gnomad-genetics-mcp-server
Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.
使うべきか
品質と安全性
B
検出事項（5）
- HIGHTool poisoning patterns detected
- MEDIUMTool description contains URL to non-standard domaingnomad_get_variant 内
- MEDIUMTool description contains URL to non-standard domaingnomad_get_gene_constraint 内
- MEDIUMTool description contains URL to non-standard domaingnomad_list_gene_variants 内
- MEDIUMTool description contains URL to non-standard domaingnomad_get_coverage 内
ツール定義とプロトコルへの準拠に関する自動分析に基づいています。
コンテキストコスト
~11,889トークン数（ツール定義）
~18.0 KB一般的なレスポンスサイズ
注意への影響は大きい（128k コンテキストの 9.29%）
これは、サーバーのツールがモデルのコンテキストに読み込まれるたびに消費されるおおよそのトークン数です。数が多いほど、ほかのタスクに使える注意が減ります。
インストール
ワンクリックインストール
これを `claude_desktop_config.json` ファイルに追加してください:
{
"mcpServers": {
"gnomad-genetics-mcp-server": {
"command": "node",
"args": [
"@cyanheads/gnomad-genetics-mcp-server"
]
}
}
}実行可能なパッケージ
npm@cyanheads/gnomad-genetics-mcp-server
0.4.0streamable-httpリモートエンドポイント
https://gnomad-genetics.caseyjhand.com/mcpstreamable-httpできること
ツール一覧
ツール（7）
🟢 読み取り専用🟡 書き込み🔴 削除⚪ 不明
🟢gnomad_get_variant(variants, dataset, reference_genome)
Fetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, homozygote and hemizygote counts, quality flags, transcript consequence, in-silico predictor scores, and joined ClinVar clinical significance. The "how common, is it benign" answer in one call. Accepts a batch of up to 25 IDs (chrom-pos-ref-alt or rsID) with per-item partial success: a malformed or absent ID lands in failed[] — with its reason and a recovery hint — without failing the others. An empty found[] for a well-formed ID means the variant is not in the chosen dataset — pair with gnomad_get_coverage to confirm the position is callable before concluding true absence. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/
入力スキーマ
{
"type": "object",
"properties": {
"variants": {
"minItems": 1,
"maxItems": 25,
"type": "array",
"items": {
"type": "string",
"minLength": 1,
"description": "Variant ID — chrom-pos-ref-alt (1-based, e.g. 1-55051215-G-GA) on chromosome 1–22, X, or Y with an optional chr prefix, or an rsID (rs11591147). Mitochondrial IDs (M, MT, chrM) are not served. Obtain a variantId from ensembl_predict_variant or a VCF. Malformed IDs are reported per-item in failed[], not rejected wholesale."
},
"description": "1–25 variant IDs (chrom-pos-ref-alt or rsID) to look up in one batched call."
},
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"type": "string",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
]
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"type": "string",
"enum": [
"GRCh38",
"GRCh37"
]
}
},
"required": [
"variants"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}出力スキーマ
{
"type": "object",
"properties": {
"found": {
"type": "array",
"items": {
"type": "object",
"properties": {
"variant_id": {
"type": "string",
"description": "Resolved chrom-pos-ref-alt variant ID."
},
"rsids": {
"type": "array",
"items": {
"type": "string"
},
"description": "dbSNP rsIDs for this variant."
},
"reference_genome": {
"type": "string",
"description": "Reference build the record is on (GRCh38 or GRCh37)."
},
"dataset": {
"type": "string",
"description": "Effective gnomAD dataset."
},
"ac": {
"type": "number",
"description": "Overall allele count across carried callset(s)."
},
"an": {
"type": "number",
"description": "Overall allele number across carried callset(s)."
},
"af": {
"description": "Overall allele frequency; null when an is 0.",
"type": [
"number",
"null"
]
},
"homozygote_count": {
"type": "number",
"description": "Overall homozygote count."
},
"hemizygote_count": {
"description": "Overall hemizygote count (X/Y only); null otherwise.",
"type": [
"number",
"null"
]
},
"populations": {
"type": "array",
"items": {
"type": "object",
"properties": {
"id": {
"type": "string",
"description": "Genetic-ancestry group: afr, amr, asj, eas, fin, mid, nfe, sas, remaining, or ami (genomes only)."
},
"source": {
"type": "string",
"enum": [
"exome",
"genome"
],
"description": "Which gnomAD callset this group vector came from."
},
"ac": {
"type": "number",
"description": "Allele count in this group."
},
"an": {
"type": "number",
"description": "Allele number (called chromosomes) in this group."
},
"af": {
"description": "Allele frequency (ac/an); null when an is 0.",
"type": [
"number",
"null"
]
},
"homozygote_count": {
"type": "number",
"description": "Homozygote count in this group."
},
"hemizygote_count": {
"description": "Hemizygote count (X/Y only); null otherwise.",
"type": [
"number",
"null"
]
}
},
"required": [
"id",
"source",
"ac",
"an",
"af",
"homozygote_count",
"hemizygote_count"
],
"additionalProperties": false,
"description": "One genetic-ancestry group AC/AN/AF vector."
},
"description": "Per-ancestry frequency vector — never collapsed to a single global AF."
},
"source": {
"type": "array",
"items": {
"type": "string",
"enum": [
"exome",
"genome"
]
},
"description": "Which gnomAD callset(s) carry this variant."
},
"flags": {
"type": "array",
"items": {
"type": "string"
},
"description": "Quality flags (e.g. lcr, segdup, lc_lof)."
},
"consequence": {
"description": "Worst/transcript VEP consequence term; null when none.",
"type": [
"string",
"null"
]
},
"transcript_id": {
"description": "Transcript the consequence is on; null when none.",
"type": [
"string",
"null"
]
},
"gene_symbol": {
"description": "Gene symbol for the reported consequence; null when none.",
"type": [
"string",
"null"
]
},
"in_silico": {
"type": "array",
"items": {
"type": "object",
"properties": {
"id": {
"type": "string",
"description": "Predictor name. Ids vary by dataset — gnomad_r4: cadd, revel_max, spliceai_ds_max, pangolin_largest_ds, phylop, sift_max, polyphen_max; gnomad_r3: cadd, revel, splice_ai, primate_ai; gnomad_r2_1 and exac carry none."
},
"value": {
"description": "Predictor score; null when not provided for this variant, or when gnomAD gave text with no number (the text is then in annotation).",
"type": [
"number",
"null"
]
},
"annotation": {
"description": "Text gnomAD attaches to the score — on gnomad_r3, the SpliceAI event (e.g. acceptor_gain, no_consequence). Holds the raw text when value is null for lack of a number; null for a plain score.",
"type": [
"string",
"null"
]
}
},
"required": [
"id",
"value",
"annotation"
],
"additionalProperties": false,
"description": "One in-silico predictor score."
},
"description": "In-silico predictor scores present for this variant."
},
"clinvar": {
"anyOf": [
{
"type": "object",
"properties": {
"clinical_significance": {
"description": "ClinVar clinical significance (e.g. Pathogenic, Likely benign); null when no entry.",
"type": [
"string",
"null"
]
},
"review_status": {
"description": "ClinVar review status text.",
"type": [
"string",
"null"
]
},
"gold_stars": {
"description": "ClinVar 0–4 star review rating.",
"type": [
"number",
"null"
]
},
"clinvar_variation_id": {
"description": "ClinVar VariationID.",
"type": [
"string",
"null"
]
}
},
"required": [
"clinical_significance",
"review_status",
"gold_stars",
"clinvar_variation_id"
],
"additionalProperties": false,
"description": "Joined ClinVar significance from gnomAD. Null when the variant has no ClinVar entry."
},
{
"type": "null"
}
],
"description": "ClinVar annotation, or null when no entry exists."
},
"clinvar_unavailable": {
"type": "boolean",
"description": "True when the optional ClinVar resolver failed; false when no entry exists."
}
},
"required": [
"variant_id",
"rsids",
"reference_genome",
"dataset",
"ac",
"an",
"af",
"homozygote_count",
"hemizygote_count",
"populations",
"source",
"flags",
"consequence",
"transcript_id",
"gene_symbol",
"in_silico",
"clinvar",
"clinvar_unavailable"
],
"additionalProperties": false,
"description": "Full population record for one variant."
},
"description": "Variants resolved to a population record."
},
"failed": {
"type": "array",
"items": {
"type": "object",
"properties": {
"variant": {
"type": "string",
"description": "The input ID that failed to resolve."
},
"error": {
"type": "string",
"description": "What went wrong for this ID."
},
"reason": {
"type": "string",
"enum": [
"invalid_variant_id",
"variant_not_found",
"mitochondrial_unsupported",
"ambiguous_rsid",
"graphql_error",
"upstream_build_mismatch",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
],
"description": "Why this ID failed — a reason declared in this tool's error contract. Branch on it rather than on the message."
},
"recovery": {
"type": "string",
"description": "The next step for this ID — the recovery hint declared for its reason."
},
"candidates": {
"description": "Concrete variant IDs to retry when an rsID is ambiguous.",
"type": "array",
"items": {
"type": "string"
}
}
},
"required": [
"variant",
"error",
"reason",
"recovery"
],
"additionalProperties": false,
"description": "One failed input ID, why it failed, and what to do next."
},
"description": "Per-item failures, in input order: malformed IDs, variants absent from the dataset, or upstream errors — each with its reason and recovery hint."
},
"dataset": {
"type": "string",
"description": "Effective gnomAD dataset used for the batch."
},
"reference_genome": {
"type": "string",
"description": "Effective reference build used for the batch."
},
"notice": {
"description": "Non-fatal notice when optional ClinVar annotation was unavailable.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_variant_id`: A variant ID is outside the chrom-pos-ref-alt or rsID grammar; reported per item in failed[]. `variant_not_found`: A well-formed ID is absent from the requested dataset; reported per item in failed[]. `mitochondrial_unsupported`: A variant ID names the mitochondrial chromosome (M, MT, or chrM); reported per item in failed[]. `ambiguous_rsid`: An rsID maps to more than one variant in the dataset; reported per item in failed[]. `graphql_error`: gnomAD rejected the lookup for one ID with a GraphQL error; reported per item in failed[]. `upstream_build_mismatch`: gnomAD answered one ID with a variant on a different reference build; reported per item in failed[]. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry for one ID; reported per item in failed[]. `upstream_timeout`: Every attempt to reach gnomAD for one ID timed out; reported per item in failed[]. `upstream_access`: gnomAD refused the request for one ID (access denied); reported per item in failed[]. `invalid_upstream_response`: gnomAD kept answering one ID with a response that failed validation; reported per item in failed[]. Other values are possible when a failure originates below the handler.",
"examples": [
"incoherent_build",
"invalid_variant_id",
"variant_not_found",
"mitochondrial_unsupported",
"ambiguous_rsid",
"graphql_error",
"upstream_build_mismatch",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"found",
"failed",
"dataset",
"reference_genome"
]
},
{
"required": [
"error"
]
}
]
}🟢gnomad_get_gene_constraint(gene, dataset, reference_genome)
Fetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric) plus its lower bound, observed/expected ratios for LoF, missense, and synonymous variation, and the three Z-scores. This is the orthogonal axis to allele frequency: a loss-of-function variant matters far more in a gene intolerant to being broken. Accepts an HGNC symbol (PCSK9) or an Ensembl gene ID (ENSG00000169174). constraint_release names the release the metrics come from: gnomAD v4.1.2 for gnomad_r4 and gnomad_r3 (gnomAD publishes no v3 constraint), gnomAD v2.1.1 for gnomad_r2_1, and ExAC r0.3 for exac. gnomAD recommends LOEUF < 0.45 to call a gene LoF-intolerant on v4.1.2 and LOEUF < 0.35 on v2.1.1. ExAC r0.3 publishes only pLI, the Z-scores, and observed/expected counts, so on exac the ratios and LOEUF are null, constraint_flags is empty, and pLI is the intolerance measure. Many genes have null constraint (sparse upstream) — null fields are reported as such, never fabricated. Echoes the effective dataset and reference build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/
入力スキーマ
{
"type": "object",
"properties": {
"gene": {
"type": "string",
"minLength": 2,
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."
},
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"type": "string",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
]
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"type": "string",
"enum": [
"GRCh38",
"GRCh37"
]
}
},
"required": [
"gene"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}出力スキーマ
{
"type": "object",
"properties": {
"gene_id": {
"type": "string",
"description": "Ensembl gene ID resolved for the gene."
},
"symbol": {
"type": "string",
"description": "HGNC gene symbol."
},
"dataset": {
"type": "string",
"description": "Effective gnomAD dataset."
},
"reference_genome": {
"type": "string",
"description": "Effective reference build."
},
"constraint_release": {
"type": "string",
"description": "Constraint release the metrics come from: gnomAD v4.1.2 for gnomad_r4 and gnomad_r3 (gnomAD publishes no v3 constraint, so gnomad_r3 serves the GRCh38 table), gnomAD v2.1.1 for gnomad_r2_1, ExAC r0.3 for exac."
},
"pli": {
"anyOf": [
{
"type": "number",
"minimum": 0,
"maximum": 1
},
{
"type": "null"
}
],
"description": "pLI — probability of LoF intolerance; >0.9 intolerant. Null when unavailable."
},
"oe_lof": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Non-negative observed/expected LoF ratio. Null when unavailable."
},
"oe_lof_lower": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "LOEUF confidence-interval lower bound. Null when unavailable."
},
"oe_lof_upper": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "LOEUF (oe_lof_upper) — the headline intolerance metric; gnomAD recommends < 0.45 on v4.1.2 and < 0.35 on v2.1.1 to call a gene LoF-intolerant. Null when unavailable, and always null on exac."
},
"oe_mis": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Observed/expected missense ratio. Null when unavailable."
},
"oe_syn": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Observed/expected synonymous ratio. Null when unavailable."
},
"lof_z": {
"description": "LoF constraint Z-score. Null when unavailable.",
"type": [
"number",
"null"
]
},
"mis_z": {
"description": "Missense constraint Z-score. Null when unavailable.",
"type": [
"number",
"null"
]
},
"syn_z": {
"description": "Synonymous constraint Z-score. Null when unavailable.",
"type": [
"number",
"null"
]
},
"obs_lof": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Non-negative observed LoF variant count. Null when unavailable."
},
"exp_lof": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Non-negative expected LoF variant count. Null when unavailable."
},
"obs_mis": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Non-negative observed missense count. Null when unavailable."
},
"exp_mis": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Non-negative expected missense count. Null when unavailable."
},
"obs_syn": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Non-negative observed synonymous count. Null when unavailable."
},
"exp_syn": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "null"
}
],
"description": "Non-negative expected synonymous count. Null when unavailable."
},
"constraint_flags": {
"type": "array",
"items": {
"type": "string"
},
"description": "Caveat flags gnomAD attaches to the gene’s constraint (e.g. no_exp_lof, mis_too_many, syn_outlier); empty when none, and always empty on exac, where ExAC publishes no flags."
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `gene_not_found`: No gene matched the symbol or Ensembl ID in this build. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_constraint_data`: gnomAD returned constraint metrics outside their valid ranges, such as a pLI above 1. `graphql_error`: gnomAD rejected the constraint query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"gene_not_found",
"incoherent_build",
"invalid_constraint_data",
"graphql_error",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"gene_id",
"symbol",
"dataset",
"reference_genome",
"constraint_release",
"pli",
"oe_lof",
"oe_lof_lower",
"oe_lof_upper",
"oe_mis",
"oe_syn",
"lof_z",
"mis_z",
"syn_z",
"obs_lof",
"exp_lof",
"obs_mis",
"exp_mis",
"obs_syn",
"exp_syn",
"constraint_flags"
]
},
{
"required": [
"error"
]
}
]
}🟢gnomad_list_gene_variants(gene, transcript_id, region, consequence_class, max_af, ...)
List every gnomAD variant in a gene, transcript, or region with allele frequencies and predicted consequences, optionally filtered to one consequence class (lof, missense, synonymous, other) and/or a maximum allele frequency. A result too large to inline is staged on a DataCanvas table named gene_variants, returned as canvas_id and table_name beside an inline preview — call gnomad_dataframe_describe for its columns, then gnomad_dataframe_query to rank by AF, count by consequence, or group across every row rather than the preview. A result that fits inline stages no table unless canvas_id is supplied. When the canvas is disabled (CANVAS_PROVIDER_TYPE != duckdb) the tool returns a capped inline preview and the SQL path is unavailable. Supply exactly one of gene, transcript_id, or region. Echoes the effective dataset and build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/
入力スキーマ
{
"type": "object",
"properties": {
"gene": {
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.",
"anyOf": [
{
"type": "string",
"minLength": 2,
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."
},
{
"type": "string",
"maxLength": 0,
"description": "Blank — the gene is treated as omitted."
}
]
},
"transcript_id": {
"description": "Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.",
"type": "string"
},
"region": {
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served), a span (stop − start) under 2,500,000 bp, and at most ~30,000 variants. Mutually exclusive with gene and transcript_id.",
"anyOf": [
{
"type": "string",
"const": ""
},
{
"type": "string",
"pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266) on chromosome 1–22, X, or Y, optional chr prefix."
}
]
},
"consequence_class": {
"description": "Keep only variants in this consequence class. Omit to return all classes.",
"type": "string",
"enum": [
"lof",
"missense",
"synonymous",
"other"
]
},
"max_af": {
"description": "Keep only variants with allele frequency ≤ this value (0–1). Variants with null AF are always kept.",
"type": "number",
"minimum": 0,
"maximum": 1
},
"canvas_id": {
"description": "Optional canvas ID from a prior call, to reuse the same canvas. When supplied, this call always writes its result to the gene_variants table on that canvas, replacing (not appending to) the previous one — even when the result fits inline; a result with no variants removes the table. Omit to stage on a fresh canvas only when the result is too large to inline.",
"type": "string",
"pattern": "^[A-Za-z0-9_-]{10}$"
},
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"type": "string",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
]
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"type": "string",
"enum": [
"GRCh38",
"GRCh37"
]
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}出力スキーマ
{
"type": "object",
"properties": {
"preview": {
"type": "array",
"items": {
"type": "object",
"properties": {
"variant_id": {
"type": "string",
"description": "chrom-pos-ref-alt variant ID."
},
"af": {
"description": "Allele frequency computed from joint allele counts; null when uncomputable.",
"type": [
"number",
"null"
]
},
"ac": {
"type": "number",
"description": "Allele count (joint across carried callsets)."
},
"an": {
"type": "number",
"description": "Allele number (joint sum across carried callsets)."
},
"consequence": {
"description": "VEP consequence term; null when none.",
"type": [
"string",
"null"
]
},
"consequence_class": {
"type": "string",
"enum": [
"lof",
"missense",
"synonymous",
"other"
],
"description": "Bucketed consequence class."
},
"homozygote_count": {
"type": "number",
"description": "Homozygote count (joint across callsets)."
},
"source": {
"type": "string",
"description": "Carried callset(s), pipe-joined (e.g. exome|genome)."
},
"flags": {
"type": "string",
"description": "Quality flags, pipe-joined (empty when none)."
}
},
"required": [
"variant_id",
"af",
"ac",
"an",
"consequence",
"consequence_class",
"homozygote_count",
"source",
"flags"
],
"additionalProperties": false,
"description": "One gene-variant row — also the canvas table column set."
},
"description": "Inline preview rows — the immediate answer; every matching variant unless spilled."
},
"canvas_id": {
"type": "string",
"description": "Canvas holding table_name (or the canvas_id you supplied) — pass it to gnomad_dataframe_describe, then gnomad_dataframe_query. Empty when this call used no canvas: the result fit inline and no canvas_id was supplied, or the canvas is disabled."
},
"table_name": {
"type": "string",
"description": "Canvas table this call staged (gene_variants), holding every matching variant — inspect it with gnomad_dataframe_describe, then query it with gnomad_dataframe_query. Empty when this call staged no table."
},
"spilled": {
"type": "boolean",
"description": "True when the result exceeded the inline preview budget, so the preview holds only the first rows and table_name holds them all."
},
"total": {
"type": "number",
"description": "Total matching variants, including any beyond the preview."
},
"dataset": {
"type": "string",
"description": "Effective gnomAD dataset."
},
"reference_genome": {
"type": "string",
"description": "Effective reference build."
},
"notice": {
"description": "Guidance when no variants matched, when the canvas is disabled and the preview is capped, and — when a table was staged — its name with the next steps: gnomad_dataframe_describe, then gnomad_dataframe_query.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_region`: The region names a chromosome outside 1–22, X, Y, or breaks the coordinate bounds. `region_too_large`: The region spans 2,500,000 bp or more, or holds more variants (~30,000) than gnomAD lists at once. `mitochondrial_unsupported`: The gene, transcript, or region is on the mitochondrial chromosome (M or MT). `graphql_error`: gnomAD rejected the variant-list query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"invalid_target",
"incoherent_build",
"invalid_region",
"region_too_large",
"mitochondrial_unsupported",
"graphql_error",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"preview",
"canvas_id",
"table_name",
"spilled",
"total",
"dataset",
"reference_genome"
]
},
{
"required": [
"error"
]
}
]
}🟢gnomad_get_coverage(gene, transcript_id, region, coverage_source, dataset, ...)
Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold (1× through 100×), separated by exome and genome track. Use this to disambiguate a true absent variant from an uncallable position: a variant missing from a well-covered region is informative, while one missing from a poorly-covered region is not. Supply exactly one of gene, transcript_id, or region. The optional coverage_source narrows to one track; by default both available tracks are returned. Echoes the effective dataset and build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/
入力スキーマ
{
"type": "object",
"properties": {
"gene": {
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.",
"anyOf": [
{
"type": "string",
"minLength": 2,
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."
},
{
"type": "string",
"maxLength": 0,
"description": "Blank — the gene is treated as omitted."
}
]
},
"transcript_id": {
"description": "Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.",
"type": "string"
},
"region": {
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop − start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id.",
"anyOf": [
{
"type": "string",
"const": ""
},
{
"type": "string",
"pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852) on chromosome 1–22, X, or Y, optional chr prefix."
}
]
},
"coverage_source": {
"description": "Restrict to one coverage track. Omit to return every available track.",
"type": "string",
"enum": [
"exome",
"genome"
]
},
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"type": "string",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
]
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"type": "string",
"enum": [
"GRCh38",
"GRCh37"
]
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}出力スキーマ
{
"type": "object",
"properties": {
"target": {
"type": "string",
"description": "The resolved target (gene symbol/ID, transcript ID, or region) the coverage describes."
},
"target_kind": {
"type": "string",
"enum": [
"gene",
"transcript",
"region"
],
"description": "Which target type was queried."
},
"summaries": {
"type": "array",
"items": {
"type": "object",
"properties": {
"source": {
"type": "string",
"enum": [
"exome",
"genome"
],
"description": "Which gnomAD coverage track this summary covers."
},
"positions": {
"type": "number",
"description": "Number of base positions summarized across the target."
},
"mean_depth": {
"description": "Mean read depth averaged across positions; null when no data.",
"type": [
"number",
"null"
]
},
"median_depth": {
"description": "Median read depth across positions; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_1": {
"description": "Mean fraction of samples covered at ≥1×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_5": {
"description": "Mean fraction of samples covered at ≥5×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_10": {
"description": "Mean fraction of samples covered at ≥10×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_15": {
"description": "Mean fraction of samples covered at ≥15×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_20": {
"description": "Mean fraction of samples covered at ≥20×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_25": {
"description": "Mean fraction of samples covered at ≥25×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_30": {
"description": "Mean fraction of samples covered at ≥30×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_50": {
"description": "Mean fraction of samples covered at ≥50×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_100": {
"description": "Mean fraction of samples covered at ≥100×; null when no data.",
"type": [
"number",
"null"
]
}
},
"required": [
"source",
"positions",
"mean_depth",
"median_depth",
"fraction_over_1",
"fraction_over_5",
"fraction_over_10",
"fraction_over_15",
"fraction_over_20",
"fraction_over_25",
"fraction_over_30",
"fraction_over_50",
"fraction_over_100"
],
"additionalProperties": false,
"description": "Aggregate coverage for one callset track over the target."
},
"description": "Per-track coverage summaries (exome and/or genome)."
},
"dataset": {
"type": "string",
"description": "Effective gnomAD dataset."
},
"reference_genome": {
"type": "string",
"description": "Effective reference build."
},
"notice": {
"description": "Guidance when no coverage data is available for the target.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_region`: The region names a chromosome outside 1–22, X, Y, or breaks the coordinate bounds. `region_too_large`: The region spans 2,500,000 bp or more, beyond what gnomAD summarizes at once. `mitochondrial_unsupported`: The gene, transcript, or region is on the mitochondrial chromosome (M or MT). `graphql_error`: gnomAD rejected the coverage query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"invalid_target",
"incoherent_build",
"invalid_region",
"region_too_large",
"mitochondrial_unsupported",
"graphql_error",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"target",
"target_kind",
"summaries",
"dataset",
"reference_genome"
]
},
{
"required": [
"error"
]
}
]
}🟢gnomad_search_clinvar(gene, clinical_significance, min_review_stars, offset, limit, ...)
Search ClinVar (NCBI E-utilities) for a gene and return its classified variants — clinical significance, review status with a 0–4 star rating, associated conditions, molecular consequences, submission counts, and gnomAD-compatible identifiers (canonical SPDI, rsIDs, GRCh38 variant ID for gnomad_get_variant) — turning the variant-level significance gnomAD joins into a gene-panel curation view. Optionally filter by clinical_significance (e.g. pathogenic) and a minimum star rating. Each call returns one window of up to 500 ClinVar records: total_found is the ClinVar candidate count for the search terms, taken before the significance and star filters narrow each window, and next_offset continues through the rest via offset. A window too large to inline is staged on a DataCanvas table named clinvar_variants, returned as canvas_id and table_name beside an inline preview — call gnomad_dataframe_describe for its columns, then gnomad_dataframe_query to rank or count across the window. A window that fits inline stages no table unless canvas_id is supplied. Keyless, but honors NCBI_API_KEY for a higher rate limit. When the canvas is disabled the tool returns a capped inline preview. Credit: ClinVar, NCBI.
入力スキーマ
{
"type": "object",
"properties": {
"gene": {
"type": "string",
"minLength": 2,
"description": "Gene HGNC symbol (e.g. PCSK9). ClinVar indexes HGNC symbols only — Ensembl gene IDs (ENSG…) are not resolved here, unlike the other gnomAD tools; resolve one to its symbol via ensembl_lookup_gene."
},
"clinical_significance": {
"description": "Filter by ClinVar clinical significance term (e.g. pathogenic, likely_pathogenic, uncertain significance), matched as whole words; underscores read as spaces. Blank means no filter.",
"type": "string"
},
"min_review_stars": {
"description": "Keep only variants with at least this gold-star review rating (0–4).",
"type": "integer",
"minimum": 0,
"maximum": 4
},
"offset": {
"default": 0,
"description": "Zero-based position of the first ClinVar record in this window. Pass next_offset from the previous call to continue.",
"type": "integer",
"minimum": 0,
"maximum": 2147483647
},
"limit": {
"default": 500,
"description": "ClinVar records to fetch in this window (1–500). Counted before the clinical_significance and min_review_stars filters, so a window can return fewer rows.",
"type": "integer",
"minimum": 1,
"maximum": 500
},
"canvas_id": {
"description": "Optional canvas ID from a prior call, to reuse the same canvas. When supplied, each search writes its window to the clinvar_variants table on that canvas, replacing (not appending to) the previous one — even when the window fits inline; a window with no rows removes the table. An Ensembl gene ID searches nothing and leaves the canvas as it was. Omit to stage on a fresh canvas only when the window is too large to inline.",
"type": "string",
"pattern": "^[A-Za-z0-9_-]{10}$"
}
},
"required": [
"gene"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}出力スキーマ
{
"type": "object",
"properties": {
"preview": {
"type": "array",
"items": {
"type": "object",
"properties": {
"clinvar_variation_id": {
"type": "string",
"description": "ClinVar VariationID (uid)."
},
"accession": {
"type": "string",
"description": "ClinVar accession (e.g. VCV004855003)."
},
"title": {
"type": "string",
"description": "Variant title (HGVS expression)."
},
"obj_type": {
"type": "string",
"description": "Variant object type (e.g. single nucleotide variant)."
},
"clinical_significance": {
"description": "Germline classification (e.g. Pathogenic); null when none.",
"type": [
"string",
"null"
]
},
"review_status": {
"description": "ClinVar review-status text; null when none.",
"type": [
"string",
"null"
]
},
"gold_stars": {
"type": "number",
"description": "0–4 star review rating derived from review status."
},
"last_evaluated": {
"description": "Date the classification was last evaluated; null when unknown.",
"type": [
"string",
"null"
]
},
"molecular_consequences": {
"type": "string",
"description": "Molecular consequences, semicolon-joined."
},
"protein_change": {
"type": "string",
"description": "Protein change(s), comma-joined as ClinVar reports them."
},
"conditions": {
"type": "string",
"description": "Associated conditions/traits, semicolon-joined."
},
"submission_count": {
"type": "number",
"description": "Number of submitted (SCV) records."
},
"canonical_spdi": {
"description": "Canonical SPDI of the variant (GRCh38, e.g. NC_000001.11:55039973:G:T); null for multi-allele records, CNVs, and records without one.",
"type": [
"string",
"null"
]
},
"rsids": {
"type": "string",
"description": "dbSNP rsIDs (e.g. rs11591147), semicolon-joined; empty when none. One rsID can match several gnomAD variants, so prefer grch38_variant_id for gnomad_get_variant."
},
"grch38_variant_id": {
"description": "gnomAD variant ID (chrom-pos-ref-alt, GRCh38) for gnomad_get_variant with the GRCh38 datasets (gnomad_r4, gnomad_r3). Set for SNVs, MNVs, and delins; null for deletions, insertions, duplications, mitochondrial variants, and multi-allele records.",
"type": [
"string",
"null"
]
}
},
"required": [
"clinvar_variation_id",
"accession",
"title",
"obj_type",
"clinical_significance",
"review_status",
"gold_stars",
"last_evaluated",
"molecular_consequences",
"protein_change",
"conditions",
"submission_count",
"canonical_spdi",
"rsids",
"grch38_variant_id"
],
"additionalProperties": false,
"description": "One ClinVar variant row — also the canvas table column set."
},
"description": "Inline preview rows — the immediate answer; the window's every row unless spilled."
},
"canvas_id": {
"type": "string",
"description": "Canvas holding table_name (or the canvas_id you supplied) — pass it to gnomad_dataframe_describe, then gnomad_dataframe_query. Empty when this call used no canvas: the window fit inline and no canvas_id was supplied, the gene was an Ensembl ID (nothing was searched), or the canvas is disabled."
},
"table_name": {
"type": "string",
"description": "Canvas table this call staged (clinvar_variants), holding this window's rows — inspect it with gnomad_dataframe_describe, then query it with gnomad_dataframe_query. Empty when this call staged no table."
},
"spilled": {
"type": "boolean",
"description": "True when this window's rows exceeded the inline preview budget, so the preview holds only the first rows and table_name holds them all."
},
"total": {
"type": "number",
"description": "Rows in this window that passed the filters, including any beyond the preview."
},
"total_found": {
"type": "number",
"description": "ClinVar records matching the gene and filter terms across every window, counted before the post-fetch significance and star filters."
},
"truncated": {
"type": "boolean",
"description": "True when ClinVar records remain past this window; continue with next_offset."
},
"next_offset": {
"description": "offset for the next window; null when this window reaches the end.",
"type": [
"number",
"null"
]
},
"unavailable_ids": {
"type": "array",
"items": {
"type": "string"
},
"description": "VariationIDs in this window that ClinVar returned no summary for, so they have no row; empty when none."
},
"notice": {
"description": "Guidance on completeness (the offset that continues the list, or an offset past the end), no-match results, a capped preview when the canvas is disabled, the staged table with its next steps (gnomad_dataframe_describe, then gnomad_dataframe_query), and which identifier to pass to gnomad_get_variant.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `upstream_unavailable`: NCBI E-utilities is unreachable, failing, or rate-limiting after retries. `upstream_timeout`: Every attempt to reach NCBI E-utilities timed out. `upstream_access`: NCBI E-utilities refused the request (access denied). `invalid_upstream_response`: NCBI E-utilities kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"preview",
"canvas_id",
"table_name",
"spilled",
"total",
"total_found",
"truncated",
"next_offset",
"unavailable_ids"
]
},
{
"required": [
"error"
]
}
]
}🟢gnomad_dataframe_query(canvas_id, sql, offset, limit)
Run a read-only SQL SELECT against a canvas table staged by gnomad_list_gene_variants (table gene_variants) or gnomad_search_clinvar (table clinvar_variants) and return one page of the result. Use the canvas_id and table_name those tools returned to rank by allele frequency, group by consequence class, count loss-of-function variants, or filter the full set the inline preview only sampled. A page holds up to limit rows (default 100, max 500) and ends early once its rows reach 10,000 characters of JSON; continue from next_offset until it is null. Each page re-runs the SQL, so stable paging needs an ORDER BY over a unique key (such as variant_id) and an unchanged table. Paging reaches the server row cap: above it total is null and later rows are reachable only by filtering or aggregating in SQL. SELECT statements only — writes, DDL, and file/HTTP table functions are rejected by the canvas gate. Call gnomad_dataframe_describe first to discover staged table and column names.
入力スキーマ
{
"type": "object",
"properties": {
"canvas_id": {
"type": "string",
"pattern": "^[A-Za-z0-9_-]{10}$",
"description": "Canvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar."
},
"sql": {
"type": "string",
"minLength": 1,
"description": "Read-only SQL SELECT. Reference tables by the names the staging tool returned (e.g. gene_variants). Add an ORDER BY over a unique key when paging."
},
"offset": {
"default": 0,
"description": "Row offset of the page to return. Start at 0, then pass next_offset from the previous page.",
"type": "integer",
"minimum": 0,
"maximum": 9007199254740991
},
"limit": {
"default": 100,
"description": "Maximum rows on the page (1–500). A page also ends before its rows pass 10,000 characters of JSON.",
"type": "integer",
"minimum": 1,
"maximum": 500
}
},
"required": [
"canvas_id",
"sql"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}出力スキーマ
{
"type": "object",
"properties": {
"rows": {
"type": "array",
"items": {
"type": "object",
"properties": {},
"additionalProperties": {},
"description": "One result row — dynamic columns per the SQL projection."
},
"description": "This page of result rows, in result order."
},
"columns": {
"type": "array",
"items": {
"type": "string"
},
"description": "Column names in the result, in order."
},
"offset": {
"type": "number",
"description": "Row offset this page starts at."
},
"returned": {
"type": "number",
"description": "Rows on this page — fewer than limit when the 10,000-character row budget or the end of the result ends it early."
},
"total": {
"description": "Rows the SQL produced; null when the result exceeds the server row cap, whose later rows paging cannot reach.",
"type": [
"number",
"null"
]
},
"truncated": {
"type": "boolean",
"description": "True when result rows exist after this page, including rows past the row cap that next_offset cannot reach."
},
"next_offset": {
"description": "offset for the next page; null when no page follows (end of the result, or the row cap reached).",
"type": [
"number",
"null"
]
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: DataCanvas is not enabled on this server instance. `row_too_large`: The first row of the requested page serializes to more than 10,000 characters of JSON, so no page can hold it. Other values are possible when a failure originates below the handler.",
"examples": [
"canvas_disabled",
"row_too_large"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"rows",
"columns",
"offset",
"returned",
"total",
"truncated",
"next_offset"
]
},
{
"required": [
"error"
]
}
]
}🟢gnomad_dataframe_describe(canvas_id)
List the tables staged on a canvas and their columns (name and type) so you can write correct SQL for gnomad_dataframe_query. Use the canvas_id returned by gnomad_list_gene_variants or gnomad_search_clinvar. Returns one entry per table with its row count and column schema.
入力スキーマ
{
"type": "object",
"properties": {
"canvas_id": {
"type": "string",
"pattern": "^[A-Za-z0-9_-]{10}$",
"description": "Canvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar)."
}
},
"required": [
"canvas_id"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}出力スキーマ
{
"type": "object",
"properties": {
"tables": {
"type": "array",
"items": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Table name to reference in SQL."
},
"row_count": {
"type": "number",
"description": "Number of rows in the table."
},
"columns": {
"type": "array",
"items": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Column name."
},
"type": {
"type": "string",
"description": "Column SQL type (DuckDB type)."
}
},
"required": [
"name",
"type"
],
"additionalProperties": false,
"description": "One column: name and SQL type."
},
"description": "Column schema, in order."
}
},
"required": [
"name",
"row_count",
"columns"
],
"additionalProperties": false,
"description": "One staged table: name, row count, and column schema."
},
"description": "Tables staged on the canvas."
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: DataCanvas is not enabled on this server instance. Other values are possible when a failure originates below the handler.",
"examples": [
"canvas_disabled"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"tables"
]
},
{
"required": [
"error"
]
}
]
}コミュニティ
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