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gbif-biodiversity-mcp-server

Match Species Name

gbif_match_species
Read-onlyIdempotent

Match a scientific name against the GBIF backbone taxonomy. Returns the best-matching taxon with full classification and a confidence score (0–100). This is the mandatory first step for any GBIF workflow — it returns the backbone taxonKey required by gbif_search_occurrences, gbif_count_occurrences, and gbif_occurrence_facets. When the queried name is a synonym, taxonKey is the accepted taxon it resolves to and matchedTaxonKey carries the synonym's own key; occurrence counts differ sharply between the two, so pass taxonKey. Below confidence 80, the match should be reviewed. matchType NONE means no usable match was found — try removing the strict flag or broadening the name.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYesScientific name to match. Examples: "Parus major", "Agaricus bisporus", "Homo sapiens". Fuzzy matching handles minor spelling variations. Common names are not supported — use gbif_search_species for vernacular name searches.
rankNoExpected taxonomic rank. Use to avoid matching a genus when you expect a species.
strictNoWhen true, only return an exact match. When false (default), GBIF applies fuzzy matching — useful for minor spelling variations and abbreviated names.
kingdomNoNarrow the match to a specific kingdom (e.g., "Animalia", "Plantae", "Fungi") to disambiguate names that appear in multiple kingdoms. Omit the field to match against the whole backbone — a blank or whitespace-only value is rejected rather than dropped, because GBIF answers one with the undisambiguated match, which is indistinguishable from a match that honored the kingdom.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
rankNoTaxonomic rank of the matched taxon.
classNoClass of the matched taxon.
errorNoPresent when the call failed. Absent on success.
genusNoGenus of the matched taxon.
orderNoOrder of the matched taxon.
familyNoFamily of the matched taxon.
noticeNoGuidance when the queried name was a synonym and taxonKey was resolved to the accepted taxon. Absent when the matched name is already the accepted one.
phylumNoPhylum of the matched taxon.
statusNoTaxonomic status: ACCEPTED, SYNONYM, or DOUBTFUL.
kingdomNoKingdom of the matched taxon.
speciesNoSpecies canonical name of the matched taxon.
classKeyNoBackbone taxon key for the class.
genusKeyNoBackbone taxon key for the genus.
orderKeyNoBackbone taxon key for the order.
taxonKeyNoGBIF backbone taxon key to pass to downstream tools. The accepted taxon's key when the queried name is a synonym, otherwise the matched taxon's own key.
familyKeyNoBackbone taxon key for the family.
matchTypeNoEXACT, FUZZY, HIGHERRANK, or NONE. NONE means no usable match.
phylumKeyNoBackbone taxon key for the phylum.
confidenceNoMatch confidence score 0–100. Below 80 warrants review.
kingdomKeyNoBackbone taxon key for the kingdom.
speciesKeyNoBackbone taxon key for the species.
canonicalNameNoScientific name without authorship.
scientificNameNoFull scientific name with authorship.
matchedTaxonKeyNoBackbone key of the name that actually matched. Present only when it differs from taxonKey — that is, when a synonym was resolved to its accepted taxon.

TDQS

A4.7/5.0
Behavior5/5

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

Annotations (readOnlyHint, openWorldHint, idempotentHint) already signal safety. The description adds high-value behavioral details like synonym resolution (taxonKey vs matchedTaxonKey), the 80-confidence review threshold, and the meaning of matchType NONE—all beyond what annotations convey.

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?

Well-structured and front-loaded: purpose first, then critical workflow context, then edge-case behavior. Every sentence serves a purpose—no filler. Approximately 200 words, acceptable given the richness of information.

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?

With an output schema present, the description complements it by explaining key output fields (taxonKey, matchedTaxonKey, matchType, confidence) and how to interpret them. Covers synonyms, confidence thresholds, and failure cases. Nothing essential for correct invocation 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%, so all parameters are well-documented. The description largely restates schema content (e.g., rank to avoid genus matching, strict flag behavior) without adding new meaning. It maintains baseline adequacy but does not elevate understanding beyond the schema.

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?

States a specific verb ('Match'), a precise resource ('scientific name against the GBIF backbone taxonomy'), and describes the output (taxon with classification and confidence). It differentiates from siblings by naming the mandatory first-step role and explicitly routing vernacular name searches to gbif_search_species.

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 declares this as the mandatory first step for GBIF workflows, lists dependent tools, names the alternative (gbif_search_species) for common names, and provides concrete troubleshooting for matchType NONE (remove strict flag or broaden name). Guidance is direct and actionable.

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.