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paleobiology-mcp-server: diversity through time

paleobiology_get_diversity
Read-onlyIdempotent

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.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
countNoWhat to count per bin: "genera" (default), "species", or "families".genera
max_maNoOlder 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.
min_maNoYounger 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.
base_idNoClade-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).
intervalNoNamed geologic interval bounding the span, e.g. "Mesozoic". Alternative to max_ma/min_ma.
base_nameNoClade-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).
resolutionNoBin resolution: "period" (default, coarse), "epoch", or "age" (finest).period

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
binsNoPer-interval diversity bins over the span, ordered oldest-first (oldest geologic interval, highest max_ma, first).
errorNoPresent when the call failed. Absent on success.
noticeNoGuidance when the clade or span produced no bins, or when the taxon name could not be resolved and was ignored.
totalCountNoNumber of geologic-interval bins returned.
attributionNoCC-BY data attribution for the Paleobiology Database.

TDQS

A4.4/5.0
Behavior5/5

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

Despite annotations already declaring readOnlyHint, idempotentHint, and openWorldHint, the description adds substantial non-obvious behavioral context: 'Counts reflect SAMPLED diversity, biased by collection effort and rock availability, not true past diversity' — an interpretive caveat that prevents an agent from drawing false conclusions about the numbers. It also discloses return semantics ('The full bin set returns inline ... so you read the curve, the turnover, and the per-bin origination/extinction directly'), which is valuable beyond any structured field.

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

Conciseness4/5

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

The description is a single dense paragraph of about four sentences, and every sentence earns its place: function, required inputs, return semantics, and the sampling caveat. The core statement and example use case are front-loaded. It is appropriately sized for a 7-parameter tool, though slight paragraph breaks would improve scannability.

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 complex tool with 7 parameters, an output schema, and no required fields in the schema, the description covers every decision an agent must make: clade selection (with the exactly-one rule), time bounding (two alternative strategies), count target, bin resolution, return semantics, and the interpretive caveat. Nothing an agent needs to invoke this correctly is missing.

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 coverage is 100%, and the individual parameter descriptions in the schema are exceptionally thorough — max_ma/min_ma even explain which is the deeper-time versus nearer-to-present bound. The tool description reinforces the exact-one-of-base_name/base_id constraint and the interval-vs-range alternative, but these are already present in the schema. Baseline 3 is appropriate: the schema carries the heavy lifting.

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 names a specific verb and resource: 'Compute a diversity / origination / extinction curve for a clade across geologic time, binned by period, epoch, or age.' It anchors the function with a concrete user query ('answers "plot dinosaur genus diversity across the Mesozoic"') and the scope is clearly distinct from every sibling — none of the dataframe, taxon, interval, collection, or occurrence tools compute curves.

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

Usage Guidelines4/5

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

The description gives explicit input-routing guidance: 'Pass a clade-inclusive base_name (or base_id ... exactly one of the two)' and 'bound the span by a named interval ... or a max_ma/min_ma range.' It clearly separates the two alternative bounding strategies. It does not explicitly name a sibling to prefer in other cases, but the sibling set is functionally so different that an agent's routing is unambiguous.

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.