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Query Genomic Region

ensembl_query_region
Read-onlyIdempotent

Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, plus the genome assembly the coordinates are on. Useful for "what's in this locus?" and for seeding follow-up lookups. Region format is chr:start-end (e.g. 13:32315086-32400268 for the BRCA2 locus), spanning at most 5,000,000 bases. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. The feature parameter defaults to gene only — requesting variation in an 85 kb region matches 44,000+ entries. Explicitly include variation, regulatory, transcript, or exon only when needed. The response returns up to max_results features (default 100) while totalCount always reports the full count; set max_results to 0 for every feature, or query a smaller region to see a different slice. Exon rows carry the parent transcript ID, so the same exon appears once per transcript it belongs to.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
regionYesGenomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl serves at most 5,000,000 bases per region; split a larger area into smaller windows. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results.
biotypeNoOptional biotype filter (e.g. protein_coding, lncRNA, SNV). Applied server-side by Ensembl. Not all feature types support biotype filtering.
featureNoFeature types to retrieve — at least one. Default is gene only. Requesting variation in a large region can match tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller).
speciesYesSpecies in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Use ensembl_list_species to discover valid values.
max_resultsNoMaximum number of features to return. A gene-length region can hold tens of thousands of variation features; the default keeps the response compact. Set to 0 to return every feature uncapped. totalCount always reports the true number found before this cap.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
capNoThe max_results limit applied to the feature list.
errorNoPresent when the call failed. Absent on success.
shownNoNumber of features returned after the max_results cap.
noticeNoGuidance about the result set: empty, large, capped, or missing assembly.
regionNoThe region queried, as provided.
speciesNoThe species queried.
featuresNoGenomic features found in the requested region, capped to max_results. totalCount reports the full count found before the cap.
truncatedNoTrue when the feature list was capped at max_results.
totalCountNoTotal number of features found in the region before the max_results cap. Exceeds the returned features count when the list was capped.
assemblyNameNoGenome assembly the coordinates are on (e.g. GRCh38). Omitted only when it could not be resolved, in which case the notice says so.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed14 schema fields changed
    • changedInput schema / properties / feature / description
      Previous value: -"Feature types to retrieve. Default is gene only. Requesting variation in a large region can return tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller)."New value: +"Feature types to retrieve — at least one. Default is gene only. Requesting variation in a large region can match tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller)."
    • addedInput schema / properties / feature / minItems
      Added value: +1
    • addedInput schema / properties / max_results
      Added value: +{
      +  "default": 100,
      +  "description": "Maximum number of features to return. A gene-length region can hold tens of thousands of variation features; the default keeps the response compact. Set to 0 to return every feature uncapped. totalCount always reports the true number found before this cap.",
      +  "maximum": 9007199254740991,
      +  "minimum": 0,
      +  "type": "integer"
      +}
    • changedInput schema / properties / region / description
      Previous value: -"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."New value: +"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl serves at most 5,000,000 bases per region; split a larger area into smaller windows. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."
    • addedInput schema / properties / region / minLength
      Added value: +1
    • addedInput schema / properties / species / minLength
      Added value: +1
    • addedOutput schema / properties / assemblyName
      Added value: +{
      +  "description": "Genome assembly the coordinates are on (e.g. GRCh38). Omitted only when it could not be resolved, in which case the notice says so.",
      +  "type": "string"
      +}
    • addedOutput schema / properties / cap
      Added value: +{
      +  "description": "The max_results limit applied to the feature list.",
      +  "type": "number"
      +}
    • changedOutput schema / properties / error / properties / data / properties / reason / description
      Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed or contains invalid coordinates. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed, contains invalid coordinates, or spans more than the 5,000,000-base maximum. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler."
    • changedOutput schema / properties / features / description
      Previous value: -"Genomic features found in the requested region."New value: +"Genomic features found in the requested region, capped to max_results. totalCount reports the full count found before the cap."
    • changedOutput schema / properties / notice / description
      Previous value: -"Warning or guidance about the result set."New value: +"Guidance about the result set: empty, large, capped, or missing assembly."
    • addedOutput schema / properties / shown
      Added value: +{
      +  "description": "Number of features returned after the max_results cap.",
      +  "type": "number"
      +}
    • changedOutput schema / properties / totalCount / description
      Previous value: -"Number of features returned. Note: very large regions may return truncated results."New value: +"Total number of features found in the region before the max_results cap. Exceeds the returned features count when the list was capped."
    • addedOutput schema / properties / truncated
      Added value: +{
      +  "description": "True when the feature list was capped at max_results.",
      +  "type": "boolean"
      +}
  2. Changed6 schema fields changed
    • changedInput schema / $schema
      Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"
    • addedInput schema / additionalProperties
      Added value: +false
    • changedOutput schema / $schema
      Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"
    • addedOutput schema / anyOf
      Added value: +[
      +  {
      +    "not": {
      +      "required": [
      +        "error"
      +      ]
      +    },
      +    "required": [
      +      "features",
      +      "totalCount",
      +      "region",
      +      "species"
      +    ]
      +  },
      +  {
      +    "required": [
      +      "error"
      +    ]
      +  }
      +]
    • addedOutput schema / properties / error
      Added value: +{
      +  "additionalProperties": {},
      +  "description": "Present when the call failed. Absent on success.",
      +  "properties": {
      +    "code": {
      +      "description": "JSON-RPC error code for this failure.",
      +      "maximum": 9007199254740991,
      +      "minimum": -9007199254740991,
      +      "type": "integer"
      +    },
      +    "data": {
      +      "additionalProperties": {},
      +      "properties": {
      +        "reason": {
      +          "description": "Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed or contains invalid coordinates. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler.",
      +          "examples": [
      +            "invalid_region",
      +            "invalid_species"
      +          ],
      +          "type": "string"
      +        },
      +        "recovery": {
      +          "additionalProperties": {},
      +          "description": "Actionable next step for the caller.",
      +          "properties": {
      +            "hint": {
      +              "type": "string"
      +            }
      +          },
      +          "required": [
      +            "hint"
      +          ],
      +          "type": "object"
      +        },
      +        "retryable": {
      +          "description": "Whether retrying may succeed.",
      +          "type": "boolean"
      +        }
      +      },
      +      "type": "object"
      +    },
      +    "message": {
      +      "description": "Human-readable description of what went wrong.",
      +      "type": "string"
      +    }
      +  },
      +  "required": [
      +    "code",
      +    "message"
      +  ],
      +  "type": "object"
      +}
    • removedOutput schema / required
      Removed value: -[
      -  "features",
      -  "totalCount",
      -  "region",
      -  "species"
      -]
  3. Changed3 schema fields changed
    • changedInput schema / properties / region / description
      Previous value: -"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Chromosome names use Ensembl format — no \"chr\" prefix for vertebrates (13, not chr13). For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."New value: +"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."
    • addedOutput schema / properties / features / items / properties / parentId
      Added value: +{
      +  "description": "Parent transcript ID (ENST…) for exon features. An exon is reported once per parent transcript it belongs to, so the same exon ID can appear on multiple rows that differ only by this field — not duplicates.",
      +  "type": "string"
      +}
    • addedOutput schema / properties / features / items / properties / rank
      Added value: +{
      +  "description": "Position (1-based) of an exon within its parent transcript.",
      +  "type": "number"
      +}
  4. First observed

TDQS

A4.4/5.0
Behavior5/5

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

The description goes well beyond the read-only, idempotent annotations by disclosing important behaviors: chromosome-name normalization, the chr-prefix acceptance, the gene-only default, the max_results cap with totalCount always reporting the full count, and the fact that exon rows can be duplicated per parent transcript. This significantly reduces the chance of misinterpreting results.

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

Conciseness5/5

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

The description is dense but efficiently organized: purpose, output shape, use case, region format, chromosome normalization, feature defaults, and response-limit semantics. Each sentence adds distinct value and there is no filler or repetition of annotation fields.

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?

Given the complexity of the tool and the presence of a rich input schema and output schema, the description covers the critical operational details: region constraints, feature selection trade-offs, response cap behavior, and exon duplication. An agent has enough context to call the tool correctly and interpret the response without needing additional external information.

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?

Schema coverage is 100%, so the schema already documents all parameters. The description adds valuable parameter-level context beyond the schema, such as the 85 kb variation example, the explicit guidance to include variation only when needed, and the semantics of max_results=0 with totalCount preserving the true count. It does not add much for species or biotype, but those are already well-covered in the schema.

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 specifies a concrete operation with a verb and resource: 'Find genomic features overlapping a chromosomal region' and enumerates feature types. It is unambiguous about what the tool returns, including stable ID, type, location, biotype, name, and assembly. However, it does not explicitly distinguish itself from sibling tools like ensembl_lookup_gene or ensembl_get_sequence, so the differentiation is implicit rather than stated.

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 gives clear usage context: it is 'useful for what's in this locus?' and 'for seeding follow-up lookups.' It also provides practical guidance on when to include variation and other feature types versus sticking with the gene default. It does not explicitly name alternatives or state when not to use this tool, but the context is strong enough for an agent to make a reasonable 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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