plant-genomics-mcp

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STRING: Interaction Network

string_interactions

Read-onlyIdempotent

Get first-neighbor interaction partners from STRING-DB for plant loci or UniProt accessions, with confidence and evidence sub-scores.

Instructions

Fetch protein-protein interaction partners from STRING-DB (string-db.org). Accepts either a UniProt accession or a locus identifier. A locus goes to STRING's own resolver, except for wheat, whose STRING proteins carry no locus alias: a wheat locus is resolved via UniProt first. Defaults to arabidopsis_thaliana; pass organism= for other plant species (slug, scientific/common name, or NCBI taxid). Returns first-neighbor partners with the combined STRING score plus per-channel sub-scores (experimental, database, textmining, predicted). The argument was called locus_or_accession before #129; that name is still accepted, deprecated.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`limit`	No	Number of partners to return
`locus`	Yes	Locus (AT1G01010) or UniProt accession (Q0WV96)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`query`	Yes	The locus or accession the user passed
`total`	No	Always null: the upstream returns the top partners asked for and states no total; null means unknown, never zero (#123)
`organism`	Yes	Plant organism canonical slug, e.g. arabidopsis_thaliana
`partners`	Yes
`returned`	Yes	Rows in this payload (#123)
`accession`	Yes	UniProt accession actually queried at STRING
`truncated`	No	Always null: without a stated total, truncation is unknown (#123)
`upstream_version`	No	STRING release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='string') reports the release its own endpoint calls current at query time, or why there is none. null means STRING 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.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.27.0Sep 27, 2026

changedOutput schema / properties / upstream_version / description

Previous value: -"STRING release that produced THIS response, — always null today: this backend states no release on its responses. null means STRING 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: +"STRING release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='string') reports the release its own endpoint calls current at query time, or why there is none. null means STRING 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."

Changed1 schema field changedv1.24.0Sep 26, 2026

removedOutput schema / $defs / StringPartner / properties / accession

Removed value: -{
-  "anyOf": [
-    {
-      "type": "string"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "description": "Deprecated (#133): always equal to string_id, a STRING id — NOT the UniProt accession other tools mean by 'accession'. Read string_id.",
-  "title": "Accession"
-}

Changed9 schema fields changedv1.22.0Sep 24, 2026

addedInput schema / properties / locus

Added value: +{
+  "description": "Locus (AT1G01010) or UniProt accession (Q0WV96)",
+  "type": "string"
+}

removedInput schema / properties / locus_or_accession

Removed value: -{
-  "description": "UniProt accession (Q0WV96) or locus (AT1G01010)",
-  "type": "string"
-}

changedInput schema / required

Previous value: -[
-  "locus_or_accession"
-]New value: +[
+  "locus"
+]

changedOutput schema / $defs / StringPartner / properties / accession / description

Previous value: -"Partner's stringId; UniProt resolution is the caller's job"New value: +"Deprecated (#133): always equal to string_id, a STRING id — NOT the UniProt accession other tools mean by 'accession'. Read string_id."

addedOutput schema / properties / returned

Added value: +{
+  "description": "Rows in this payload (#123)",
+  "title": "Returned",
+  "type": "integer"
+}

addedOutput schema / properties / total

Added value: +{
+  "anyOf": [
+    {
+      "type": "integer"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Always null: the upstream returns the top partners asked for and states no total; null means unknown, never zero (#123)",
+  "title": "Total"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "anyOf": [
+    {
+      "type": "boolean"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Always null: without a stated total, truncation is unknown (#123)",
+  "title": "Truncated"
+}

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "STRING release that produced THIS response, — always null today: this backend states no release on its responses. null means STRING 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: -[
-  "query",
-  "accession",
-  "organism",
-  "partners"
-]New value: +[
+  "returned",
+  "query",
+  "accession",
+  "organism",
+  "partners"
+]

First observedv1.8.0May 30, 2026

TDQS

A4.7/5.0

Behavior5/5

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

Annotations already declare read-only, open-world, idempotent, and non-destructive behavior. The description adds substantial behavioral detail beyond that: resolution quirks for wheat, accepted organism name forms, the returned first-neighbor scores, and the deprecated argument name that remains accepted. This gives an agent a clear mental model of observable behavior.

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 slightly long at six sentences, but every sentence adds useful information. The most important action and output are front-loaded, and the deprecated alias note is the only mildly tangential detail, though still valuable.

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?

With a rich output schema, clear annotations, and only three parameters, the description covers all necessary invocation knowledge: accepted inputs, resolver behavior, defaults, organism selection, and return fields. Nothing essential for correct use is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Even though schema description coverage is 100%, the description enriches parameter meaning: it explains that locus may be a UniProt accession or a locus, that wheat loci are resolved via UniProt first, that organism accepts slug/scientific/common name/taxid, and that the prior argument name locus_or_accession is deprecated. This goes well beyond what the schema alone states.

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?

The description opens with a specific verb and resource: 'Fetch protein-protein interaction partners from STRING-DB.' It further specifies accepted identifiers, default organism, and returned fields, making it easy to distinguish from sibling interaction tools such as experimental_interactions or bar_aiv_interactions.

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: bases of resolution (STRING resolver vs UniProt for wheat), the default organism, and how to pass other organisms. It does not explicitly name alternative tools or state when not to use this tool, so it stops short of a 5.

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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