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ensembl_feature_overlap

Identify genomic features overlapping a specified region or feature in Ensembl, handling assembly variations and supporting multiple species and feature types.

Instructions

Find genomic features (genes, transcripts, regulatory elements) that overlap with a genomic region or specific feature. Automatically handles assembly-specific format variations (GRCh38/hg38, chromosome naming conventions, coordinate systems). Covers /overlap/region and /overlap/id endpoints.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
regionNoGenomic region in format 'chromosome:start-end' (e.g., '17:7565096-7590856', 'X:1000000-2000000', '1:100000-200000'). Use this OR feature_id, not both.
feature_idNoFeature ID (gene, transcript, etc.) to find overlapping features for (e.g., 'ENSG00000141510', 'ENST00000288602', 'BRCA1'). Use this OR region, not both.
speciesNoSpecies name (e.g., 'homo_sapiens', 'mus_musculus', 'danio_rerio')homo_sapiens
feature_typesNoTypes of features to include (e.g., ['gene', 'transcript', 'exon'], ['regulatory', 'enhancer'])
biotypeNoFilter by biotype (e.g., 'protein_coding', 'lncRNA', 'miRNA', 'pseudogene')
Behavior3/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It adds useful context: 'Automatically handles assembly-specific format variations' and 'Covers /overlap/region and /overlap/id endpoints,' which helps the agent understand implementation details. However, it doesn't cover critical behavioral aspects like rate limits, error handling, response format, or whether this is a read-only operation (though 'Find' implies it likely is).

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 appropriately sized (three sentences) and front-loaded with the core purpose. Every sentence adds value: the first states the purpose, the second adds behavioral context (format handling), and the third specifies endpoints. There's no wasted text, though it could be slightly more structured for 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?

Given the tool's moderate complexity (5 parameters, no output schema, no annotations), the description is partially complete. It covers the purpose and some behavioral context but lacks details on output format, error cases, or performance characteristics. Without annotations or output schema, the agent might struggle to interpret results fully, making this description adequate but with clear gaps.

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 all parameters thoroughly. The description doesn't add any parameter-specific semantics beyond what's in the schema (e.g., it doesn't explain format variations for 'region' beyond the schema's examples). Baseline 3 is appropriate when the schema does the heavy lifting, though the description could have enhanced understanding of parameter interactions.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: 'Find genomic features (genes, transcripts, regulatory elements) that overlap with a genomic region or specific feature.' It specifies the verb ('Find') and resource ('genomic features'), and mentions the types of features covered. However, it doesn't explicitly differentiate this tool from its siblings (e.g., ensembl_lookup, ensembl_mapping), which would be needed for a score of 5.

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 context by mentioning 'genomic region or specific feature' and the endpoints covered, but it doesn't provide explicit guidance on when to use this tool versus alternatives like ensembl_lookup or ensembl_mapping. The input schema's 'oneOf' constraint (region OR feature_id) offers some usage rules, but the description itself lacks clear when/when-not instructions or named alternatives.

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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