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plant-genomics-mcp

by musharna
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Python
Remote

Batch: STRING Interactions

batch_string_interactions
Read-onlyIdempotent

Fetch protein-protein interactions for up to 50 plant loci in one request. Use batch queries to obtain STRING-DB interaction networks for multiple genes simultaneously.

Instructions

Batch version of string_interactions. Up to 50 inputs per call. The argument was called loci_or_accessions before #129; that name is still accepted, deprecated.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYes
limitNo
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
toolYesThe batch tool name, e.g. batch_resolve_locus_to_uniprot
countYesNumber of distinct loci queried, returned (== len(results) + len(errors)). The input list is de-duplicated first, so this is LOWER than the number of loci you sent if you sent a duplicate — that is de-duplication, not a dropped locus.
errorsYeslocus → '[ClassName] message' for PlantGenomicsError failures
resultsYeslocus → per-locus result dict (same shape as the single-locus tool)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changedv1.22.0
    • addedInput schema / properties / loci
      Added value: +{
+  "items": {
+    "type": "string"
+  },
+  "maxItems": 50,
+  "minItems": 1,
+  "type": "array"
+}
    • removedInput schema / properties / loci_or_accessions
      Removed value: -{
-  "items": {
-    "type": "string"
-  },
-  "maxItems": 50,
-  "type": "array"
-}
    • changedInput schema / required
      Previous value: -[
-  "loci_or_accessions"
-]New value: +[
+  "loci"
+]
  2. Changed1 schema field changedv1.19.4
    • changedOutput schema / properties / count / description
      Previous value: -"Number of loci in the input list"New value: +"Number of distinct loci queried, returned (== len(results) + len(errors)). The input list is de-duplicated first, so this is LOWER than the number of loci you sent if you sent a duplicate — that is de-duplication, not a dropped locus."
  3. First observedv1.8.0

TDQS

B3.1/5.0
Behavior3/5

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

Annotations already cover read-only, idempotent, and non-destructive behavior. The description adds the batch limit and a deprecation note about the parameter name change, which are useful. However, it does not disclose how partial failures are handled, rate limits, or other batch-specific behaviors, leaving some gaps beyond the annotations.

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 two sentences with no wasted words. It front-loads the key batch limit and then adds the deprecation note. It is efficient and easy to parse, though it could have included a bit more context without becoming verbose.

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?

For a batch tool with three parameters and an output schema present, the description is minimal. It doesn't explain batch semantics (e.g., whether a single failed locus invalidates the whole call), pagination, or how the limit interacts with the batch. The deprecation note is helpful but not sufficient for a tool that likely has complex edge cases. The output schema mitigates some return-format ambiguity, but operational details are missing.

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

Parameters2/5

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

Schema coverage is only 33% (only organism has a description). The description adds semantic info for the loci parameter by noting its deprecated name (loci_or_accessions), which helps. But it provides no explanation for the limit parameter or how batching interacts with it, and the organism parameter's flexible types are not elaborated. Given the low schema coverage, more parameter guidance is needed.

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 this is the batch version of string_interactions, which distinguishes it from the single-input sibling. It also specifies the batch limit (up to 50 inputs), making the tool's scope explicit. However, it doesn't restate what string_interactions does, relying on the sibling name for context.

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 usage for multiple loci ('up to 50 inputs') but does not explicitly state when to choose this over the single version or how to decide between other batch tools. The deprecation note provides some usage guidance about accepted parameter names, but no exclusions or alternatives are mentioned.

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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