paleobiology-mcp-server

v0.3.4 pre-1.0

Search fossil occurrences, resolve taxon fossil ranges, plot diversity through deep time, and look up the geologic time scale via MCP. STDIO or Streamable HTTP.

paleobiology.caseyjhand.com/mcp
claude mcp add --transport http paleobiology-mcp-server https://paleobiology.caseyjhand.com/mcp
codex mcp add paleobiology-mcp-server --url https://paleobiology.caseyjhand.com/mcp
{
  "mcpServers": {
    "paleobiology-mcp-server": {
      "url": "https://paleobiology.caseyjhand.com/mcp"
    }
  }
}
gemini mcp add --transport http paleobiology-mcp-server https://paleobiology.caseyjhand.com/mcp
{
  "mcpServers": {
    "paleobiology-mcp-server": {
      "command": "bunx",
      "args": [
        "mcp-remote",
        "https://paleobiology.caseyjhand.com/mcp"
      ]
    }
  }
}
{
  "mcpServers": {
    "paleobiology-mcp-server": {
      "type": "http",
      "url": "https://paleobiology.caseyjhand.com/mcp"
    }
  }
}
curl -X POST https://paleobiology.caseyjhand.com/mcp \
  -H "Content-Type: application/json" \
  -H "MCP-Protocol-Version: 2025-11-25" \
  -d '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-11-25","capabilities":{},"clientInfo":{"name":"curl","version":"1.0.0"}}}'

Tools

7

paleobiology_search_occurrences

open-world

Search fossil occurrences filtered by taxon, geologic time, geography, and depositional environment — the flagship. Use base_name for a clade and all its descendants (what "Tyrannosaurus occurrences" usually means), base_id for that same clade by resolved taxon id, or taxon_name for an exact taxon. Bound the age by a named interval (e.g. "Maastrichtian") or a max_ma/min_ma range, and/or a lng/lat bounding box; scope to a single locality with collection_no (take it from a paleobiology_search_collections row). At least one filter is required — taxon, time, place, environment, or collection_no. Every row carries two distinct coordinate systems — modern lng/lat (where the rock is today) and paleo lng/lat (where the landmass sat at deposition) — plus the formation, age interval, and higher classification (phylum through genus); never plot a deep-time occurrence on a modern coastline. Resolve a name with paleobiology_get_taxon first if unsure. Broad queries return many rows: an inline preview answers the immediate question, and when the set outgrows that preview the matching occurrences — up to the per-call cap — stage on a DataCanvas (canvas_id + table_name, returned only then) for SQL via paleobiology_dataframe_query (count by interval, group by formation/country, map by region). The response reports how many occurrences matched in total, which rows this page covers, and the offset that reaches the next page — page through the whole match set with limit/offset.

read
invocation
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "paleobiology_search_occurrences",
    "arguments": {}
  }
}
schema
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "base_name": {
      "description": "Clade-inclusive taxon filter — this taxon and all descendants, e.g. \"Dinosauria\". The usual choice. Supply this or base_id, never both.",
      "type": "string"
    },
    "base_id": {
      "description": "Clade-inclusive taxon filter by PBDB taxon id — the taxon_no from paleobiology_get_taxon, or accepted_no on an occurrence row. Same clade-inclusive semantics as base_name, but unambiguous where a name is not (homonyms, synonyms, unresolved spellings). Supply this or base_name, never both.",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "taxon_name": {
      "description": "Exact taxon filter — only this taxon, not descendants. Use instead of base_name when you want a single taxon.",
      "type": "string"
    },
    "collection_no": {
      "description": "Restrict to one collection (locality) by its PBDB collection_no — the fauna found together at that site. Take the id from a paleobiology_search_collections row to drill from a locality into its occurrences.",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "interval": {
      "description": "Named geologic interval bounding the age, e.g. \"Cretaceous\" or \"Maastrichtian\". Alternative to max_ma/min_ma.",
      "type": "string"
    },
    "max_ma": {
      "description": "Older age bound in millions of years ago. Alternative to interval. When paired with min_ma it must be strictly greater — max_ma is the deeper-time end of the window.",
      "type": "number",
      "minimum": 0
    },
    "min_ma": {
      "description": "Younger age bound in millions of years ago. Alternative to interval. When paired with max_ma it must be strictly smaller — min_ma is the nearer-to-present end of the window.",
      "type": "number",
      "minimum": 0
    },
    "lngmin": {
      "description": "Western edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmax with it or neither.",
      "type": "number",
      "minimum": -180,
      "maximum": 180
    },
    "lngmax": {
      "description": "Eastern edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmin with it or neither.",
      "type": "number",
      "minimum": -180,
      "maximum": 180
    },
    "latmin": {
      "description": "Southern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.",
      "type": "number",
      "minimum": -90,
      "maximum": 90
    },
    "latmax": {
      "description": "Northern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.",
      "type": "number",
      "minimum": -90,
      "maximum": 90
    },
    "environment": {
      "description": "Depositional environment: \"marine\", \"terrestrial\", or \"freshwater\" (lacustrine + fluvial). Omit for all.",
      "type": "string",
      "enum": [
        "marine",
        "terrestrial",
        "freshwater"
      ]
    },
    "limit": {
      "default": 100,
      "description": "Maximum occurrences to pull per page (1–500). Caps the pull (further bounded by PBDB_MAX_OCCURRENCES); broad queries stage that page on the canvas for SQL. Pair with offset to walk the whole match set.",
      "type": "integer",
      "minimum": 1,
      "maximum": 500
    },
    "offset": {
      "default": 0,
      "description": "Number of matching occurrences to skip before this page — page with limit by advancing offset. The response notice names the exact offset that reaches the next page.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    },
    "canvas_id": {
      "description": "Canvas id from a prior call to re-stage onto the same workspace. Reusing it REPLACES (overwrites) the prior occurrence table — each search restages the full result, it does not append to or accumulate across earlier ones. Omit to start fresh; the response returns a new id.",
      "type": "string"
    }
  },
  "required": [
    "limit",
    "offset"
  ],
  "additionalProperties": false
}
view source ↗

paleobiology_get_taxon

open-world

Resolve a taxon by name (e.g. "Tyrannosaurus") or by integer taxon_no to its accepted name, rank, higher classification, immediate parent, fossil occurrence count, and first/last appearance (FAD/LAD) range in millions of years — "when did this clade exist, and what is it." Run this first to resolve a name into the accepted name and taxon_no, then pass that id as base_id to paleobiology_search_occurrences, paleobiology_get_diversity, or paleobiology_search_collections for a clade-inclusive filter that carries no name ambiguity (the same id also appears as accepted_no on occurrence rows). Set show_children to also list immediate child taxa. PBDB taxonomy is opinionated and can differ from GBIF's backbone, so the accepted name may differ from the name you searched.

read
invocation
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "paleobiology_get_taxon",
    "arguments": {}
  }
}
schema
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "name": {
      "description": "Taxon name to resolve, e.g. \"Tyrannosaurus\" or \"Ammonoidea\". Provide this or taxon_no.",
      "type": "string"
    },
    "taxon_no": {
      "description": "PBDB taxon id from a prior get_taxon, or accepted_no on an occurrence row. Provide this or name.",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "show_children": {
      "default": false,
      "description": "When true, include a page of the immediate child taxa of this taxon (at most 200 per call — children_truncated says whether more remain).",
      "type": "boolean"
    },
    "children_offset": {
      "default": 0,
      "description": "Number of immediate children to skip before the returned page — used only when show_children is true. Advance it by 200 while children_truncated is true to walk the whole child list.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    }
  },
  "required": [
    "show_children",
    "children_offset"
  ],
  "additionalProperties": false
}
view source ↗

paleobiology_get_diversity

open-world

Compute a diversity / origination / extinction curve for a clade across geologic time, binned by period, epoch, or age — answers "plot dinosaur genus diversity across the Mesozoic." Pass a clade-inclusive base_name (or base_id, the same clade by resolved taxon id — exactly one of the two) and bound the span by a named interval (e.g. "Mesozoic") or a max_ma/min_ma range; choose what to count (genera, species, or families) and the bin resolution. The full bin set returns inline — a diversity series is a bounded set of geologic intervals — so you read the curve, the turnover, and the per-bin origination/extinction directly. Counts reflect SAMPLED diversity, biased by collection effort and rock availability, not true past diversity.

read
invocation
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "paleobiology_get_diversity",
    "arguments": {}
  }
}
schema
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "base_name": {
      "description": "Clade-inclusive taxon to count, e.g. \"Dinosauria\" or \"Ammonoidea\" — this taxon and all descendants. Supply this or base_id (exactly one is required, never both).",
      "type": "string"
    },
    "base_id": {
      "description": "Clade-inclusive taxon to count, by PBDB taxon id — the taxon_no from paleobiology_get_taxon, or accepted_no on an occurrence row. Same semantics as base_name, but unambiguous where a name is not (homonyms, synonyms, unresolved spellings). Supply this or base_name (exactly one is required, never both).",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "count": {
      "default": "genera",
      "description": "What to count per bin: \"genera\" (default), \"species\", or \"families\".",
      "type": "string",
      "enum": [
        "genera",
        "species",
        "families"
      ]
    },
    "resolution": {
      "default": "period",
      "description": "Bin resolution: \"period\" (default, coarse), \"epoch\", or \"age\" (finest).",
      "type": "string",
      "enum": [
        "period",
        "epoch",
        "age"
      ]
    },
    "interval": {
      "description": "Named geologic interval bounding the span, e.g. \"Mesozoic\". Alternative to max_ma/min_ma.",
      "type": "string"
    },
    "max_ma": {
      "description": "Older bound of the span in millions of years ago. Alternative to interval. When paired with min_ma it must be strictly greater — max_ma is the deeper-time end of the span.",
      "type": "number",
      "minimum": 0
    },
    "min_ma": {
      "description": "Younger bound of the span in millions of years ago. Alternative to interval. When paired with max_ma it must be strictly smaller — min_ma is the nearer-to-present end of the span.",
      "type": "number",
      "minimum": 0
    }
  },
  "required": [
    "count",
    "resolution"
  ],
  "additionalProperties": false
}
view source ↗

paleobiology_list_intervals

open-world

Look up the geologic time scale — eons, eras, periods, epochs, and ages with their absolute-age boundaries in millions of years (Ma) and nesting. This is the reference that grounds every temporal filter on the other tools and translates a named interval like "Late Cretaceous" to its 100.5–66.0 Ma boundaries (and back). Filter by a name substring, a Ma range (overlap match), and/or a level; call with no filters to browse the full scale. Browsing and every name on the bundled ICS international-scale snapshot are answered offline. A name the snapshot does not carry — the sub-stage and regional names that occurrence and collection rows report, such as "Late Maastrichtian" or "Lancian" — costs one PBDB lookup across its other time scales; the response names which source answered and which scale the interval belongs to.

read
invocation
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "paleobiology_list_intervals",
    "arguments": {}
  }
}
schema
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "name": {
      "description": "Case-insensitive substring of the interval name, e.g. \"cretaceous\" or \"Jurassic\". A name the bundled international scale does not carry is matched exactly against PBDB's other time scales.",
      "type": "string"
    },
    "min_ma": {
      "description": "Younger bound of an age window (Ma); intervals overlapping [min_ma, max_ma] match.",
      "type": "number",
      "minimum": 0
    },
    "max_ma": {
      "description": "Older bound of an age window (Ma); intervals overlapping [min_ma, max_ma] match.",
      "type": "number",
      "minimum": 0
    },
    "level": {
      "description": "Restrict to one rank of the international scale: eon, era, period, epoch, or age (finest). Browsing is bounded to that scale, so the sub-stage and regional ranks are not selectable here.",
      "type": "string",
      "enum": [
        "eon",
        "era",
        "period",
        "epoch",
        "age"
      ]
    }
  },
  "additionalProperties": false
}
view source ↗

paleobiology_search_collections

open-world

Find fossil collections (localities) by area and geologic time — "what has been dug up here, and from what rock." Each locality returns its location, age (named interval and Ma), formation and strata, lithology, depositional environment, and the count of co-occurring fossils. Filter by a clade-inclusive base_name (or base_id, the same clade by resolved taxon id), a named interval or max_ma/min_ma range, a lng/lat bounding box, a formation or lithology name, and/or an environment. Results page inline via limit/offset (the response discloses when more remain). Take a collection_no from a row and pass it — or the same bbox+interval — to paleobiology_search_occurrences to see the actual fauna found together.

read
invocation
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "paleobiology_search_collections",
    "arguments": {}
  }
}
schema
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "base_name": {
      "description": "Clade-inclusive taxon filter — localities yielding this taxon or its descendants, e.g. \"Dinosauria\". Supply this or base_id, never both.",
      "type": "string"
    },
    "base_id": {
      "description": "Clade-inclusive taxon filter by PBDB taxon id — the taxon_no from paleobiology_get_taxon, or accepted_no on an occurrence row. Same semantics as base_name, but unambiguous where a name is not (homonyms, synonyms, unresolved spellings). Supply this or base_name, never both.",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "interval": {
      "description": "Named geologic interval bounding the age, e.g. \"Maastrichtian\". Alternative to max_ma/min_ma.",
      "type": "string"
    },
    "max_ma": {
      "description": "Older age bound in millions of years ago. When paired with min_ma it must be strictly greater — max_ma is the deeper-time end of the window.",
      "type": "number",
      "minimum": 0
    },
    "min_ma": {
      "description": "Younger age bound in millions of years ago. When paired with max_ma it must be strictly smaller — min_ma is the nearer-to-present end of the window.",
      "type": "number",
      "minimum": 0
    },
    "lngmin": {
      "description": "Western edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmax with it or neither.",
      "type": "number",
      "minimum": -180,
      "maximum": 180
    },
    "lngmax": {
      "description": "Eastern edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmin with it or neither.",
      "type": "number",
      "minimum": -180,
      "maximum": 180
    },
    "latmin": {
      "description": "Southern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.",
      "type": "number",
      "minimum": -90,
      "maximum": 90
    },
    "latmax": {
      "description": "Northern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.",
      "type": "number",
      "minimum": -90,
      "maximum": 90
    },
    "formation": {
      "description": "Geologic formation name to filter by, e.g. \"Hell Creek\".",
      "type": "string"
    },
    "lithology": {
      "description": "Lithology (rock type) to filter by, e.g. \"sandstone\".",
      "type": "string"
    },
    "environment": {
      "description": "Depositional environment: \"marine\", \"terrestrial\", or \"freshwater\" (lacustrine + fluvial). Omit for all.",
      "type": "string",
      "enum": [
        "marine",
        "terrestrial",
        "freshwater"
      ]
    },
    "limit": {
      "default": 100,
      "description": "Maximum localities to return per page (1–500).",
      "type": "integer",
      "minimum": 1,
      "maximum": 500
    },
    "offset": {
      "default": 0,
      "description": "Number of localities to skip — page with limit by advancing offset.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    }
  },
  "required": [
    "limit",
    "offset"
  ],
  "additionalProperties": false
}
view source ↗

paleobiology_dataframe_query

Run a read-only SQL SELECT against occurrence result sets staged on a DataCanvas by paleobiology_search_occurrences. This is how you analyze a large fossil set without re-fetching it: count occurrences by early_interval, group by formation, country (cc), or accepted_name, or filter by a paleo/modern coordinate range. The classification column is JSON — roll up by rank with json_extract_string(classification, '$.family') (also $.phylum, $.class, $.order, $.genus). Staged rows are occurrences, so collection-only fields such as lithology are not present. Reference tables by the table_name that search_occurrences returned — call paleobiology_dataframe_describe first if you do not know the table or column names. SELECT only; writes and file-reading functions are rejected.

read
invocation
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "paleobiology_dataframe_query",
    "arguments": {
      "canvas_id": "<canvas_id>",
      "sql": "<sql>"
    }
  }
}
schema
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "canvas_id": {
      "type": "string",
      "description": "Canvas id returned by paleobiology_search_occurrences when its result spilled."
    },
    "sql": {
      "type": "string",
      "description": "A read-only SQL SELECT. Reference tables by the names paleobiology_search_occurrences / _describe returned."
    }
  },
  "required": [
    "canvas_id",
    "sql"
  ],
  "additionalProperties": false
}
view source ↗

paleobiology_dataframe_describe

List the tables and their columns staged on a DataCanvas by paleobiology_search_occurrences. Call this before paleobiology_dataframe_query to discover the exact table_name and column names to reference in SQL.

read
invocation
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "paleobiology_dataframe_describe",
    "arguments": {
      "canvas_id": "<canvas_id>"
    }
  }
}
schema
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "canvas_id": {
      "type": "string",
      "description": "Canvas id returned by paleobiology_search_occurrences when its result spilled."
    }
  },
  "required": [
    "canvas_id"
  ],
  "additionalProperties": false
}
view source ↗

Resources

2

Read one fossil occurrence by its integer occurrence_no (obtained from paleobiology_search_occurrences output rows). Returns the accepted and identified names, age as both a named interval and a Ma range, modern and paleo coordinates distinctly, formation/strata, locality, and an attribution field carrying the CC BY 4.0 source credit.

uri paleobiology://occurrence/{occurrence_no} mime application/json

Read one taxon by its integer taxon_no (from paleobiology_get_taxon, or accepted_no on an occurrence row). Returns the accepted name, rank, higher classification, immediate parent, fossil occurrence count, first/last appearance (FAD/LAD) range in millions of years, and an attribution field carrying the CC BY 4.0 source credit.

uri paleobiology://taxon/{taxon_no} mime application/json