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paleobiology-mcp-server

by io.github.cyanheads

paleobiology-mcp-server: get taxon record and fossil range

paleobiology_get_taxon
Read-onlyIdempotent

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.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameNoTaxon name to resolve, e.g. "Tyrannosaurus" or "Ammonoidea". Provide this or taxon_no.
taxon_noNoPBDB taxon id from a prior get_taxon, or accepted_no on an occurrence row. Provide this or name.
show_childrenNoWhen true, include a page of the immediate child taxa of this taxon (at most 200 per call — children_truncated says whether more remain).
children_offsetNoNumber 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.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
rankNoTaxonomic rank, e.g. "genus", "family", "order".
errorNoPresent when the call failed. Absent on success.
extantNoTrue if the clade survives to the present day; false if entirely extinct.
noticeNoGuidance when the child list was cut off at the per-page cap (naming the children_offset that reaches the next page), or when children_offset ran past the end of the child list.
childrenNoOne page of immediate child taxa, at most 200 — present only when show_children was true. A taxon with more children than that returns a page, not the full list; read children_truncated before treating it as complete.
taxon_noNoAccepted PBDB taxon id — the canonical id for this taxon. Pass it as base_id to paleobiology_search_occurrences, paleobiology_get_diversity, or paleobiology_search_collections to filter on this clade without re-sending a name.
parent_noNoPBDB taxon id of the immediate parent, when known.
attributionNoCC-BY data attribution for the Paleobiology Database.
parent_nameNoName of the immediate parent taxon, when known.
accepted_nameNoPBDB accepted name (may differ from the searched name).
classificationNoHigher classification of the taxon. Each level is present only when PBDB resolves it.
children_offsetNoPosition in the child list this page started at (0 is the first child). Present only when show_children was true.
last_appearanceNoA first- or last-appearance window. Empty when PBDB has no dated occurrences.
first_appearanceNoA first- or last-appearance window. Empty when PBDB has no dated occurrences.
occurrence_countNoNumber of fossil occurrences recorded in PBDB, when reported.
children_truncatedNoTrue when more immediate children remain past this page — re-call with children_offset advanced by 200 to read the next. False means this page runs to the end of the child list. Present only when show_children was true.

TDQS

A4.5/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already cover readOnly and idempotent. The description adds useful behavioral context: PBDB taxonomy is opinionated, the accepted name may differ from GBIF, and the resolved id appears as accepted_no on occurrence rows. It doesn't describe unresolved-name failure behavior, but the output schema and annotations cover most safety and side-effect concerns.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is reasonably dense but every sentence earns its place: what it returns, when to run it, how to chain it, when to use show_children, and a relevant caveat. It is front-loaded with the main purpose and avoids boilerplate.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a read-only, idempotent tool with a complete input schema and output schema, this description covers all the essential context: purpose, workflow, sibling routing, optional children retrieval, and taxonomy differences. An agent has enough to select and invoke it correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description cover age is 100%, so the description doesn't need to re-explain parameters. It does add workflow context about choosing name vs taxon_no and using show_children, but this is more about orchestration than parameter syntax or semantics.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's job: resolve a taxon by name or taxon_no and return accepted name, rank, higher classification, parent, occurrence count, and FAD/LAD range. It also names the sibling tools it belongs with, distinguishing this lookup-and-resolve step from the later search tools.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly instructs the agent to run this tool first to resolve a name into accepted name and taxon_no, then pass that id as base_id to three named siblings. It also tells when to use show_children, and warns that accepted names may differ from the searched name due to PBDB taxonomy.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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TDQS

A4.7/5.0
Disambiguation5/5

Each tool targets a clearly distinct resource or workflow: taxa, intervals, occurrences, collections, diversity curves, and staged dataframe inspection. Even the two analysis-oriented tools (get_diversity and dataframe_query) are separated by whether the user needs a precomputed curve or arbitrary SQL over staged results.

Naming Consistency4/5

All tools share the paleobiology_ prefix and use clear snake_case names, so the set is predictable overall. The minor deviation is that dataframe_describe and dataframe_query place the object before the verb, while the other five tools use verb_object ordering (get_diversity, get_taxon, list_intervals, search_collections, search_occurrences).

Tool Count5/5

Seven tools is a well-scoped size for a Paleobiology Database client: two search tools, two lookup tools, two dataframe-analysis tools, and a diversity-curve tool. Each tool earns its place without redundancy or bloat.

Completeness5/5

The surface covers the full read-only workflow: resolve taxa, look up time intervals, search occurrences and collections, compute diversity curves, and run SQL analysis over large staged occurrence sets. No obvious gaps exist for the stated domain; pagination and staging hand-offs create no dead ends.

Resources