SciX MCP Server

A Model Context Protocol (MCP) server for the SciX API. This server enables LLMs to search astronomical literature, retrieve paper metadata, analyze citation metrics, and export bibliographic data.

Quick Start (MCP clients)

Get an API Key

1. Create an account at SciX
2. Generate an API token at https://scixplorer.org/user/settings/token
3. Set the environment variable:

export SCIX_API_TOKEN=your_api_key_here

Or create a .env file:

cp .env.example .env
# Edit .env and add your key

Configure your MCP client (Claude, Codex, etc.)

Add to your MCP client configuration:

{
  "mcpServers": {
    "scix": {
      "command": "npx",
      "args": ["scix-mcp"],
      "env": {
        "SCIX_API_TOKEN": "your_api_key_here"
      }
    }
  }
}

Common locations: Claude Desktop (~/Library/Application Support/Claude/claude_desktop_config.json on macOS or %AppData%\\Claude\\claude_desktop_config.json on Windows) and Codex CLI (~/.config/codex/config.json). Restart your client after editing.

Local MCP clients that read .mcp/server.json can also pick up the packaged config in .mcp/server.json; just drop in your SCIX_API_TOKEN.

Environment variables

• SCIX_API_TOKEN (required for stdio): your SciX API key. Not used by the
  HTTP transport, which takes the token from each request.
• SCIX_API_BASE (optional): override the API base URL. Defaults to
  https://api.scixplorer.org/v1 when unset. Primarily used to point the
  server at a local mock during the e2e test suite.
• SCIX_WEB_BASE (optional): override the host used when building the
  scixplorer.org links in tool output. Defaults to https://scixplorer.org.
• PORT / HOST (HTTP only): where the HTTP transport listens. Default
  8000 on 0.0.0.0.

HTTP transport

scix-mcp-http serves the same tools over Streamable HTTP instead of stdio:
POST /mcp for JSON-RPC, GET /healthz as an unauthenticated probe.

Unlike stdio, the server holds no token of its own — each request must carry
the caller's, and requests without one get a 401:

Authorization: Bearer <your SciX API token>

Tool calls act as the calling user and spend that user's rate limit. Clients
that cannot set the header (ChatGPT connectors, which need OAuth or no auth)
cannot use this endpoint.

Example Prompts

- Find refereed JWST exoplanet papers from 2022-2024 sorted by citation_count, return the top 5 in markdown with bibcodes, titles, first author, and citation counts.
- Build a query for gravitational wave kilonova follow-ups since 2017 (fielded abstract search), add the first 50 results to library <library_id>, and then give me metrics (h-index, total cites) for those bibcodes in JSON.
- Fetch paper 2020ApJ...905....3A, list its first 10 references with titles, and also list the first 10 forward citations with publication years.
- Create a public library named “Cosmic Web Reviews”, seeded with bibcodes [...], then share the public URL and export the contents in BibTeX.
- For bibcodes [...], return citation metrics plus a ranked list of which papers cite the most recent one (rows=25) in markdown.
- Get all my libraries, pick the one with the most documents, and return its metadata plus the first 5 document titles in JSON.

Features

• Literature Search: Full-text search with advanced Solr query syntax
• Faceting: Break a result set down by any of the 16 SciX facets and feed the counts back as filters via the get_facets tool
• Paper Details: Retrieve metadata for any publication
• Citation Metrics: Calculate h-index, citation counts, and usage statistics
• Citation Network: Explore forward and backward citations
• Export: Generate citations in 23 bibliographic formats (BibTeX, AASTeX, EndNote, RIS, and more) — see the export tool's format enum in src/types.ts for the full list
• Documentation Search: Query SciX help/docs content via the search_docs tool
• Health Check: Diagnose setup (token, API reachability, tool registry) via the health_check tool
• Dual Format: Support for both human-readable Markdown and machine-readable JSON

Available Tools

Search & Metadata

• search: Solr-powered search across SciX. Params: query (required), filter_query (up to 20 Solr fq strings, each sent as its own repeated parameter and ANDed together), rows (1-100, default 10), start (offset, default 0), sort (score desc | citation_count desc | date desc | date asc | read_count desc, default score desc), response_format (markdown | json, default markdown).
  • Example queries: author:"Einstein, A." title:relativity, black holes year:2020-2023, author:^Smith, dark energy AND galaxy clusters.
• get_facets: Count how a result set breaks down across facets, so a search can be narrowed. Params: query (required), filter_query, facets (default author, year, publications, keywords, refereed, collections), limit (1-200 buckets per facet, default 10), sort (count desc | count asc | index asc | index desc), prefix (drill into a hierarchy; only valid with exactly one facet), response_format.

  • Every bucket carries a filter string ready to pass straight back as a search filter_query entry.

  • Available facets, with the Solr field each one counts:

    Facet	Solr field	Hierarchical
    author	author_facet_hier	yes (2 levels)
    collections	database	no
    refereed	property	no
    institutions	aff_facet_hier	yes (2 levels)
    keywords	keyword_facet	no
    publications	pub_abbrev	no
    bibgroups	bibgroup_facet	no
    simbad	simbad_object_facet_hier	yes (2 levels)
    ned	ned_object_facet_hier	yes (2 levels)
    award	grant_facet_hier	yes (2 levels)
    data	data_facet	no
    vizier	vizier_facet	no
    pubtype	doctype_facet_hier	yes (2 levels)
    planetary	planetary_feature_facet_hier_3level	yes (3 levels)
    uat	uat	no
    year	year	no

  • Hierarchical facet values are prefixed with their level, e.g. 0/Smith, J at the root and 1/Smith, J/Smith, John one level down. Expandable buckets report a child_prefix to pass back as prefix.

• get_paper: Fetch a paper by bibcode, DOI, arXiv ID, or SciX ID (scix:...) with optional response_format.
• get_metrics: Metrics for bibcodes (1-2000) with optional response_format; returns h-index, g-index, citation counts, usage stats.

Citation Network

• get_citations: Forward citations for a paper (bibcode, DOI, arXiv ID, or SciX ID); optional rows (1-100, default 20) and response_format.
• get_references: Backward references for a paper (bibcode, DOI, arXiv ID, or SciX ID); optional rows (1-100, default 20) and response_format.

Export

• export: Export bibcodes (1-2000) in format — one of the 23 formats in the ExportInputSchema enum in src/types.ts (e.g. bibtex, aastex, endnote, ris, ieee, mnras). Use custom_format with format: custom for a template. Returns plain text in the chosen format.

Documentation

• search_docs: Search SciX help documentation. Params: query (required, natural language), limit (1-20, default 5). Returns a ranked list with title, section/subsection, source URL, relevance score, and a focused snippet.

Libraries

• get_libraries: List libraries; optional type (all | owner | collaborator, default all) and response_format.
• get_library: Metadata + documents for library_id; optional response_format.
• create_library: Create with name (required), optional description, public (default false), bibcodes, and response_format.
• delete_library: Permanently delete by library_id; optional response_format.
• edit_library: Update name, description, or public for library_id; optional response_format.
• manage_documents: Add/remove documents with library_id, bibcodes (1-2000), action (add | remove), and optional response_format.
• add_documents_by_query: Add search results to a library with library_id, query, optional rows (1-2000, default 25), and response_format.
• library_operation: Run set ops on a library with library_id, operation (union | intersection | difference | copy | empty), optional source_library_ids, name/description (for copy), and response_format.

Permissions & Sharing

• get_permissions: View owners/collaborators for library_id; optional response_format.
• update_permissions: Grant/change a user's access with library_id, email, permission (owner | admin | write | read), and optional response_format.
• transfer_library: Transfer ownership with library_id, email, and optional response_format.

Annotations

• get_annotation: Fetch note content for library_id + bibcode; optional response_format.
• manage_annotation: Add/update note with library_id, bibcode, content, and optional response_format.
• delete_annotation: Remove note for library_id + bibcode; optional response_format.

Diagnostics

• health_check: Diagnose the server setup. No required params (optional response_format). Reports server name/version, API base URL, whether a token is configured, an authentication probe result (ok | unauthorized | rate_limited | unreachable | skipped), and the registered tool names. Never emits the token value. Runs without a token (probe is skipped); use it to tell setup problems apart from ordinary API errors.

Rate Limits

• 5000 requests per day per API key
• Rate limit info is returned in response headers
• Request higher limits at https://scixplorer.org/feedback/general

SciX Search Syntax

The SciX search supports Solr query syntax:

Values discovered through get_facets are better applied as filter_query
entries than folded into query: Solr caches filters separately, and the
facet/filter split is what the SciX web UI does.

Outbound request tagging

Every request this server makes to the SciX API carries:

• X-Client-Source: scix-mcp — a stable, low-cardinality tag so SciX access
  logs can attribute MCP traffic without parsing User-Agent.
• User-Agent: scix-mcp/<version> (transport=stdio|http) — version and
  transport detail.

Development

Install & Build

pnpm install
pnpm build

Local commands

# Watch mode
pnpm dev

# Test with MCP Inspector
npx @modelcontextprotocol/inspector node build/index.js

Testing

The project uses Vitest.

Running Tests

# Run all tests
pnpm test

# Run tests in watch mode
pnpm test:watch

# Run tests with coverage
pnpm test:coverage

# Run the end-to-end protocol smoke suite (builds first, then drives the
# built server over stdio against a local mock SciX API)
pnpm test:e2e

The e2e suite (test/e2e/protocol.test.ts) spawns node build/index.js,
connects a real MCP client over stdio, and asserts the live tool/prompt/
resource surface plus one canned call per tool. It points the server at a
local mock via the SCIX_API_BASE environment variable (see below); no real
network access is required.

Test Structure

Tests are organized in the test/ directory:

test/
├── helpers/
│   └── mockFetch.ts        # Fetch mocking utilities
├── client.test.ts          # HTTP client tests
├── search-docs.test.ts     # Documentation search tests
└── tools/
    ├── search.test.ts      # Search tool tests
    ├── facets.test.ts      # Facet counts tool tests
    ├── paper.test.ts       # Paper details tests
    ├── metrics.test.ts     # Metrics tests
    ├── citations.test.ts   # Citations/references tests
    ├── export.test.ts      # Export tests
    └── library.test.ts     # Library management tests

Test Coverage

The test suite covers:

• HTTP Client: GET/POST/PUT/DELETE methods, error handling (401/404/429), timeouts, request formatting
• Search Tools: Query parameter encoding, repeated fq filters, pagination, result limiting, response formatting
• Facets: Registry/field mapping, json.facet request bodies, hierarchical prefix handling, bucket parsing
• Paper Tools: Bibcode validation, field selection, error handling for missing papers
• Metrics Tools: Batch bibcode processing, MAX_BIBCODES limits, metric type selection
• Citation Tools: Forward/backward citations, sorting, row limits
• Export Tools: Multiple export formats (BibTeX, AASTeX, EndNote, etc.), batch processing
• Library Tools: All CRUD operations, permissions, annotations, library operations

API Token for Tests

Tests use mock fetch and don't require a real API token. Individual tests set SCIX_API_TOKEN='test-api-key' as needed.

Project Structure

src/
├── index.ts             # Main server entry point
├── client.ts            # SciX API client wrapper
├── types.ts             # TypeScript/Zod type definitions
├── formatters.ts        # Response formatting utilities
├── config.ts            # Configuration constants
├── identifier-query.ts  # Identifier (bibcode/DOI/arXiv/SciX) resolution
├── facets.ts            # Facet registry, json.facet building, bucket parsing
├── scix-urls.ts         # scixplorer.org link builders
├── search-docs.ts       # Offline docs search (search_docs tool)
└── tools/
    ├── search.ts        # Search tool
    ├── facets.ts        # Facet counts tool
    ├── paper.ts         # Paper details tool
    ├── metrics.ts       # Metrics tool
    ├── citations.ts     # Citation network tools
    ├── export.ts        # Export tool
    └── library.ts       # Library management tools

Example Usage

Search for papers

Use search with query "supernova 2023" to find recent supernova papers

Narrow a search with facets

Use get_facets with query "exoplanet atmospheres" to see the top authors,
journals and years, then call search with the filter_query values it returns.

Get paper details

Use get_paper with bibcode "2023ApJ...950..123S"

Calculate metrics

Use get_metrics with bibcodes ["2023ApJ...950..123S", "2022MNRAS.517.1234T"]

Export citations

Use export with bibcodes ["2023ApJ...950..123S"] and format "bibtex"

Error Handling

The server provides clear error messages:

• 401: Token missing or rejected - check SCIX_API_TOKEN (stdio) or the
  Authorization: Bearer header (HTTP)
• 404: Resource not found - check bibcode format
• 429: Rate limit exceeded - wait until reset
• Timeout: Request took > 30 seconds

Resources

• SciX Homepage
• SciX API Documentation
• SciX Search Syntax
• MCP Documentation

License

MIT

Support

For API issues: https://scixplorer.org/feedback/general
For server issues: Open an issue on GitHub