Scholar MCP

io.github.pvliesdonk/scholar-mcpv2.0.0Documents & Spreadsheets

FastMCP server for scholarly papers, patents, books and standards with docling PDF conversion

The current version, v2.0.0, was published to the official MCP registry on 2026-09-11. It is distributed as pvliesdonk-scholar-mcp on PyPI and as the Docker image ghcr.io/pvliesdonk/scholar-mcp:v2.0.0, filed under Documents & Spreadsheets by this index, and declares 42 environment variables. Removals and unreachable sources are measured across every server this index tracks, contract drift across the servers that answer in consecutive snapshots; the index's current counts put this record in context.

In-path gate · all MCP tools

Using Scholar MCP in Claude, Cursor, Gemini CLI, Cline, or Zed?

MCP tool contracts can change remotely with no version bump. The mcpindex gate pins each contract and HOLDs the call when it drifts-before your agent acts. Zero credentials. This is not the package install for this server itself (use Install this server for that).

Install the mcpindex gate (one command)

Rewrites your MCP host config so each server launches behind the gate. Inspect first: curl -fsSL https://mcpindex.ai/install.sh | less

uv tool install mcpindex-gate && mcpindex-config-wire

Auditable install path →Watch it hold a drift →

Trust verdict · v1 advisory · method

REVIEWstatus: PARTIALfresh until 2026-09-28 15:53 UTC

screened 2026-08-29tier: scannedgranularity: description-levelsource: registry

Semantic screen found no manipulation pattern in the description. Conformance probe not yet run.

mcpindex.integrity.descriptionpassINFO

evidence“Normal capability description”via static_description

Limits of this verdict

- Semantic screen only - the deterministic conformance probe has not run on this server
- Confidence is reported but not yet calibrated (v1)
- Screen reads the tool description, not the live behavior
- advisory
- registry description only no input schema
- screen model 8b
- The registry listing (version, packages, links) changed after this screen ran - the description we assessed did not

Semantic screen: an LLM judge reads the tool description for hidden instructions (status PARTIAL). A pass means the description is not lying, not that the tool is safe: a high-capability tool with an honest description still warrants caution. The deterministic conformance probe has not been run on this server yet, so the screen here is semantic-only. Posture: advisory. Confidences are reported but not yet calibrated (calibrated=false at v1). Full verdict history is not shown on this page.

Own this server? Screen its description →

That verdict was true at screening time (snapshot 2026-09-14).

Contracts can change after screening, with no version bump. The gate pins Scholar MCP’s tool contracts on first sight and holds any silent change before your agent acts - the check that keeps being true on Tuesday.

See your first HOLD in 2 minutes →

Cite this record

People vet a server before wiring it in. One line on your project site or docs answers that with an independent record: screening verdict, registry provenance, contract drift history. It stays current as new screens and drift events land.

Markdown

[Independent trust record for Scholar MCP](https://mcpindex.ai/server/io-github-pvliesdonk-scholar-mcp) - screening verdict, registry provenance, and contract drift monitoring.

HTML

<a href="https://mcpindex.ai/server/io-github-pvliesdonk-scholar-mcp">Independent trust record for Scholar MCP</a> - screening verdict, registry provenance, and contract drift monitoring.

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A live verdict badge for your README or listing. It reflects the current screen, links back here, and updates when the verdict does.

Markdown

[![mcpindex](https://mcpindex.ai/api/v1/badge/io-github-pvliesdonk-scholar-mcp)](https://mcpindex.ai/server/io-github-pvliesdonk-scholar-mcp)

HTML

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Environment variables

SCHOLAR_MCP_KV_STORE_URL

Persistent-state backend URL shared by every pvl-core subsystem that needs state. `memory://` is in-process and lost on restart; `file:///path` persists on one server; `redis://`, `dynamodb://` and `mongodb://` each need their matching extra. When unset, defaults to `file:///data/state` (the volume family Docker images mount), or to `memory://` (with a warning) on a host where that directory is not usable.

SCHOLAR_MCP_TOOLS_ALLOW

Comma-separated explicit tool names this instance exposes; every other tool is hidden from listings and cannot be invoked. Names matching no registered tool are inert. Mutually exclusive with `tools_deny`. Takes effect through `apply_tool_visibility`.

SCHOLAR_MCP_TOOLS_DENY

Comma-separated explicit tool names hidden from this instance (absent from listings, cannot be invoked). Names matching no registered tool are inert. Mutually exclusive with `tools_allow`. Takes effect through `apply_tool_visibility`.

SCHOLAR_MCP_SERVER_NAME

Rename this server instance; defaults to the project name.

SCHOLAR_MCP_INSTANCE_DESCRIPTION

Concise routing context that distinguishes this deployment's material or responsibility.

SCHOLAR_MCP_INSTRUCTIONS_EXTRA

Deployment-specific behavioral policy added to the generated MCP instructions.

SCHOLAR_MCP_INSTRUCTIONS

Legacy: replaces all generated MCP instructions (deprecated; use _INSTANCE_DESCRIPTION for routing and _INSTRUCTIONS_EXTRA for policy).

FASTMCP_LOG_LEVEL

Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG.

FASTMCP_ENABLE_RICH_LOGGING

Set false for plain or structured JSON log output.

SCHOLAR_GITHUB_TOKEN

secret

GitHub token used to raise rate limits when fetching standards documents from GitHub. Optional; unauthenticated requests work at reduced limits.

SCHOLAR_MCP_READ_ONLY

When true, write-tagged tools (PDF download and conversion cache writes) are hidden. Set false to enable them.

SCHOLAR_MCP_S2_API_KEY

secret

Semantic Scholar API key. Optional but strongly recommended: unauthenticated requests are limited to ~1 req/s. Request one at https://www.semanticscholar.org/product/api#api-key-form.

SCHOLAR_MCP_DOCLING_URL

Base URL of a running docling-serve instance for PDF conversion (e.g. http://localhost:5001). When unset, PDF conversion tools return an error.

SCHOLAR_MCP_VLM_API_URL

OpenAI-compatible VLM endpoint for formula and figure enrichment during PDF conversion.

SCHOLAR_MCP_VLM_API_KEY

secret

API key for the VLM endpoint.

SCHOLAR_MCP_VLM_MODEL

Model name to use with the VLM endpoint.

SCHOLAR_MCP_CACHE_DIR

Directory for the SQLite cache database (cache.db) and downloaded PDFs (pdfs/, md/).

SCHOLAR_MCP_CONTACT_EMAIL

Contact email for the OpenAlex polite pool (improves rate limits). Also enables Unpaywall lookups as a PDF fallback source.

SCHOLAR_MCP_EPO_CONSUMER_KEY

EPO Open Patent Services consumer key. Optional; patent tools are hidden when unset. Register at https://developers.epo.org/user/register.

SCHOLAR_MCP_EPO_CONSUMER_SECRET

secret

EPO Open Patent Services consumer secret. Optional; patent tools are hidden when unset.

SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY

secret

Google Books API key. Optional; book tools work unauthenticated at reduced rate limits.

SCHOLAR_MCP_JOBS_SOFT_DEADLINE_S

Seconds a long-running tool call may run in the foreground before it is promoted to a background job and a job handle is returned instead.

SCHOLAR_MCP_JOBS_RESULT_TTL_S

Seconds a background-job record (working or finished) is retained for polling before it expires from the store.

SCHOLAR_MCP_JOBS_MAX_PER_SUBJECT

Maximum live background jobs per calling subject; further promotions are rejected until older records expire.

SCHOLAR_MCP_BASE_URL

Public base URL of the deployed server, for example `https://mcp.example.com`. Required for OIDC. Also the fallback source of the MCP Apps domain when `app_domain` is unset.

SCHOLAR_MCP_BEARER_TOKEN

secret

Single shared bearer token; enables bearer auth unless `bearer_tokens_file` is set, which takes precedence.

SCHOLAR_MCP_OIDC_CONFIG_URL

OIDC discovery document URL, for example `https://auth.example.com/.well-known/openid-configuration`.

SCHOLAR_MCP_OIDC_CLIENT_ID

OIDC client identifier registered with the provider.

SCHOLAR_MCP_OIDC_CLIENT_SECRET

secret

OIDC client secret registered with the provider.

SCHOLAR_MCP_OIDC_AUDIENCE

Expected `aud` claim; tokens issued for another audience are rejected.

SCHOLAR_MCP_OIDC_REQUIRED_SCOPES

Scopes a caller must present, space- or comma-separated. Defaults to `openid` in oidc-proxy mode.

SCHOLAR_MCP_OIDC_ADVERTISED_SCOPES

Scopes advertised to MCP clients in protected-resource metadata, space- or comma-separated. Overrides the default `openid offline_access`; `oidc_required_scopes` is always added on top. Set this when the registered client is not permitted `offline_access`, or to have clients request extra claim scopes (such as `groups`) without also requiring them in every token.

SCHOLAR_MCP_OIDC_JWT_SIGNING_KEY

secret

Signing key for issued tokens; used in oidc-proxy mode only. When unset, the key is derived deterministically from `oidc_client_secret`, so tokens survive a restart. Rotating that secret then invalidates every issued token. Set this explicitly to decouple token validity from secret rotation. Generate with `openssl rand -hex 32`.

SCHOLAR_MCP_OIDC_VERIFY_ACCESS_TOKEN

Validate the access token instead of the id token.

SCHOLAR_MCP_KV_STORE_URL

SCHOLAR_MCP_APP_DOMAIN

MCP Apps iframe domain, used for CSP sandboxing. Overrides the host derived from `base_url`.

SCHOLAR_MCP_TOOLS_ALLOW

SCHOLAR_MCP_TOOLS_DENY

SCHOLAR_MCP_AUTH_MODE

Explicit auth-mode override, accepting `remote` or `oidc-proxy` (case- and whitespace-insensitive). When unset the mode is auto-detected from which auth variables are set; the override exists because having all four OIDC variables set is ambiguous between those two modes. Other values are ignored with a warning.

SCHOLAR_MCP_BEARER_TOKENS_FILE

Path to a TOML file mapping bearer tokens to subjects; overrides the single-token `bearer_token` mode.

SCHOLAR_MCP_BEARER_DEFAULT_SUBJECT

Subject assigned to the single-token bearer mode; ignored when `bearer_tokens_file` is set, since mapped mode carries per-token subjects.

SCHOLAR_MCP_SERVER_NAME

Rename this server instance; defaults to the project name.

SCHOLAR_MCP_INSTANCE_DESCRIPTION

Concise routing context that distinguishes this deployment's material or responsibility.

SCHOLAR_MCP_INSTRUCTIONS_EXTRA

Deployment-specific behavioral policy added to the generated MCP instructions.

SCHOLAR_MCP_INSTRUCTIONS

Legacy: replaces all generated MCP instructions (deprecated; use _INSTANCE_DESCRIPTION for routing and _INSTRUCTIONS_EXTRA for policy).

SCHOLAR_MCP_HTTP_PATH

Mount path for the MCP endpoint; the health routes derive their prefix from it.

SCHOLAR_MCP_HEALTH_DETAIL

How much the unauthenticated /health and /health/ready bodies say: status, standard (adds name, version and per-check verdicts), or full (adds redacted reasons; trusted networks only).

PUID

Run the server process as this UID; the container entrypoint reassigns ownership of writable paths to match.

PGID

Run the server process as this GID; pair with PUID to match the owner of a mounted volume.

FASTMCP_LOG_LEVEL

Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG.

FASTMCP_ENABLE_RICH_LOGGING

Set false for plain or structured JSON log output.

SCHOLAR_GITHUB_TOKEN

secret

GitHub token used to raise rate limits when fetching standards documents from GitHub. Optional; unauthenticated requests work at reduced limits.

SCHOLAR_MCP_READ_ONLY

When true, write-tagged tools (PDF download and conversion cache writes) are hidden. Set false to enable them.

SCHOLAR_MCP_S2_API_KEY

secret

Semantic Scholar API key. Optional but strongly recommended: unauthenticated requests are limited to ~1 req/s. Request one at https://www.semanticscholar.org/product/api#api-key-form.

SCHOLAR_MCP_DOCLING_URL

Base URL of a running docling-serve instance for PDF conversion (e.g. http://localhost:5001). When unset, PDF conversion tools return an error.

SCHOLAR_MCP_VLM_API_URL

OpenAI-compatible VLM endpoint for formula and figure enrichment during PDF conversion.

SCHOLAR_MCP_VLM_API_KEY

secret

API key for the VLM endpoint.

SCHOLAR_MCP_VLM_MODEL

Model name to use with the VLM endpoint.

SCHOLAR_MCP_CACHE_DIR

Directory for the SQLite cache database (cache.db) and downloaded PDFs (pdfs/, md/).

SCHOLAR_MCP_CONTACT_EMAIL

Contact email for the OpenAlex polite pool (improves rate limits). Also enables Unpaywall lookups as a PDF fallback source.

SCHOLAR_MCP_EPO_CONSUMER_KEY

EPO Open Patent Services consumer key. Optional; patent tools are hidden when unset. Register at https://developers.epo.org/user/register.

SCHOLAR_MCP_EPO_CONSUMER_SECRET

secret

EPO Open Patent Services consumer secret. Optional; patent tools are hidden when unset.

SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY

secret

Google Books API key. Optional; book tools work unauthenticated at reduced rate limits.

SCHOLAR_MCP_JOBS_SOFT_DEADLINE_S

Seconds a long-running tool call may run in the foreground before it is promoted to a background job and a job handle is returned instead.

SCHOLAR_MCP_JOBS_RESULT_TTL_S

Seconds a background-job record (working or finished) is retained for polling before it expires from the store.

SCHOLAR_MCP_JOBS_MAX_PER_SUBJECT

Maximum live background jobs per calling subject; further promotions are rejected until older records expire.

MCP quality score · maturity, not trust · methodology

freshness

completeness

installability

documentation

stability

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Install this server

Claude Desktop (uvx)

{
  "mcpServers": {
    "scholar-mcp": {
      "command": "uvx",
      "args": [
        "--",
        "pvliesdonk-scholar-mcp"
      ],
      "env": {
        "SCHOLAR_MCP_KV_STORE_URL": "file:///data/state",
        "SCHOLAR_MCP_TOOLS_ALLOW": "<scholar_mcp_tools_allow>",
        "SCHOLAR_MCP_TOOLS_DENY": "<scholar_mcp_tools_deny>",
        "SCHOLAR_MCP_SERVER_NAME": "<scholar_mcp_server_name>",
        "SCHOLAR_MCP_INSTANCE_DESCRIPTION": "<scholar_mcp_instance_description>",
        "SCHOLAR_MCP_INSTRUCTIONS_EXTRA": "<scholar_mcp_instructions_extra>",
        "SCHOLAR_MCP_INSTRUCTIONS": "<scholar_mcp_instructions>",
        "FASTMCP_LOG_LEVEL": "INFO",
        "FASTMCP_ENABLE_RICH_LOGGING": "true",
        "SCHOLAR_GITHUB_TOKEN": "<your-scholar_github_token>",
        "SCHOLAR_MCP_READ_ONLY": "true",
        "SCHOLAR_MCP_S2_API_KEY": "<your-scholar_mcp_s2_api_key>",
        "SCHOLAR_MCP_DOCLING_URL": "<scholar_mcp_docling_url>",
        "SCHOLAR_MCP_VLM_API_URL": "<scholar_mcp_vlm_api_url>",
        "SCHOLAR_MCP_VLM_API_KEY": "<your-scholar_mcp_vlm_api_key>",
        "SCHOLAR_MCP_VLM_MODEL": "gpt-4o",
        "SCHOLAR_MCP_CACHE_DIR": "/data/scholar-mcp",
        "SCHOLAR_MCP_CONTACT_EMAIL": "<scholar_mcp_contact_email>",
        "SCHOLAR_MCP_EPO_CONSUMER_KEY": "<scholar_mcp_epo_consumer_key>",
        "SCHOLAR_MCP_EPO_CONSUMER_SECRET": "<your-scholar_mcp_epo_consumer_secret>",
        "SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY": "<your-scholar_mcp_google_books_api_key>",
        "SCHOLAR_MCP_JOBS_SOFT_DEADLINE_S": "25.0",
        "SCHOLAR_MCP_JOBS_RESULT_TTL_S": "3600.0",
        "SCHOLAR_MCP_JOBS_MAX_PER_SUBJECT": "256",
        "SCHOLAR_MCP_BASE_URL": "<scholar_mcp_base_url>",
        "SCHOLAR_MCP_BEARER_TOKEN": "<your-scholar_mcp_bearer_token>",
        "SCHOLAR_MCP_OIDC_CONFIG_URL": "<scholar_mcp_oidc_config_url>",
        "SCHOLAR_MCP_OIDC_CLIENT_ID": "<scholar_mcp_oidc_client_id>",
        "SCHOLAR_MCP_OIDC_CLIENT_SECRET": "<your-scholar_mcp_oidc_client_secret>",
        "SCHOLAR_MCP_OIDC_AUDIENCE": "<scholar_mcp_oidc_audience>",
        "SCHOLAR_MCP_OIDC_REQUIRED_SCOPES": "openid",
        "SCHOLAR_MCP_OIDC_ADVERTISED_SCOPES": "openid offline_access",
        "SCHOLAR_MCP_OIDC_JWT_SIGNING_KEY": "<your-scholar_mcp_oidc_jwt_signing_key>",
        "SCHOLAR_MCP_OIDC_VERIFY_ACCESS_TOKEN": "false",
        "SCHOLAR_MCP_APP_DOMAIN": "<scholar_mcp_app_domain>",
        "SCHOLAR_MCP_AUTH_MODE": "<scholar_mcp_auth_mode>",
        "SCHOLAR_MCP_BEARER_TOKENS_FILE": "<scholar_mcp_bearer_tokens_file>",
        "SCHOLAR_MCP_BEARER_DEFAULT_SUBJECT": "bearer-anon",
        "SCHOLAR_MCP_HTTP_PATH": "/mcp",
        "SCHOLAR_MCP_HEALTH_DETAIL": "standard",
        "PUID": "1000",
        "PGID": "1000"
      }
    }
  }
}

Claude Desktop (Docker)

{
  "mcpServers": {
    "scholar-mcp": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "--",
        "ghcr.io/pvliesdonk/scholar-mcp:v2.0.0"
      ],
      "env": {
        "SCHOLAR_MCP_KV_STORE_URL": "file:///data/state",
        "SCHOLAR_MCP_TOOLS_ALLOW": "<scholar_mcp_tools_allow>",
        "SCHOLAR_MCP_TOOLS_DENY": "<scholar_mcp_tools_deny>",
        "SCHOLAR_MCP_SERVER_NAME": "<scholar_mcp_server_name>",
        "SCHOLAR_MCP_INSTANCE_DESCRIPTION": "<scholar_mcp_instance_description>",
        "SCHOLAR_MCP_INSTRUCTIONS_EXTRA": "<scholar_mcp_instructions_extra>",
        "SCHOLAR_MCP_INSTRUCTIONS": "<scholar_mcp_instructions>",
        "FASTMCP_LOG_LEVEL": "INFO",
        "FASTMCP_ENABLE_RICH_LOGGING": "true",
        "SCHOLAR_GITHUB_TOKEN": "<your-scholar_github_token>",
        "SCHOLAR_MCP_READ_ONLY": "true",
        "SCHOLAR_MCP_S2_API_KEY": "<your-scholar_mcp_s2_api_key>",
        "SCHOLAR_MCP_DOCLING_URL": "<scholar_mcp_docling_url>",
        "SCHOLAR_MCP_VLM_API_URL": "<scholar_mcp_vlm_api_url>",
        "SCHOLAR_MCP_VLM_API_KEY": "<your-scholar_mcp_vlm_api_key>",
        "SCHOLAR_MCP_VLM_MODEL": "gpt-4o",
        "SCHOLAR_MCP_CACHE_DIR": "/data/scholar-mcp",
        "SCHOLAR_MCP_CONTACT_EMAIL": "<scholar_mcp_contact_email>",
        "SCHOLAR_MCP_EPO_CONSUMER_KEY": "<scholar_mcp_epo_consumer_key>",
        "SCHOLAR_MCP_EPO_CONSUMER_SECRET": "<your-scholar_mcp_epo_consumer_secret>",
        "SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY": "<your-scholar_mcp_google_books_api_key>",
        "SCHOLAR_MCP_JOBS_SOFT_DEADLINE_S": "25.0",
        "SCHOLAR_MCP_JOBS_RESULT_TTL_S": "3600.0",
        "SCHOLAR_MCP_JOBS_MAX_PER_SUBJECT": "256",
        "SCHOLAR_MCP_BASE_URL": "<scholar_mcp_base_url>",
        "SCHOLAR_MCP_BEARER_TOKEN": "<your-scholar_mcp_bearer_token>",
        "SCHOLAR_MCP_OIDC_CONFIG_URL": "<scholar_mcp_oidc_config_url>",
        "SCHOLAR_MCP_OIDC_CLIENT_ID": "<scholar_mcp_oidc_client_id>",
        "SCHOLAR_MCP_OIDC_CLIENT_SECRET": "<your-scholar_mcp_oidc_client_secret>",
        "SCHOLAR_MCP_OIDC_AUDIENCE": "<scholar_mcp_oidc_audience>",
        "SCHOLAR_MCP_OIDC_REQUIRED_SCOPES": "openid",
        "SCHOLAR_MCP_OIDC_ADVERTISED_SCOPES": "openid offline_access",
        "SCHOLAR_MCP_OIDC_JWT_SIGNING_KEY": "<your-scholar_mcp_oidc_jwt_signing_key>",
        "SCHOLAR_MCP_OIDC_VERIFY_ACCESS_TOKEN": "false",
        "SCHOLAR_MCP_APP_DOMAIN": "<scholar_mcp_app_domain>",
        "SCHOLAR_MCP_AUTH_MODE": "<scholar_mcp_auth_mode>",
        "SCHOLAR_MCP_BEARER_TOKENS_FILE": "<scholar_mcp_bearer_tokens_file>",
        "SCHOLAR_MCP_BEARER_DEFAULT_SUBJECT": "bearer-anon",
        "SCHOLAR_MCP_HTTP_PATH": "/mcp",
        "SCHOLAR_MCP_HEALTH_DETAIL": "standard",
        "PUID": "1000",
        "PGID": "1000"
      }
    }
  }
}

Verdict API

curl -s mcpindex.ai/api/v1/trust/server/io-github-pvliesdonk-scholar-mcp

Free-tier verdict as JSON: decision + dimensions + severity. Call it from your agent before it invokes a tool it just discovered.

Details

version: v2.0.0
category: Documents & Spreadsheets
verdict expires: 2026-09-28
quality: 95 / 100
operator: pvliesdonk

Listing

Listed from the official MCP registry. Unclaimed by its maintainer. Maintainer? Email us →

Provenance

Each verdict is bound to a hash of the exact description it judged, so a re-crawl that changes the text produces a new record rather than silently inheriting this one. Verdict history is hash-chained and anchored to Bitcoin via OpenTimestamps (latest confirmed at block 966,775). Verify it yourself.

Links

Repository →Website →