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Bioregistry

by io.github.pipeworx-io

Prefix

prefix
Read-onlyIdempotent

Fetch full Bioregistry metadata for a biological database prefix (e.g. "chebi", "hpo", "uniprot"), including canonical URI pattern, synonyms, homepage, and cross-registry mappings.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
prefixYese.g. "chebi", "hpo"

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameNoHuman-readable name
prefixNoThe prefix identifier
exampleNoExample identifier
uri_formatNoURI format template
descriptionNoDescription of the prefix

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint false. The description adds valuable context about what metadata is returned (canonical URI pattern, synonyms, homepage, cross-registry mappings), which goes beyond the structured annotations.

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?

Single sentence, no filler, includes key details upfront. Every word adds value, making it efficient and easy to parse.

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 the single parameter, rich annotations, and presence of an output schema, the description covers all essential aspects. No gaps in explaining what the tool does or returns.

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 coverage is 100% with a well-described string parameter and examples. The description adds the biological database context but no additional syntax or format details beyond the schema, meeting the baseline for high-coverage schemas.

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?

Description clearly states the action ('Fetch'), the resource ('full Bioregistry metadata for a biological database prefix'), and provides two concrete examples. This distinguishes it from the sibling tool 'prefixes' which likely returns a list, making purpose unambiguous.

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?

Implicitly differentiates from sibling 'prefixes' by focusing on a single prefix. No explicit when-not or alternatives, but the context is clear enough for an AI agent to infer the right scenario.

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

All Bioregistry toolsInspect
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TDQS

A3.5/5.0
Disambiguation2/5

Severe overlap exists between ask_pipeworx, ask_pipeworx_beta, ask_pipeworx_grounded, and deep_research, all of which route to the same 5,743-tool catalog with only subtle differences. The pair resolve (CURIE-to-URL) and resolve_entity (name-to-ID) share the same verb but mean completely different things in different domains, and the five polymarket tools have heavily overlapping purposes.

Naming Consistency2/5

The set mixes multiple conventions: noun-only names (prefix, prefixes, search, resolve), verb_noun names (generate_llms_txt, scan_dependency, validate_claim), adjective_noun names (recent_alerts, recent_changes), and vendor-prefixed names (ask_pipeworx*, pipeworx_*, polymarket_*). Some names break the pattern entirely, like forget and remember, and the plural prefix/prefixes pair is inconsistent.

Tool Count2/5

35 tools is heavy for any single server, but the bigger problem is that roughly 31 tools are Pipeworx platform utilities (asking, memory, subscriptions, feedback) while only 4 serve the stated 'Bioregistry' purpose. A server named Bioregistry carrying prediction-market arbitrage and AI-visibility tools is poorly scoped regardless of the absolute count.

Completeness2/5

The Bioregistry surface is thin: search, prefix, prefixes, and resolve cover lookup/pagination but no registry management, and the remaining tools belong to an entirely different, unrelated domain. The server's apparent purpose ('Bioregistry') is barely served, while the Pipeworx functionality, though broad, is buried under an incongruent server name, making the overall surface incomplete and incoherent.

Resources