@pipeworx/mcp-bold-systems

@pipeworx/bold-systems

The global DNA barcode reference library from BOLD Systems (Barcode of Life Data System, Centre for Biodiversity Genomics, University of Guelph) — specimen vouchers with locality, institution and taxonomy, the COI/rbcL/matK barcode sequences themselves, and BIN species-proxy clusters.

Part of Pipeworx — an MCP gateway connecting AI agents to 1863+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider.

Tools

• bold_specimens(taxon?, country?, bin?, institution?, query?, limit?, offset?) — specimen records: process ID, full taxonomy, BIN, collection date, locality with coordinates, holding institution, marker and GenBank accession. Filters AND together.
• bold_sequences(taxon?, country?, bin?, institution?, marker?, query?, limit?, offset?) — the barcode sequences, with primers, base count, INSDC accession and a ready-to-paste FASTA block.
• bold_taxonomy(name, rank?) — resolve a name against BOLD's own index: lineage, record/species/BIN counts at each rank above it, a plain-language description, and alternative matches with counts.

Auth

Keyless.

Data sources

• https://portal.boldsystems.org/api/terms — term index; resolves a plain name to a query triplet.
• https://portal.boldsystems.org/api/query — turns a triplet query into a query_id.
• https://portal.boldsystems.org/api/documents/{query_id} — the records, nuc sequence inline.
• https://portal.boldsystems.org/api/taxonomy/{description,hierarchy} — lineage, counts, prose.
• Swagger: https://portal.boldsystems.org/api/docs (the spec itself is at https://portal.boldsystems.org/openapi.json, NOT under /api/).

Traps

The v4 API is dead. v4.boldsystems.org/index.php/API_Public/{specimen,sequence,combined} — what every tutorial and most R packages still point at — answers with a "BOLD Public Offline" HTML page, not JSON, so a naive client reports a parse error rather than a retirement. Everything here is the v5 portal API.

The query language is scope:field:value triplets and the scope/field pair is not guessable from the value. Canada is geo:country/ocean, Danaus is tax:genus, BOLD:AAA9566 is bin:uri, Smithsonian Institution is inst:name. Free text gets a 400 {"detail":"Invalid triplet token"}. The pack resolves every typed argument through /api/terms first, which is what turns a plain name into a query that matches instead of a 400 or a silent zero.

/api/counts reports the SUM of the per-term counts, not the size of the intersection. For tax:species:Danaus plexippus;geo:country/ocean:Canada it says 2,520,553 records; the actual match set is 7. That is a clean 200 carrying a number wrong by five orders of magnitude, and it is the number a naive integration would quote. The pack does not use it — matchingRecords comes from recordsTotal on the document query, which is the real count. (Semicolon-separated triplets AND on /documents even though they sum on /counts.)

/api/query/preprocessor falls back to ID-field matching on a multi-word string. Feeding it "Danaus plexippus Canada" returns ids:processid:...;ids:sampleid:...;ids:insdcacs:... — a query that matches nothing and errors nowhere. Resolve each filter separately, which is what resolveTriplet does.

BOLD holds specimen records that were never sequenced. bold_sequences filters to records with a nuc field and says so in note when the result is empty, so "this taxon has no barcodes" is distinguishable from "this taxon has no records".

The marker filter is applied to the returned page, not upstream (BOLD's term index has no entry for COI-5P). The pack over-fetches 5× when a marker is set and reports which markers were actually present in the page it scanned, so an empty result names the markers you could have asked for.

identifier_email is dropped before anything leaves the pack — it is a contact address on a person, not specimen data. Collector and identifier NAMES are kept: those are the published attribution on a museum voucher and appear on every biodiversity record.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "bold-systems": {
      "url": "https://gateway.pipeworx.io/bold-systems/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/bold-systems/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — ask_pipeworx, discover_tools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Both URLs reach the same gateway and the same 1863+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/bold_specimens \
  -H 'Content-Type: application/json' \
  -d '{"taxon":"Danaus plexippus","country":"Canada","limit":3}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/bold_specimens. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Run it from npm

@pipeworx/mcp-bold-systems is a local stdio bridge to the Pipeworx gateway: your MCP client starts it with npx, and it forwards every call to the same https://gateway.pipeworx.io/bold-systems/mcp endpoint shown above. It needs network access; there is no offline mode.

{
  "mcpServers": {
    "bold-systems": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-bold-systems"]
    }
  }
}

Without a key it calls anonymously, capped at 50 calls a day. A free account raises that to 200 a day: get a key at https://pipeworx.io/signup and add "env": { "PIPEWORX_API_KEY": "<your key>" } to the server entry. The key is sent as a Bearer token, the same way a hosted connection sends it, so calls are metered and billed exactly as they are there.

It lists only this pack's tools by default. Set PIPEWORX_META_TOOLS=1 to also list ask_pipeworx and the other gateway-wide tools.

Behind an HTTPS proxy: Node's built-in fetch does not read HTTPS_PROXY by default. Newer Node releases honour it when NODE_USE_ENV_PROXY=1 is set; check your Node version's documentation.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Bold Systems data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT