[{"_1":2,"_3":-5,"_4":-5},"loaderData",{"_5":6,"_7":8,"_9":10},"actionData","errors","root",{"_120":121},"routes/modules.$creator.$moduleId",{"_14":15,"_16":17,"_18":19,"_20":21},"routes/modules.$creator.$moduleId.endpoints",{"_11":12,"_13":-5},"error","Module '@cyanheads/gbif-biodiversity-mcp-server' is not configured","tools","module",{"_20":22,"_23":24,"_25":26,"_27":28,"_29":30,"_31":32,"_33":26,"_34":-5,"_35":36,"_37":-5,"_38":-5,"_39":40,"_41":42,"_43":44,"_45":46,"_47":48,"_49":50,"_51":52,"_53":54,"_55":48,"_56":57,"_58":59,"_60":61,"_62":63,"_64":65,"_66":48,"_67":68,"_69":70,"_71":72,"_73":74,"_75":76,"_77":-5,"_78":-5,"_79":-5,"_80":48,"_81":-5,"_82":83,"_84":85,"_86":87,"_88":89,"_90":91,"_92":93,"_94":95},"apiUrl","https://odel.app/api","creator","cyanheads","moduleId","gbif-biodiversity-mcp-server","@cyanheads/gbif-biodiversity-mcp-server","displayName","gbif biodiversity mcp server","tagline","Search GBIF species taxonomy, occurrence records, datasets, and publishers.","iconKey","https://avatars.githubusercontent.com/u/10339515?v=4","category","data","status","published","metaDescription","metaKeywords","deploymentType","external","workerName","bindingName","mcpConfig","{\"url\":\"https://gbif-biodiversity.caseyjhand.com/mcp\",\"transport\":\"streamable-http\",\"authType\":\"none\"}","pricingModel","free","creatorUserId","system:external-import","createdAt",1781363414000,"updatedAt",1781583623000,"sourceRegistry","official-mcp-registry","sourceUrl","https://registry.modelcontextprotocol.io/v0/servers?search=io.github.cyanheads%2Fgbif-biodiversity-mcp-server","sourceVerified",true,"importedAt","upstreamStars",1,"upstreamUpdatedAt",1781570358000,"detectedTransport","streamable-http","detectedAuthType","none","probeStatus","ok","lastProbedAt","githubRepoUrl","https://github.com/cyanheads/gbif-biodiversity-mcp-server","githubRepoFullName","cyanheads/gbif-biodiversity-mcp-server","releaseId","ext-cyanheads-gbif-biodiversity-mcp-server","version","0.2.8","descriptionMarkdown","

@cyanheads/gbif-biodiversity-mcp-server

Search GBIF species taxonomy, occurrence records, datasets, and publishers via MCP. STDIO or Streamable HTTP.\n

12 Tools • 2 Resources

\n\n

\n\n[![Version](https://img.shields.io/badge/Version-0.2.8-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/gbif-biodiversity-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/gbif-biodiversity-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/gbif-biodiversity-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)\n\n

\n\n

\n\n[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/gbif-biodiversity-mcp-server/releases/latest/download/gbif-biodiversity-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=gbif-biodiversity-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvZ2JpZi1iaW9kaXZlcnNpdHktbWNwLXNlcnZlciJdfQ==) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22gbif-biodiversity-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fgbif-biodiversity-mcp-server%22%5D%7D)\n\n[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)\n\n**Public Hosted Server:** [https://gbif-biodiversity.caseyjhand.com/mcp](https://gbif-biodiversity.caseyjhand.com/mcp)\n\n

\n\n---\n\n## Tools\n\n12 tools for working with GBIF species taxonomy, occurrence records, datasets, and publishers:\n\n| Tool | Description |\n|:---|:---|\n| `gbif_match_species` | Match a species name against the GBIF backbone taxonomy — returns taxonKey, confidence score, and full classification |\n| `gbif_get_species` | Fetch a single backbone taxon by key — full classification, authorship, synonymy, vernacular name, descendant count |\n| `gbif_search_species` | Search or browse the GBIF backbone taxonomy by name fragment, rank, kingdom, family, or genus |\n| `gbif_get_species_classification` | Return the complete parent chain for a taxon — root-first ordered array from kingdom to immediate parent |\n| `gbif_get_species_children` | List direct children of a backbone taxon — genera within a family, species within a genus |\n| `gbif_search_occurrences` | Search 2.4B+ GBIF occurrence records with Darwin Core filters — country, bounding box, WKT geometry, year, month, basis of record |\n| `gbif_count_occurrences` | Count occurrences matching a filter without fetching records — fast single-number response |\n| `gbif_get_occurrence` | Fetch a single occurrence record by key — full Darwin Core record with GADM geography, media, and quality flags |\n| `gbif_occurrence_facets` | Aggregate occurrence counts by a dimension — country, year, basis of record, dataset, kingdom, and more |\n| `gbif_search_datasets` | Search GBIF datasets by keyword, type, country, or publishing organization |\n| `gbif_get_dataset` | Fetch full dataset metadata by UUID — title, description, citation, contacts, license, DOI, coverage |\n| `gbif_search_publishers` | Search GBIF-registered publishing organizations by name fragment or country |\n\n### `gbif_match_species`\n\nMatch a scientific or common name against the GBIF backbone taxonomy.\n\n- Fuzzy matching handles minor typos and vernacular names; set `strict: true` for exact-only matching\n- Returns `taxonKey` — the backbone key required by `gbif_search_occurrences`, `gbif_count_occurrences`, and `gbif_occurrence_facets`\n- Confidence score 0–100; below 80 warrants review\n- Full classification hierarchy with keys at each rank: kingdom, phylum, class, order, family, genus, species\n- `matchType NONE` indicates no usable match — try removing strict mode or broadening the name\n- Resolves synonyms: always returns the accepted backbone key regardless of which name form was queried\n\n---\n\n### `gbif_get_species`\n\nFetch a complete taxon record by GBIF backbone key.\n\n- Full classification, authorship string, and vernacular (English) name when available\n- `taxonomicStatus`: ACCEPTED, SYNONYM, DOUBTFUL — when SYNONYM, `acceptedKey` and `accepted` identify the current name\n- `numDescendants` and `numOccurrences` for scope at a glance\n- `extinct` field present only when explicitly flagged — not false on unlabeled taxa\n- `publishedIn` carries the original description citation when available\n\n---\n\n### `gbif_search_species`\n\nSearch or browse the GBIF backbone taxonomy.\n\n- Accepts name fragments matching scientific and vernacular names\n- Filter by rank, kingdom, family, or genus to scope browsing\n- `isExtinct` filter for extinct vs. extant taxa\n- Scope to a specific checklist dataset with `datasetKey` (omit for the GBIF backbone)\n- Paginated — limit up to 1000, use offset to walk through large groups\n\n---\n\n### `gbif_get_species_classification`\n\nReturn the full parent chain for a taxon as an ordered array.\n\n- Root-first (kingdom → phylum → class → order → family → genus → species → up to parent of queried taxon)\n- Each entry: rank, canonical name, scientific name, taxon key\n- Useful for building taxonomic trees or placing an unfamiliar taxon in context without manual backbone navigation\n\n---\n\n### `gbif_get_species_children`\n\nList direct children of a backbone taxon.\n\n- Genera within a family, species within a genus, subspecies within a species\n- Each child: key, name, rank, taxonomic status, common name, occurrence count, descendant count\n- Paginated — limit up to 1000, iterate with offset for large groups like Coleoptera\n\n---\n\n### `gbif_search_occurrences`\n\nSearch 2.4B+ GBIF occurrence records with full Darwin Core filtering.\n\n- Use `taxonKey` from `gbif_match_species` for reliable results — resolves synonyms automatically; `scientificName` filter does not\n- Geographic filters: `country` (ISO 3166-1 alpha-2), bounding box (`decimalLatitude`/`decimalLongitude` ranges as \"min,max\"), or WKT polygon (`geometry`)\n- Temporal filters: `year` as single year or range, `month` (1–12) for seasonal queries\n- `basisOfRecord` enum: `HUMAN_OBSERVATION`, `PRESERVED_SPECIMEN`, `MACHINE_OBSERVATION`, and more\n- `hasCoordinate` to require or exclude georeferenced records\n- Pagination capped at offset+limit ≈ 100,000 — use `gbif_occurrence_facets` for aggregate analysis beyond this\n\n---\n\n### `gbif_count_occurrences`\n\nCount occurrences matching a filter without fetching any records.\n\n- Backed by the lightweight `/occurrence/count` endpoint — fast single-number response\n- Supported filters: `taxonKey`, `country`, `isGeoreferenced`, `datasetKey`, `year`\n- Use to assess result set size before deciding whether to paginate a full search\n\n---\n\n### `gbif_get_occurrence`\n\nFetch a single occurrence record by GBIF occurrence key.\n\n- Complete Darwin Core record — all coordinate fields, GADM administrative geography (continent, country, state/province, locality), dates\n- Collections metadata: institution code, collection code, catalog number\n- Collector and identifier names, individual count, sex, life stage\n- Associated media (images, audio, video) with URLs and license\n- GBIF data quality issue flags for provenance assessment\n\n---\n\n### `gbif_occurrence_facets`\n\nAggregate occurrence counts across a dimension.\n\n- Facets: `COUNTRY`, `YEAR`, `BASIS_OF_RECORD`, `DATASET_KEY`, `KINGDOM_KEY`, `PHYLUM_KEY`, `CLASS_KEY`, `ORDER_KEY`, `FAMILY_KEY`, `GENUS_KEY`, `SPECIES_KEY`, `PUBLISHING_COUNTRY`, `MONTH`\n- Scope with `taxonKey`, `country`, `year`, `geometry`, or `basisOfRecord` filters\n- Returns top-N values (up to 100) ranked by count — no record payloads\n- Core tool for distribution analysis (\"which countries have the most records?\") and trend queries (\"how has observation volume changed since 2010?\")\n\n---\n\n### `gbif_search_datasets`\n\nSearch GBIF datasets by keyword, type, country, or publishing organization.\n\n- Filters: free-text query, dataset type (`OCCURRENCE`, `CHECKLIST`, `METADATA`, `SAMPLING_EVENT`), publishing country, hosting organization UUID\n- Returns title, type, description, license, DOI, and record count\n- Use `hostingOrg` from `gbif_search_publishers` to scope to datasets from one organization\n- Paginated — limit up to 1000\n\n---\n\n### `gbif_get_dataset`\n\nFetch full dataset metadata by UUID.\n\n- Full description, citation text (for academic reference), license, DOI\n- Contacts with role, name, organization, and email\n- `numConstituents` for aggregate datasets (e.g. iNaturalist, eBird)\n- Use after `gbif_search_datasets` or when an occurrence record's `datasetKey` needs provenance detail\n\n---\n\n### `gbif_search_publishers`\n\nSearch organizations registered with GBIF.\n\n- Filter by name fragment or country\n- Returns organization key, title, and country — sufficient to chain into `gbif_search_datasets` with `hostingOrg`\n- Paginated — limit up to 1000\n\n## Resources\n\n| Type | Name | Description |\n|:---|:---|:---|\n| Resource | `gbif://species/{taxonKey}` | Taxon record from the GBIF backbone — classification, authorship, synonymy status, vernacular name |\n| Resource | `gbif://dataset/{datasetKey}` | Dataset metadata — title, description, citation, license, contacts, coverage |\n\n## Features\n\nBuilt on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core):\n\n- Declarative tool definitions — single file per tool, framework handles registration and validation\n- Unified error handling across all tools\n- Pluggable auth (`none`, `jwt`, `oauth`)\n- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`\n- Structured logging with optional OpenTelemetry tracing\n- Runs locally (stdio/HTTP) or on Cloudflare Workers from the same codebase\n\nGBIF-specific:\n\n- Full GBIF REST API v1 coverage: species taxonomy, occurrences, datasets, and publishers\n- `gbif_match_species` as the entry point — resolves synonyms to backbone taxon keys used throughout\n- Occurrence pagination cap detection with `paginationNote` — redirects to facet aggregation before hitting the ~100,000 row limit\n- WKT polygon geometry support for geographic occurrence queries\n- Darwin Core field mapping with explicit provenance on sparse upstream fields\n\nAgent-friendly output:\n\n- `gbif_match_species` is the mandatory first step — all downstream tools document which key they expect\n- Graceful sparse-field handling — optional fields absent from the API response are omitted rather than null-filled\n- Discriminated error contracts with typed reasons, structured recovery hints, and `when` documentation per tool\n\n## Getting started\n\n### Self-Hosted / Local\n\nAdd the following to your MCP client configuration file.\n\n```json\n{\n \"mcpServers\": {\n \"gbif-biodiversity-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"bunx\",\n \"args\": [\"@cyanheads/gbif-biodiversity-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with npx (no Bun required):\n\n```json\n{\n \"mcpServers\": {\n \"gbif-biodiversity-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"npx\",\n \"args\": [\"-y\", \"@cyanheads/gbif-biodiversity-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with Docker:\n\n```json\n{\n \"mcpServers\": {\n \"gbif-biodiversity-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"docker\",\n \"args\": [\"run\", \"-i\", \"--rm\", \"-e\", \"MCP_TRANSPORT_TYPE=stdio\", \"ghcr.io/cyanheads/gbif-biodiversity-mcp-server:latest\"]\n }\n }\n}\n```\n\nFor Streamable HTTP, set the transport and start the server:\n\n```sh\nMCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http\n# Server listens at http://localhost:3010/mcp\n```\n\n### Prerequisites\n\n- [Bun v1.3.2](https://bun.sh/) or higher.\n- Optional: [GBIF API key](https://www.gbif.org/developer/summary) for higher rate limits.\n\n### Installation\n\n1. **Clone the repository:**\n\n```sh\ngit clone https://github.com/cyanheads/gbif-biodiversity-mcp-server.git\n```\n\n2. **Navigate into the directory:**\n\n```sh\ncd gbif-biodiversity-mcp-server\n```\n\n3. **Install dependencies:**\n\n```sh\nbun install\n```\n\n## Configuration\n\nAll configuration is validated at startup via Zod schemas in `src/config/server-config.ts`. Key environment variables:\n\n| Variable | Description | Default |\n|:---|:---|:---|\n| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http` | `stdio` |\n| `MCP_HTTP_PORT` | HTTP server port | `3010` |\n| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path where the MCP server is mounted | `/mcp` |\n| `MCP_PUBLIC_URL` | Public origin override for TLS-terminating reverse-proxy deployments | none |\n| `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth` | `none` |\n| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.) | `info` |\n| `MCP_GC_PRESSURE_INTERVAL_MS` | Opt-in Bun-only forced-GC pressure loop (ms). Try `60000` if RSS grows under sustained HTTP load. | `0` (disabled) |\n| `LOGS_DIR` | Directory for log files (Node.js only) | `/logs` |\n| `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |\n| `GBIF_BASE_URL` | GBIF API base URL override | `https://api.gbif.org/v1` |\n| `GBIF_REQUEST_TIMEOUT_MS` | HTTP request timeout in milliseconds | `10000` |\n| `OTEL_ENABLED` | Enable OpenTelemetry | `false` |\n\n## Running the server\n\n### Local development\n\n- **Build and run the production version**:\n\n ```sh\n # One-time build\n bun run rebuild\n\n # Run the built server\n bun run start:http\n # or\n bun run start:stdio\n ```\n\n- **Run checks and tests**:\n ```sh\n bun run devcheck # Lints, formats, type-checks, and more\n bun run test # Runs the test suite\n ```\n\n## Project structure\n\n| Directory | Purpose |\n|:---|:---|\n| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Twelve tools across species taxonomy, occurrences, datasets, and publishers. |\n| `src/mcp-server/resources` | Resource definitions. Species and dataset stable-URI resources. |\n| `src/services/gbif` | GBIF REST API service layer — client, request handling, type definitions. |\n| `src/config` | Server-specific environment variable parsing and validation with Zod. |\n| `tests/` | Unit and integration tests, mirroring the `src/` structure. |\n\n## Development guide\n\nSee [`CLAUDE.md`](https://github.com/cyanheads/gbif-biodiversity-mcp-server/blob/main/CLAUDE.md) for development guidelines and architectural rules. The short version:\n\n- Handlers throw, framework catches — no `try/catch` in tool logic\n- Use `ctx.log` for logging, `ctx.state` for storage\n- Register new tools and resources in the `createApp()` arrays\n\n## Contributing\n\nIssues and pull requests are welcome. Run checks and tests before submitting:\n\n```sh\nbun run devcheck\nbun run test\n```\n\n## License\n\nThis project is licensed under the Apache 2.0 License. See the [LICENSE](https://github.com/cyanheads/gbif-biodiversity-mcp-server/blob/main/LICENSE) file for details.\n","changelogMarkdown","videoKey","requiredSecretsJson","publishedAt","priceCents","trialDays",0,"categoryDisplayName","Data & Analytics","upstream",{"_98":99,"_100":101,"_102":103,"_104":105,"_106":107},"requiredSecrets",[],"tags",[],"assets",[],"stats",{"_96":83,"_97":83},"ratingAvg","reviewCount","topics",[108,109,19,110,111,112,113,114,115,116,117,118,119],"license","Apache-2.0","language","TypeScript","registryName","io.github.cyanheads/gbif-biodiversity-mcp-server","homepage","https://www.npmjs.com/package/@cyanheads/gbif-biodiversity-mcp-server","biodiversity","bun","darwin-core","gbif","mcp","mcp-server","model-context-protocol","natural-history","occurrences","species","taxonomy","typescript","ENV",{"_122":123,"_124":125,"_126":127},"ENVIRONMENT","production","TURNSTILE_SITE_KEY","0x4AAAAAAB8-rEI2gNDf_QhU","SENTRY_DSN","https://45fd1229f78089d5c3ee78be128030e1@o4510583261757440.ingest.de.sentry.io/4510584253448272"]