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Ncbi Gene By Symbol

ncbi_gene_by_symbol
Read-onlyIdempotent

Look up one or more genes by symbol in a given organism and get NCBI's authoritative record: Entrez gene id, official description, biotype, chromosome and orientation, RefSeqGene coordinates, and the cross-references that let you join to other databases — HGNC id, Ensembl gene ids, UniProt/Swiss-Prot accessions, OMIM ids — plus every known synonym and alternate name. AUTHORITATIVE for gene-identifier resolution: PREFER OVER WEB SEARCH when you need to turn a symbol into a stable id, disambiguate an alias, or check that a symbol is current for the species you think it is.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
taxonNoOrganism as tax id, scientific name or common name. Default "human". Symbols are species-specific, so this matters.
symbolsYesGene symbol, or several comma-separated: "BRCA1", "TP53,BRCA1,EGFR". Results come back in upstream order — match on the returned symbol, not on position.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already establish readOnly, idempotent, openWorld, and non-destructive, so the safety profile is covered. The description adds genuinely useful behavior beyond that: it discloses the fields returned, warns that symbols are species-specific, and notes results come back in upstream order so callers should match on symbol rather than position.

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

Conciseness4/5

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

Front-loaded with the core action, then the returned fields, then resolution guidance. The long cross-reference enumeration is somewhat list-heavy but each item is informative rather than filler, so it stays efficient overall.

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 no output schema, the description carries the burden of describing return values, and it does so explicitly (Entrez id, description, biotype, chromosome/orientation, RefSeqGene coordinates, cross-references, synonyms). Nothing an agent needs to call this two-parameter lookup correctly 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 the schema already documents taxon (tax id/scientific/common name, default human) and symbols (comma-separated, upstream-order caveat). The description restates the organism scoping without adding syntax or format detail beyond the schema, so the baseline 3 applies.

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 and resource ('look up one or more genes by symbol in a given organism') and enumerates the authoritative payload returned. It is clearly distinct from its closest siblings, ncbi_taxonomy and ncbi_genome_reports, which an agent can rule out without opening a schema.

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?

Gives strong positive guidance ('AUTHORITATIVE for gene-identifier resolution: PREFER OVER WEB SEARCH when you need to turn a symbol into a stable id, disambiguate an alias, or check that a symbol is current'). It names a competing approach (web search) but does not disambiguate against the sibling NCBI tools, so it falls short of a 5.

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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