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uniprot_resolve_orthology

Read-only

Group orthology cross-references in a UniProt entry by source database to compare inference methods and identify consensus across species.

Instructions

Group every orthology cross-reference in a UniProt entry by source database (KEGG / OMA / OrthoDB / eggNOG / HOGENOM / PhylomeDB / InParanoid / TreeFam / GeneTree / PAN-GO / PANTHER / OrthoInspector). Different databases use different inference methods; surfacing them side-by-side lets the agent reason about consensus when comparing orthologs across species. Pure-Python — no extra HTTP call beyond the entry fetch.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYes
response_formatNomarkdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Annotations indicate readOnlyHint=true and openWorldHint=true; the description adds valuable context: it is 'Pure-Python — no extra HTTP call beyond the entry fetch,' clarifying performance and data source. It also explains the grouping behavior (by database), which goes beyond annotations.

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?

Three sentences, front-loaded with the main action. The second sentence adds rationale, and the third adds implementation detail. No waste, though it could be slightly more concise by omitting the database list if it's already in the schema (but it's not).

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?

Given the existence of an output schema (unseen), return values need not be explained. However, the tool lacks parameter explanations, which is a gap. The description adequately covers the purpose and behavior for a tool that processes data from a prior entry fetch.

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?

The input schema has 0% description coverage, and the tool description does not explain the parameters. 'accession' is not defined, and 'response_format' (with default 'markdown') is not described. The description fails to add meaning beyond the schema field names.

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 groups orthology cross-references by source database, lists the specific databases, and explains the purpose of surfacing side-by-side for consensus reasoning. This is specific and distinguishes it from sibling tools like uniprot_get_cross_refs.

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 implicitly suggests use when comparing orthologs across species, but lacks explicit guidance on when to use this tool versus alternatives, such as uniprot_get_cross_refs or other resolve tools. No exclusions or when-not-to-use are provided.

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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