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Map HPO Cross-Ontology

map_cross_ontology
Read-onlyIdempotent

Map HPO terms to cross-references in external ontologies like UMLS, SNOMEDCT_US, and ICD-10, optionally filtered by target prefix.

Instructions

List an HPO term's cross-references to other ontologies/vocabularies, grouped by target prefix (UMLS/SNOMEDCT_US/NCIT/MEDDRA/ICD-10/ICD-9/MONDO/DOID/ORPHA/EFO/MSH/MESH). Optionally restrict to a subset of prefixes. Signature: map_cross_ontology(term, prefixes=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
termYesAn HP id (HP:0000118), a phenotype label/synonym, or an external xref CURIE that resolves to a single HPO term.
prefixesNoRestrict to these target prefixes, e.g. ['UMLS','SNOMEDCT_US'].
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
candidatesNo
hpo_idNo
nameNo
mappingsNo
hpo_versionNo
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and idempotentHint=true. Description adds value by specifying that results are grouped by target prefix and listing all supported prefixes, which goes beyond annotations to inform the agent of output structure.

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?

Two concise sentences, front-loaded with the core action and enumeration of prefixes. Includes signature for quick reference. No redundant phrases.

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 high schema coverage, explicit annotations, and output schema presence, the description adequately covers everything needed: what the tool does, parameter semantics with examples, optional filtering, and response mode choice.

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

Parameters4/5

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

Schema coverage is 100% for all three parameters. The description adds extra context for the 'term' parameter, explaining it accepts HP IDs, labels, or external xref CURIEs, which aids the agent in formatting inputs. Other parameters are consistent with 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?

Description clearly states the tool lists an HPO term's cross-references to other ontologies/vocabularies, grouped by target prefix. It enumerates common prefixes like UMLS, SNOMEDCT_US, etc., distinguishing it from sibling tools like resolve_xref which likely map to a single ontology.

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?

Description explains optional restriction to a subset of prefixes via the 'prefixes' parameter. While it doesn't explicitly compare to alternatives or specify when not to use, the grouping behavior and prefix listing provide clear context for selection.

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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