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gbif-biodiversity-mcp-server

Search Species Taxonomy

gbif_search_species
Read-onlyIdempotent

Search or browse the GBIF backbone taxonomy. Accepts scientific name fragments, rank filters, and higher-taxon constraints. Useful for exploring what species exist under a higher taxon (e.g., "list all families of Coleoptera"), for simple name-fragment searches, or when gbif_match_species returns too narrow a result. kingdom, family, and genus scope the browse to a higher taxon: each is resolved to its backbone key before the search runs, so the narrowest one supplied is what scopes, an alternative name resolves to the taxon it is a synonym of, and a name that matches no backbone taxon at that rank fails rather than returning the whole index. Names are capitalized as GBIF writes them ("Paridae", not "paridae") and are matched exactly, not fuzzily. Paginated — use limit and offset to walk through results.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
qNoName fragment to search for. Matches scientific and vernacular names. Omit the field to browse without a name term — a blank or whitespace-only value is rejected rather than sent, because GBIF answers a blank one with the whole 46,623,754-name index and a whitespace-only one with nothing, and neither is the search a caller who filled the field was asking for.
rankNoFilter to a specific taxonomic rank.
genusNoScope the search to a genus, by name — "Quercus", "Parus". Resolved to its backbone key before the search runs, and it is the narrowest of the three, so it is what scopes when kingdom or family is supplied too. Matched exactly and capitalized as GBIF writes it; a name shared across kingdoms ("Prunella", "Oenanthe") resolves only when kingdom is supplied with it. Omit the field to browse every genus; a blank or whitespace-only value is rejected rather than dropped.
limitNoNumber of records to return (default 20, max 1000).
familyNoScope the search to a family, by name — "Paridae", "Fagaceae". Resolved to its backbone key before the search runs, so an alternative family name lands on the taxon it is a synonym of ("Compositae" scopes to Asteraceae). Matched exactly and capitalized as GBIF writes it; a name that is not a backbone family fails rather than being ignored. Supplied with genus, it must be that genus's own family. Omit the field to browse every family; a blank or whitespace-only value is rejected rather than dropped.
offsetNoPagination offset.
kingdomNoScope the search to a kingdom, by name — "Animalia", "Plantae", "Fungi". Resolved to its backbone key before the search runs, and matched exactly: capitalize it as GBIF writes it, since "animalia" resolves to nothing. Supplied alongside family or genus it disambiguates that name rather than scoping on its own — "Prunella" alone names both a bird genus and a plant genus and resolves to neither. Omit the field to browse every kingdom; a blank or whitespace-only value is rejected rather than dropped.
isExtinctNoFilter to extinct (true) or extant (false) taxa.
datasetKeyNoScope to a specific checklist dataset UUID (8-4-4-4-12 hex). Omit the field to search the GBIF backbone — an empty string is rejected rather than read as no scope, because GBIF answers a blank datasetKey with the unfiltered backbone result.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
taxaNoMatching taxa.
errorNoPresent when the call failed. Absent on success.
limitNoRecords returned in this page.
noticeNoGuidance when results are empty or paging overshot. Absent on successful result pages.
offsetNoCurrent pagination offset.
taxonScopeNoThe higher-taxon scope actually applied — which of kingdom, family, or genus scoped the search, the backbone taxon its name resolved to, and that taxon key. Absent when none of the three was supplied.
totalCountNoTotal matches before pagination.
endOfRecordsNoTrue when there are no more results after this page.

TDQS

A5/5.0
Behavior5/5

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

The description goes well beyond the readOnlyHint/openWorldHint/idempotentHint annotations, disclosing concrete behaviors: higher-taxon names are resolved to backbone keys, alternative names resolve to synonyms, unmatched names fail rather than returning everything, matching is exact and capitalization-sensitive, blank values are rejected, and pagination works via limit/offset. All of this adds value beyond the annotations, and there is no contradiction.

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?

Although long, every sentence is information-dense and earns its place. The structure front-loads purpose, then usage, then behavioral nuances, and then parameter specifics. It is not padded or redundant; the length is justified by the complexity of GBIF's matching and scoping behavior.

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?

Given 9 parameters, an output schema exists, and annotations cover safety, the description thoroughly covers the operational context: matching rules, synonym resolution, exact capitalization, blank-value pitfalls, pagination, and failure modes. No critical information an agent needs to call this correctly is missing.

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

Parameters5/5

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

Schema coverage is 100%, yet the description adds substantial meaning to every parameter: it explains why blank values are rejected (GBIF returns the whole 46M-name index), how genus/family/kingdom interact and disambiguate (e.g., 'Prunella'), how synonym resolution works (Compositae → Asteraceae), and constraints like genus-specific families. This is far more than the schema provides, richly compensating for the 9-parameter surface.

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 opens with a specific verb-resource pair ('Search or browse the GBIF backbone taxonomy') and immediately clarifies what it accepts (name fragments, rank filters, higher-taxon constraints). It distinguishes itself from a sibling by stating it is useful 'when gbif_match_species returns too narrow a result,' so an agent can tell them apart without inspecting schemas.

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?

Explicit usage contexts are given: exploring what species exist under a higher taxon, simple name-fragment searches, and as a fallback when gbif_match_species is too narrow. It also differentiates browsing vs searching and explains when higher-taxon scope applies, giving clear when-to-use and when-not-to-use guidance.

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

A4.5/5.0
Disambiguation5/5

Each tool targets a distinct action and resource pair: matching (single and batch), retrieving species details, hierarchy traversal, searching occurrences, counting, aggregating by facets, and searching datasets/publishers. There is no functional overlap or ambiguity between tools.

Naming Consistency4/5

The naming is largely consistent with the gbif_ prefix followed by a verb and noun (e.g., gbif_match_species, gbif_count_occurrences, gbif_get_dataset). However, a few tools use a search_<noun> pattern (e.g., gbif_search_datasets) and one uses a noun phrase without a verb (gbif_occurrence_facets), introducing a minor inconsistency.

Tool Count5/5

13 tools is well within the optimal range for a domain-specific API. The tools cover taxonomy resolution, species lookup and hierarchy, occurrence search/count/aggregation, and dataset/publisher discovery—no unnecessary bloat or sparse coverage.

Completeness4/5

The surface covers the core GBIF workflows: match → search/get occurrences, get species details and classification, and find datasets/publishers. Missing bulk download is explicitly acknowledged and not served by this tool, and searching datasets by taxon is indirect (via occurrence datasetKey), but these are workable gaps rather than blockers.