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togoid_convertId

Map identifiers between biological databases, such as converting NCBI Gene IDs to UniProt accessions or UniProt to PDB structure IDs. Accepts lists of IDs and a route string.

Instructions

Convert identifiers from one database to another.

Maps IDs between biological databases — e.g., NCBI Gene IDs to UniProt accessions, or UniProt accessions to PDB structure IDs.

RETURNS a JSON string of a bare array of [source_id, target_id] pairs, e.g. '[["672", "P38398"], ["675", "O15129"]]'. An empty array means none of the input IDs converted along the route.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idsYesSource IDs. Accepts either a list of strings (e.g., ["672", "675", "7157"]) or a comma-separated string ("672,675,7157"). Examples: "672,675,7157" (NCBI Gene IDs), "P38398,P04637" (UniProt)
limitNoMaximum number of results (default 10000)
routeYesComma-separated pair of dataset keys: 'source,target'. NOTE: this is a single joined string, NOT separate `source`/`target` args (as in countId/getRelation) — because a route may be multi-hop (3+ datasets). Examples: - 'ncbigene,uniprot' (Gene → Protein) - 'uniprot,pdb' (Protein → 3D Structure) - 'ncbigene,ensembl_gene' (NCBI Gene → Ensembl Gene) - 'chembl_target,uniprot' (Drug Target → Protein) - 'uniprot,chembl_target' (Protein → Drug Target) - 'ncbigene,hgnc' (Gene → HGNC symbol) Multi-hop routes are also supported: - 'ncbigene,uniprot,pdb' (Gene → Protein → Structure)
offsetNoPagination offset for large result sets

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations are provided, so the description must carry the full burden of behavioral disclosure. It describes the return format (JSON string of pairs) and explains that an empty array means no conversion. However, it does not mention whether the operation is read-only, requires authentication, has rate limits, or any side effects. Given the tool's nature (conversion), it is likely safe, but more detail would improve transparency.

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?

The description is three sentences plus a bullet list of examples, which is appropriately sized. It front-loads the core action, then provides examples, then explains the return format. Every sentence adds information without redundancy.

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

Completeness4/5

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

Given that an output schema exists (as indicated by context signals), the description adequately explains the return value structure. It covers the two required parameters and provides extensive route examples. For a conversion tool with moderate complexity, the description is sufficiently complete.

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?

The input schema already describes all 4 parameters with 100% coverage. The description adds value by clarifying the route parameter's format (comma-separated single string, not separate args) and explicitly noting multi-hop support. This goes beyond what the schema provides, aiding correct usage.

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 ('Convert') and clearly identifies the resource ('identifiers from one database to another'). It provides concrete examples (NCBI Gene IDs to UniProt, UniProt to PDB) that immediately distinguish it from sibling tools like togoid_getRelation or togoid_countId, which handle related but distinct operations.

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?

The description explains the tool's primary use case (mapping IDs between biological databases) and gives multiple route examples. While it does not explicitly state when not to use it or list alternatives, the context is clear enough for an AI agent to recognize when ID conversion is needed versus other operations like counting relations or retrieving dataset descriptions.

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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