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berntpopp
by berntpopp

Map Cross-Ontology

map_cross_ontology
Read-onlyIdempotent

Map an Orphanet disorder to its cross-references in external ontologies (OMIM, MONDO, ICD, etc.), grouped by source with mapping relations. Optionally restrict to selected ontologies.

Instructions

List an Orphanet disorder's cross-references to other ontologies, grouped by source (OMIM/MONDO/ICD-10/ICD-11/UMLS/GARD/MeSH/MedDRA), each with its mapping relation. Optionally restrict to a subset of sources, or pass fields=['xrefs.OMIM'] for a sparse projection. Signature: map_cross_ontology(term, prefixes=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
termYesAn ORPHAcode (ORPHA:166024 or 166024), a disease label/synonym, or an external xref CURIE that resolves to a single Orphanet term.
prefixesNoRestrict to these source prefixes, e.g. ['OMIM', 'MONDO'].
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
orpha_codeNo
nameNo
mappingsNo
countNo
prefixes_filterNo
orphanet_versionNo
Behavior2/5

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

Annotations already declare readOnlyHint, destructiveHint, idempotentHint, openWorldHint. The description adds grouping and mapping relations. However, it mentions a 'fields' parameter not present in the input schema, which contradicts the schema and could mislead an agent about available options.

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

Conciseness3/5

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

The description is two sentences plus a signature, which is brief. However, the inconsistent mention of 'fields' introduces confusion and wastes space. Front-loading is adequate but the inconsistency hurts clarity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The description covers the tool's purpose and main parameters. An output schema exists, so return values are documented elsewhere. The description is mostly complete but the 'fields' inconsistency raises questions about the true behavior, harming completeness.

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%, so the schema fully describes parameters. The description adds value by explaining how to use each parameter (e.g., term accepts ORPHAcode, label, or xref; prefixes restricts; response_mode controls verbosity) and provides examples. This exceeds the baseline of 3.

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 uses a specific verb ('list') and resource ('cross-references to other ontologies'), clearly distinguishing it from sibling tools that focus on genes, phenotypes, or disease details. It also clarifies grouping by source and mapping relations.

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?

Provides explicit guidance on when to use the tool and optional filters (prefixes, response_mode). Mentions sparse projection with 'fields' but lacks a clear when-not-to-use statement. Sibling differentiation is implicit.

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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