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paleobiology-mcp-server: Instructions file for Claude Code

CLAUDE.md

paleobiology-mcp-server CLAUDE.md is an instructions file for Claude Code from cyanheads/paleobiology-mcp-server. It costs 8,843 tokens per session, scanned A, a copy of obsidian-mcp-server AGENTS.md, Apache-2.0.

A project instruction file for an MCP server that searches the Paleobiology Database, a public collection of fossil records. It explains the server's available searches, data access rules, and development setup.

In plain words
What is it for?
Use it when developing or maintaining tools that find fossil species, occurrences, collections, geological time intervals, or diversity changes.
Why use it?
It gives an AI coding assistant the project context needed to work safely on a fossil-biodiversity data service.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md. Also seen: reads .claude/ paths; mentions .claude-plugin; mentions CLAUDE.md.

This is cyanheads/paleobiology-mcp-server's own configuration. It tells Claude Code how to work on paleobiology-mcp-server itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything paleobiology-mcp-server configures →

not rated 2repo changed 5d ago A scan 8,843 tokens copy · 81% Apache-2.0
View source ↗ cyanheads/paleobiology-mcp-server npmjs.com
Reuse

Borrowing it

Nothing to install: this file belongs to cyanheads/paleobiology-mcp-server. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/cyanheads/paleobiology-mcp-server/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/cyanheads/paleobiology-mcp-server

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

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README.md
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Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

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Per session 8,843 This file is loaded in full into every session.
When invoked 8,843 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin 81% copy Near-identical to another mod in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.08843 $0.08843
Opus 5.5 $0.03537 $0.03537
Sonnet 5.5 $0.01769 $0.01769
Haiku 4.5 $0.00884 $0.00884

Measured 5d ago against content hash 0f8c254733e4, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

paleobiology-mcp-server CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

81% identical to obsidian-mcp-server AGENTS.md — 430 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

CLAUDE.md · 492 lines

How it starts

The opening of the file, as written. The whole thing — 492 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Agent Protocol

Server: paleobiology-mcp-server Version: 0.5.0 Framework: @cyanheads/mcp-ts-core ^0.13.18 Engines: Bun ≥1.4.0, Node ≥24.0.0 MCP SDK: @modelcontextprotocol/server ^2.4.0 Zod: ^4.6.7

Dependency hold: Keep @duckdb/node-api on ^1.5.6-r.2 until mcp-ts-core#800 ships: DuckDB 2 currently rejects supported SHOW <table> canvas queries.

Fossil biodiversity over the Paleobiology Database (PBDB, paleobiodb.org/data1.2) — keyless, CC BY 4.0. Six domain paleobiology_* tools, plus three dataframe tools listed only when DataCanvas is on (CANVAS_PROVIDER_TYPE=duckdb), and three paleobiology:// data resources plus the published guide: get_taxon (name/id → matched and accepted identities, classification, FAD/LAD range — the name-resolution gateway), search_occurrences (the flagship; large results spill to a DataCanvas when it is on, read via dataframe_describe then dataframe_query, freed via the opt-in dataframe_drop), get_diversity (origination/extinction curve through time), search_collections (fossil localities), get_references (row reference_no → citation, batched), and list_intervals (the bundled ICS geologic time scale — offline, with a PBDB fallback for sub-stage and regional names outside it). No auth, no API key. Domain env vars: PBDB_BASE_URL, PBDB_TIMEOUT_MS, PBDB_MAX_OCCURRENCES, PALEOBIOLOGY_DATAFRAME_DROP_ENABLED.

Read the framework docs first: node_modules/@cyanheads/mcp-ts-core/CLAUDE.md contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.

What's Next?

When the user asks what's next or needs direction, suggest options based on the current project state. Common next steps:

  1. Re-run the setup skill — ensures CLAUDE.md, skills, structure, and metadata are populated and up to date with the current codebase
  2. Run the design-mcp-server skill — if the tool/resource surface hasn't been mapped yet, work through domain design
  3. Add tools/resources/prompts — scaffold new definitions using the add-tool, add-app-tool, add-resource, add-prompt skills
  4. Add services — scaffold domain service integrations using the add-service skill
  5. Add tests — scaffold tests for existing definitions using the add-test skill
  6. Field-test definitions — exercise tools/resources/prompts with real inputs using the field-test skill, get a report of issues and pain points
  7. Run devcheck — lint, format, typecheck, and security audit
  8. Run the security-pass skill — audit handlers for MCP-specific security gaps: output injection, scope blast radius, input sinks, tenant isolation
  9. Run the polish-docs-meta skill — finalize README, CHANGELOG, metadata, and agent protocol for shipping
  10. Run the maintenance skill — investigate changelogs, adopt upstream changes, and sync skills after bun update --latest

Read the full file on GitHub · 492 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 5d ago Changed · +6 lines · +100 tokens per session 0f8c254733e4
  2. 21d ago Changed · +20 lines · +395 tokens per session 10c765adbe14
  3. 1mo ago Changed · +1 lines · +148 tokens per session 7c626bdd8248
  4. 1mo ago Changed · +29 lines · +1,277 tokens per session 34291d213a31
  5. 2mo ago First seen · 436 lines · 6,923 tokens per session scan A 16683e3e7cfc

Subscribe to this mod's changes

paleobiology-mcp-server CLAUDE.md is an instructions file published in the GitHub repository cyanheads/paleobiology-mcp-server (2 stars, last pushed 5d ago), licensed Apache-2.0. It adds 8,843 tokens to every session, about $0.0354 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 81% identical to obsidian-mcp-server AGENTS.md, differing in 430 lines, and is treated as a copy.

ResearchScientificbiodiversitycyanheadsdeep-timefossilsgeologic-timemcp
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