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namespace.reconcile

Resolve gene symbols to Entrez IDs by building a crosswalk between PPI hits and model genes, using a resolver for unmatched symbols with provenance tracking.

Instructions

Build a symbol<->entrez crosswalk between PPI hits and model genes. Symbols without a table entrez (or absent from the model) are resolved via the id-map resolver (model gene table + symbol map + MyGene); each entry carries authority/confidence/matched_by provenance.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
session_idYes
resolve_unmappedNo
Behavior4/5

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

With no annotations provided, the description carries full burden. It discloses that unresolved symbols go through an id-map resolver using multiple sources and that results include authority/confidence/matched_by provenance. This provides good insight into behavior and side effects.

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?

The description is two sentences, front-loading the core purpose. Every word adds value—no redundancy, fluff, or restatement of the tool name. Highly efficient.

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

Completeness2/5

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

Given no output schema and zero parameter descriptions, the description is incomplete. It explains the high-level algorithm but fails to document the input parameters (session_id and resolve_unmapped) or the output structure, leaving significant gaps for an agent to invoke correctly.

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

Parameters1/5

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

Schema coverage is 0% (no parameter descriptions in schema) and the description does not mention or explain either parameter (session_id or resolve_unmapped). The agent cannot infer how these parameters affect the crosswalk building or resolution process.

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 clearly states the tool builds a symbol<->entrez crosswalk between PPI hits and model genes. It specifies the resolution process and provenance details, giving a specific verb ('Build') and resource ('crosswalk'). While not explicitly distinguishing from siblings, the unique combination of PPI hits and model genes differentiates it.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage when reconciling PPI symbols to model gene entrez IDs but provides no explicit guidance on when to use versus alternatives (e.g., metabolic.id_map). It lacks exclusion criteria or when-not scenarios.

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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