Scholar MCP Setup & Guide

{
  "id": "io.github.pvliesdonk/scholar-mcp",
  "type": "mcp-server",
  "version": "2.0.0",
  "displayName": "Scholar MCP",
  "description": "FastMCP server for scholarly papers, patents, books and standards with docling PDF conversion",
  "repository": {
    "url": "https://github.com/pvliesdonk/scholar-mcp",
    "source": "github"
  },
  "homepage": "https://pvliesdonk.github.io/scholar-mcp/",
  "distribution": {
    "packages": [
      {
        "registryType": "pypi",
        "identifier": "pvliesdonk-scholar-mcp",
        "version": "2.0.0",
        "runtimeHint": "uvx",
        "transport": "stdio",
        "environmentVariables": [
          {
            "name": "SCHOLAR_MCP_KV_STORE_URL",
            "description": "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."
          },
          {
            "name": "SCHOLAR_MCP_TOOLS_ALLOW",
            "description": "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`."
          },
          {
            "name": "SCHOLAR_MCP_TOOLS_DENY",
            "description": "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`."
          },
          {
            "name": "SCHOLAR_MCP_SERVER_NAME",
            "description": "Rename this server instance; defaults to the project name."
          },
          {
            "name": "SCHOLAR_MCP_INSTANCE_DESCRIPTION",
            "description": "Concise routing context that distinguishes this deployment's material or responsibility."
          },
          {
            "name": "SCHOLAR_MCP_INSTRUCTIONS_EXTRA",
            "description": "Deployment-specific behavioral policy added to the generated MCP instructions."
          },
          {
            "name": "SCHOLAR_MCP_INSTRUCTIONS",
            "description": "Legacy: replaces all generated MCP instructions (deprecated; use _INSTANCE_DESCRIPTION for routing and _INSTRUCTIONS_EXTRA for policy)."
          },
          {
            "name": "FASTMCP_LOG_LEVEL",
            "description": "Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG."
          },
          {
            "name": "FASTMCP_ENABLE_RICH_LOGGING",
            "description": "Set false for plain or structured JSON log output."
          },
          {
            "name": "SCHOLAR_GITHUB_TOKEN",
            "description": "GitHub token used to raise rate limits when fetching standards documents from GitHub. Optional; unauthenticated requests work at reduced limits.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_READ_ONLY",
            "description": "When true, write-tagged tools (PDF download and conversion cache writes) are hidden. Set false to enable them."
          },
          {
            "name": "SCHOLAR_MCP_S2_API_KEY",
            "description": "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.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_DOCLING_URL",
            "description": "Base URL of a running docling-serve instance for PDF conversion (e.g. http://localhost:5001). When unset, PDF conversion tools return an error."
          },
          {
            "name": "SCHOLAR_MCP_VLM_API_URL",
            "description": "OpenAI-compatible VLM endpoint for formula and figure enrichment during PDF conversion."
          },
          {
            "name": "SCHOLAR_MCP_VLM_API_KEY",
            "description": "API key for the VLM endpoint.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_VLM_MODEL",
            "description": "Model name to use with the VLM endpoint."
          },
          {
            "name": "SCHOLAR_MCP_CACHE_DIR",
            "description": "Directory for the SQLite cache database (cache.db) and downloaded PDFs (pdfs/, md/)."
          },
          {
            "name": "SCHOLAR_MCP_CONTACT_EMAIL",
            "description": "Contact email for the OpenAlex polite pool (improves rate limits). Also enables Unpaywall lookups as a PDF fallback source."
          },
          {
            "name": "SCHOLAR_MCP_EPO_CONSUMER_KEY",
            "description": "EPO Open Patent Services consumer key. Optional; patent tools are hidden when unset. Register at https://developers.epo.org/user/register."
          },
          {
            "name": "SCHOLAR_MCP_EPO_CONSUMER_SECRET",
            "description": "EPO Open Patent Services consumer secret. Optional; patent tools are hidden when unset.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY",
            "description": "Google Books API key. Optional; book tools work unauthenticated at reduced rate limits.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_JOBS_SOFT_DEADLINE_S",
            "description": "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."
          },
          {
            "name": "SCHOLAR_MCP_JOBS_RESULT_TTL_S",
            "description": "Seconds a background-job record (working or finished) is retained for polling before it expires from the store."
          },
          {
            "name": "SCHOLAR_MCP_JOBS_MAX_PER_SUBJECT",
            "description": "Maximum live background jobs per calling subject; further promotions are rejected until older records expire."
          }
        ]
      },
      {
        "registryType": "oci",
        "identifier": "ghcr.io/pvliesdonk/scholar-mcp:v2.0.0",
        "transport": "streamable-http",
        "environmentVariables": [
          {
            "name": "SCHOLAR_MCP_BASE_URL",
            "description": "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."
          },
          {
            "name": "SCHOLAR_MCP_BEARER_TOKEN",
            "description": "Single shared bearer token; enables bearer auth unless `bearer_tokens_file` is set, which takes precedence.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_OIDC_CONFIG_URL",
            "description": "OIDC discovery document URL, for example `https://auth.example.com/.well-known/openid-configuration`."
          },
          {
            "name": "SCHOLAR_MCP_OIDC_CLIENT_ID",
            "description": "OIDC client identifier registered with the provider."
          },
          {
            "name": "SCHOLAR_MCP_OIDC_CLIENT_SECRET",
            "description": "OIDC client secret registered with the provider.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_OIDC_AUDIENCE",
            "description": "Expected `aud` claim; tokens issued for another audience are rejected."
          },
          {
            "name": "SCHOLAR_MCP_OIDC_REQUIRED_SCOPES",
            "description": "Scopes a caller must present, space- or comma-separated. Defaults to `openid` in oidc-proxy mode."
          },
          {
            "name": "SCHOLAR_MCP_OIDC_ADVERTISED_SCOPES",
            "description": "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."
          },
          {
            "name": "SCHOLAR_MCP_OIDC_JWT_SIGNING_KEY",
            "description": "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`.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_OIDC_VERIFY_ACCESS_TOKEN",
            "description": "Validate the access token instead of the id token."
          },
          {
            "name": "SCHOLAR_MCP_KV_STORE_URL",
            "description": "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."
          },
          {
            "name": "SCHOLAR_MCP_APP_DOMAIN",
            "description": "MCP Apps iframe domain, used for CSP sandboxing. Overrides the host derived from `base_url`."
          },
          {
            "name": "SCHOLAR_MCP_TOOLS_ALLOW",
            "description": "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`."
          },
          {
            "name": "SCHOLAR_MCP_TOOLS_DENY",
            "description": "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`."
          },
          {
            "name": "SCHOLAR_MCP_AUTH_MODE",
            "description": "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."
          },
          {
            "name": "SCHOLAR_MCP_BEARER_TOKENS_FILE",
            "description": "Path to a TOML file mapping bearer tokens to subjects; overrides the single-token `bearer_token` mode."
          },
          {
            "name": "SCHOLAR_MCP_BEARER_DEFAULT_SUBJECT",
            "description": "Subject assigned to the single-token bearer mode; ignored when `bearer_tokens_file` is set, since mapped mode carries per-token subjects."
          },
          {
            "name": "SCHOLAR_MCP_SERVER_NAME",
            "description": "Rename this server instance; defaults to the project name."
          },
          {
            "name": "SCHOLAR_MCP_INSTANCE_DESCRIPTION",
            "description": "Concise routing context that distinguishes this deployment's material or responsibility."
          },
          {
            "name": "SCHOLAR_MCP_INSTRUCTIONS_EXTRA",
            "description": "Deployment-specific behavioral policy added to the generated MCP instructions."
          },
          {
            "name": "SCHOLAR_MCP_INSTRUCTIONS",
            "description": "Legacy: replaces all generated MCP instructions (deprecated; use _INSTANCE_DESCRIPTION for routing and _INSTRUCTIONS_EXTRA for policy)."
          },
          {
            "name": "SCHOLAR_MCP_HTTP_PATH",
            "description": "Mount path for the MCP endpoint; the health routes derive their prefix from it."
          },
          {
            "name": "SCHOLAR_MCP_HEALTH_DETAIL",
            "description": "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)."
          },
          {
            "name": "PUID",
            "description": "Run the server process as this UID; the container entrypoint reassigns ownership of writable paths to match."
          },
          {
            "name": "PGID",
            "description": "Run the server process as this GID; pair with PUID to match the owner of a mounted volume."
          },
          {
            "name": "FASTMCP_LOG_LEVEL",
            "description": "Log level for FastMCP internals and app loggers (DEBUG / INFO / WARNING / ERROR / CRITICAL). The -v CLI flag overrides to DEBUG."
          },
          {
            "name": "FASTMCP_ENABLE_RICH_LOGGING",
            "description": "Set false for plain or structured JSON log output."
          },
          {
            "name": "SCHOLAR_GITHUB_TOKEN",
            "description": "GitHub token used to raise rate limits when fetching standards documents from GitHub. Optional; unauthenticated requests work at reduced limits.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_READ_ONLY",
            "description": "When true, write-tagged tools (PDF download and conversion cache writes) are hidden. Set false to enable them."
          },
          {
            "name": "SCHOLAR_MCP_S2_API_KEY",
            "description": "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.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_DOCLING_URL",
            "description": "Base URL of a running docling-serve instance for PDF conversion (e.g. http://localhost:5001). When unset, PDF conversion tools return an error."
          },
          {
            "name": "SCHOLAR_MCP_VLM_API_URL",
            "description": "OpenAI-compatible VLM endpoint for formula and figure enrichment during PDF conversion."
          },
          {
            "name": "SCHOLAR_MCP_VLM_API_KEY",
            "description": "API key for the VLM endpoint.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_VLM_MODEL",
            "description": "Model name to use with the VLM endpoint."
          },
          {
            "name": "SCHOLAR_MCP_CACHE_DIR",
            "description": "Directory for the SQLite cache database (cache.db) and downloaded PDFs (pdfs/, md/)."
          },
          {
            "name": "SCHOLAR_MCP_CONTACT_EMAIL",
            "description": "Contact email for the OpenAlex polite pool (improves rate limits). Also enables Unpaywall lookups as a PDF fallback source."
          },
          {
            "name": "SCHOLAR_MCP_EPO_CONSUMER_KEY",
            "description": "EPO Open Patent Services consumer key. Optional; patent tools are hidden when unset. Register at https://developers.epo.org/user/register."
          },
          {
            "name": "SCHOLAR_MCP_EPO_CONSUMER_SECRET",
            "description": "EPO Open Patent Services consumer secret. Optional; patent tools are hidden when unset.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY",
            "description": "Google Books API key. Optional; book tools work unauthenticated at reduced rate limits.",
            "isSecret": true
          },
          {
            "name": "SCHOLAR_MCP_JOBS_SOFT_DEADLINE_S",
            "description": "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."
          },
          {
            "name": "SCHOLAR_MCP_JOBS_RESULT_TTL_S",
            "description": "Seconds a background-job record (working or finished) is retained for polling before it expires from the store."
          },
          {
            "name": "SCHOLAR_MCP_JOBS_MAX_PER_SUBJECT",
            "description": "Maximum live background jobs per calling subject; further promotions are rejected until older records expire."
          }
        ]
      }
    ],
    "remotes": []
  },
  "dependencies": [],
  "installTargets": [
    "claude-code",
    "claude-desktop",
    "cursor",
    "vscode",
    "trae",
    "cherry-studio",
    "lingma",
    "windsurf",
    "cline",
    "workbuddy"
  ],
  "keywords": [],
  "provenance": {
    "origin": "official-mcp-registry",
    "originalId": "io.github.pvliesdonk/scholar-mcp",
    "originalUrl": "https://registry.modelcontextprotocol.io/v0.1/servers/io.github.pvliesdonk%2Fscholar-mcp/versions/latest",
    "isOfficial": true,
    "status": "active"
  }
}