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AraGWAS: GWAS Associations

aragwas_associations

Read-onlyIdempotent

Fetch Arabidopsis GWAS hits for a locus, returning significant SNPs with scores, minor-allele frequency, predicted molecular effects, phenotypes, and study thresholds.

Instructions

Fetch AraGWAS genome-wide association study hits for an Arabidopsis locus (aragwas.1001genomes.org; free, no key). Returns each significant SNP association overlapping the gene with its score (-log10 p), minor-allele frequency, the SNP's predicted molecular effect (impact, amino-acid change), and the phenotype/study it came from, including the study's own significance thresholds on the score's scale (study.thresholds), which the over_bonferroni / over_fdr / over_permutation flags are taken against. Rows come strongest first, 25 per answer by default (limit, up to 100); next_cursor resumes at the first row not returned. association_count is the true total even when page-capped. ARABIDOPSIS-ONLY — any other organism raises OrganismNotSupported. Defaults to arabidopsis_thaliana.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`limit`	No	Max associations, strongest first (1–100, default 25)
`locus`	Yes	Arabidopsis AGI locus, e.g. AT1G01060
`cursor`	No	next_cursor from the previous page; omit for the first (#123)
`organism`	No	Arabidopsis only (the 1001 Genomes panel is A. thaliana)	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`found`	Yes	True once the associations endpoint returned 200
`locus`	Yes
`total`	Yes	How many associations exist upstream for this query, all pages (pre-cap) (#123)
`organism`	Yes	Always arabidopsis_thaliana
`returned`	Yes	Associations returned (post page-cap)
`truncated`	Yes	True if pagination was capped
`next_cursor`	No	Pass back as cursor= to get the rows after this page; null on the last page. Opaque, and bound to this tool and query (#123)
`associations`	No	Per-hit {score, maf, mac, over_bonferroni, over_fdr, over_permutation, snp{…}, study{…, thresholds}}. score is -log10(p); study.thresholds holds that study's bonferroni_threshold05/01, bh_threshold and permutation_threshold on the same scale, which over_bonferroni / over_fdr / over_permutation compare score against
`upstream_version`	No	AraGWAS release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='aragwas') reports the release its own endpoint calls current at query time, or why there is none. null means AraGWAS did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.
`association_count`	Yes	Total associations (pre-cap)

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.28.0Sep 30, 2026

addedInput schema / properties / limit

Added value: +{
+  "default": 25,
+  "description": "Max associations, strongest first (1–100, default 25)",
+  "maximum": 100,
+  "minimum": 1,
+  "type": "integer"
+}

Changed1 schema field changedv1.27.0Sep 27, 2026

changedOutput schema / properties / upstream_version / description

Previous value: -"AraGWAS release that produced THIS response, — always null today: this backend states no release on its responses. null means AraGWAS did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."New value: +"AraGWAS release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='aragwas') reports the release its own endpoint calls current at query time, or why there is none. null means AraGWAS did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."

Changed6 schema fields changedv1.22.0Sep 24, 2026

addedInput schema / properties / cursor

Added value: +{
+  "description": "next_cursor from the previous page; omit for the first (#123)",
+  "type": "string"
+}

changedOutput schema / properties / associations / description

Previous value: -"Per-hit {score, maf, mac, snp{…}, study{…}}"New value: +"Per-hit {score, maf, mac, over_bonferroni, over_fdr, over_permutation, snp{…}, study{…, thresholds}}. score is -log10(p); study.thresholds holds that study's bonferroni_threshold05/01, bh_threshold and permutation_threshold on the same scale, which over_bonferroni / over_fdr / over_permutation compare score against"

addedOutput schema / properties / next_cursor

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Pass back as cursor= to get the rows after this page; null on the last page. Opaque, and bound to this tool and query (#123)",
+  "title": "Next Cursor"
+}

addedOutput schema / properties / total

Added value: +{
+  "description": "How many associations exist upstream for this query, all pages (pre-cap) (#123)",
+  "title": "Total",
+  "type": "integer"
+}

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "AraGWAS release that produced THIS response, — always null today: this backend states no release on its responses. null means AraGWAS did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.",
+  "title": "Upstream Version"
+}

changedOutput schema / required

Previous value: -[
-  "locus",
-  "organism",
-  "found",
-  "association_count",
-  "returned",
-  "truncated"
-]New value: +[
+  "total",
+  "locus",
+  "organism",
+  "found",
+  "association_count",
+  "returned",
+  "truncated"
+]

Addedv1.19.4Jul 28, 2026

TDQS

A4.4/5.0

Behavior5/5

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

Annotations already cover the safety profile (readOnly/idempotent/destructive=false), and the description goes well beyond them: it discloses no-auth access, deterministic ordering (strongest first), page size and cap, cursor semantics, the guarantee that association_count is the true total even when page-capped, and the OrganismNotSupported failure mode. That is substantial operational context.

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?

A single dense paragraph with the core action front-loaded and pagination/organism constraints at the end. Nearly every clause carries unique information, though it is long enough that mild trimming would improve scannability.

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?

For a read-only, output-schema-backed tool, the description covers everything an agent needs: what is returned, ordering, pagination, the true-total caveat, authentication needs, and the error condition. Nothing essential is missing.

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 baseline is 3, but the description adds meaning the schema lacks: the ordering guarantee behind limit (strongest first), the resume semantics of next_cursor (first row not returned), and the organism constraint ('Arabidopsis only'). This raises it above baseline.

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?

States a specific verb (fetch) and resource (AraGWAS GWAS association hits) scoped to an Arabidopsis locus, and enumerates the returned fields (score, MAF, predicted effect, phenotype/study, thresholds). This clearly distinguishes it from neighbors like arabidopsis_natural_variation and locus_variants without opening any schema.

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 its use case (pull GWAS hits for a locus) and notes it is free/no key, plus a hard constraint that non-Arabidopsis input raises OrganismNotSupported. However it never routes the agent among the many sibling locus tools (e.g., arabidopsis_natural_variation, locus_variants) or states when this source is preferable, leaving usage to inference.

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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