semitica, Yod, Topoi (OAI-PMH, CC0); multilingual FR/EN	implemented
search_gnomon	Gnomon Bibliographische Datenbank (via K10plus SRU) — classical studies bibliography	implemented
search_perse	Persée — French humanities journals (SPARQL backend)	planned
search_tocs_in	TOCS-IN — Toronto Classics journal tables of contents	planned

Install / Run

Via uvx directly from GitHub:

uvx --from git+https://github.com/leiverkus/dao-paper-search-mcp \
  python -m dao_paper_search_mcp.server

Or clone the repo and run from the working tree:

uvx --from git+file:///path/to/dao-paper-search-mcp \
  python -m dao_paper_search_mcp.server

OpenCode integration

Add to ~/.config/opencode/opencode.jsonc under the mcp block:

"dao-paper-search": {
  "type": "local",
  "command": [
    "uvx",
    "--from", "git+https://github.com/leiverkus/dao-paper-search-mcp",
    "python", "-m", "dao_paper_search_mcp.server"
  ],
  "enabled": true,
  "environment": {
    "CORE_API_KEY": "your-core-api-key",
    "DAO_PAPER_SEARCH_CONTACT_EMAIL": "[e-mail]",
    "DAO_PAPER_SEARCH_RATE_LIMIT_MS": "1000"
  }
}

Then update ~/.config/opencode/agent/research.md to route Levant/IAA/DoA-Jordan queries to this server first.

Environment variables

Variable	Required	Default	Purpose
CORE_API_KEY	yes (for search_core)	—	Bearer token for the CORE v3 API. Register free at core.ac.uk/services/api. Without it search_core raises an error on every call.
DAO_PAPER_SEARCH_CONTACT_EMAIL	no	"anonymous"	Your e-mail, sent as mailto: in User-Agent headers to polite-pool APIs (OpenAlex, Crossref, CORE, arXiv). Improves rate-limit priority on those APIs.
SEMANTIC_SCHOLAR_API_KEY	no	—	API key for Semantic Scholar. Without it the adapter runs on the public bucket (~100 req/min); with it limits rise substantially. Register at semanticscholar.org/product/api.
DAO_PAPER_SEARCH_RATE_LIMIT_MS	no	1000	Minimum milliseconds between outbound requests (simple rate limiter).

Architecture principles

• Vertical scope. Only sources paper-search-mcp does not cover.
• Tool independence. No internal calls to paper-search-mcp. Citation-graph delegation is the agent's responsibility. This preserves the cross-validation property of research.md.
• Schema fidelity. All search tools return the same Pydantic model (DAOPaper).
• Structured verification notes. When uncertain, the adapter sets verification_note, never guesses.
• Stdio cleanliness. MCP stdout is reserved for JSON-RPC; all logging goes to stderr.
• Output-shape lock-in for citations. Every hit carries an inline_citation block whose markdown field is a pre-rendered Markdown link (with ⚠️-prefix when audit.warn_marker or audit.aggregator is set). The agent copies this verbatim instead of formatting citations itself — structural enforcement of the AGENTS.md inline-link rule. Two extra fields (authoritative_authors_label, authoritative_bibliography_line) carry the tool-authoritative Author-Year and reference-list strings to prevent DOI-consistent author-year hallucinations.
• Centralised DOI normalisation. All adapters run DOIs through utils.doi.normalize_doi() — stripping resolver prefixes (https://doi.org/, info:doi/, doi: …) and lower-casing (DOI Handbook §2.4). Produces bare, case-insensitive 10.<registrant>/… strings for reliable deduplication. The render layer always reconstructs the full link from the bare string, so case drift in upstream APIs never leaks into bibliography output.

Inline citations

Each DAOPaper carries three blocks the agent should consume directly:

• identifiers: structured DOI / Zenon / IAA / ADAJ IDs (coexists with the legacy doi_or_id string).
• audit: primary_source, aggregator, verification_note, warn_marker — flags that drive the citation renderer.
• inline_citation: pre-rendered Markdown plus the tool-authoritative bibliography strings.

inline_citation fields (Schema v2.1, since v0.7.1)

Field	Purpose
url	Canonical URL (priority: DOI > OpenAlex > Zenon > IAA > ADAJ > arXiv > Semantic Scholar > CORE > Europe PMC > open_access_url > landing_page_url).
markdown	Finished in-text Markdown link. Author-Year form for academic hits ([(Cohen 1979)](https://doi.org/…)), Domain-Title form for web hits ([(example.org — Title…)](url)), Domain-only as last resort, and ⚠️-prefixed for aggregator/warn-flagged hits. Print-only hits (no URL) collapse to fallback_text. Copy this verbatim in prose.
authoritative_authors_label	Plain-text Author-Year string ("Finkelstein 1999") — None when no author context exists. Use this when you want to render Author-Year yourself instead of copying markdown; do not reconstruct from authors/year.
authoritative_bibliography_line	Full reference-list line with a trailing clickable link: "Finkelstein, I. (1999). Title. *BASOR* 314, 55–70. DOI: [10.2307/1357451](https://doi.org/10.2307/1357451)". DOI takes priority over primary_url; no suffix when neither is present. None when author/year/title metadata is incomplete. Copy verbatim in the references list.
fallback_text	"Cohen 1979: 61–79" — used when no url exists (print-only).

Author-label rules (inline):

• 1 author → "Cohen 1979".
• 2 authors → "Cohen & Yisrael 1995".
• 3 authors → "Boaretto, Finkelstein & Shahack-Gross 2010" (explicit, no et al.).
• ≥4 authors → "Bruins et al. 2011".
• Particle names (van der Plicht, von Daniken) stay intact in both inline and bibliography forms.

Bibliography author-rules: family + initials, Oxford comma before &, full list (no et al.). 1 author: "Cohen, R."; 2: "Cohen, R., & Yisrael, Y."; ≥3: "Boaretto, E., Finkelstein, I., & Shahack-Gross, R.".

markdown cascade: print-only → fallback_text; aggregator → ⚠️[(domain — Title…)](url); Author + Year → [(Author-Label Year)](url); URL + Title without Author-Year → [(domain — Title…)](url); URL only → [(domain)](url); audit.warn_marker prepends ⚠️ to the link form.

Authority overrides

src/dao_paper_search_mcp/data/authority_overrides.yml is the DAO-curated disambiguation list. To add an entry:

- canonical: "Steven A. Rosen"
  variants: ["S.A. Rosen", "Rosen, S.A.", "Steven Rosen"]
  q_id: "Q7613131"
  domain: "Levant archaeology, lithics, Negev Highlands Survey"
  affiliation: "Ben Gurion University"
  sites: ["Negev Highlands", "Camel Site"]

resolve_author checks the override list before consulting Wikidata. Add an entry whenever you encounter a misattribution in real research output.

Tests

uv sync --extra test
uv run pytest -v

The verification suite (tests/test_verification_suite.py) contains five frozen reference fingerprints drawn from the 2026-05-15 Negev-fortress test. One of them is a negative test — a hallucinated reference (Ben-Ami 2026 Levant 58(1):25–42) that converged across three LLM outputs. The suite asserts the server returns no result for this query; a false positive would mean the server is echoing the LLM hallucination.

Known limitations

search_iaa has no full-text search

The IAA backend (BePress/Solr) does not expose a public free-text search API. The v0.5.0 OAI-PMH-backed adapter compensates by AND-matching query tokens against title + description + subject + author fields client-side — broad enough for most archaeology queries, but not as deep as a real Solr q= would be. Recommendation: always pass at least a 5-year year_from/year_to window so the OAI listing stays manageable.

The reverse-engineered /do/search/results/json endpoint pulled from the page's 2019 JS bundle has been retired — BePress migrated the route without updating the bundle. See docs/2026-05-15-iaa-solr-probe.md for the full sondierungsbericht.

Disclaimer

MIT licensed. No cloud upload, runs entirely locally. GDPR-compliant: no personal data is collected or transmitted by the server itself.