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ensembl_regulatory

Retrieve regulatory features, binding matrices, and annotations from Ensembl genomic data to analyze gene regulation mechanisms.

Instructions

Get regulatory features, binding matrices, and regulatory annotations. Covers regulatory overlap endpoints and binding matrix data.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
regionNoGenomic region in format 'chromosome:start-end' (e.g., '17:7565096-7590856', 'X:1000000-2000000', '6:25000000-35000000')
protein_idNoProtein ID for regulatory features affecting translation (e.g., 'ENSP00000288602', 'ENSP00000350283')
binding_matrix_idNoBinding matrix stable ID (e.g., 'ENSPFM0001', 'ENSPFM0123')
speciesNoSpecies name (e.g., 'homo_sapiens', 'mus_musculus')homo_sapiens
feature_typeNoType of regulatory feature (e.g., 'RegulatoryFeature', 'MotifFeature', 'TF_binding_site')
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It states 'Get' which implies a read-only operation, but doesn't specify if this requires authentication, has rate limits, returns paginated results, or details error conditions. The mention of 'regulatory overlap endpoints' hints at API behavior but lacks specifics like response format or performance characteristics, leaving significant gaps for a tool with 5 parameters.

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 concise and front-loaded, stating the core purpose in the first clause. Both sentences earn their place: the first defines what the tool gets, and the second clarifies the scope of coverage. There's no redundant or vague language, making it efficient for quick understanding.

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 the complexity (5 parameters, no annotations, no output schema), the description is incomplete. It lacks behavioral details (e.g., read/write nature, error handling), usage guidelines compared to siblings, and explanation of return values. While the schema covers parameters well, the description doesn't compensate for missing annotations or output schema, making it inadequate for full agent understanding.

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?

The input schema has 100% description coverage, providing clear documentation for all 5 parameters (region, protein_id, binding_matrix_id, species, feature_type). The description adds no additional parameter semantics beyond what's in the schema—it doesn't explain relationships between parameters (e.g., that region, protein_id, and binding_matrix_id are alternative inputs) or provide usage examples. Baseline 3 is appropriate since the schema does the heavy lifting.

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: 'Get regulatory features, binding matrices, and regulatory annotations.' It specifies the types of data retrieved (regulatory features, binding matrices, annotations) and mentions coverage of regulatory overlap endpoints and binding matrix data. However, it doesn't explicitly differentiate this tool from its siblings like 'ensembl_feature_overlap' or 'ensembl_protein_features', which likely handle related genomic data.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives. It mentions 'Covers regulatory overlap endpoints and binding matrix data' but doesn't clarify if this is exclusive to this tool or shared with siblings. There's no mention of prerequisites, typical use cases, or comparisons to other tools in the Ensembl suite, leaving the agent without context for selection.

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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