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plant-genomics-mcp

by musharna
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Python
Remote

Batch: Any Locus Tool

batch_locus_call
Read-onlyIdempotent

Apply one locus-keyed plant-genomics tool to up to 50 loci in a single call; shared arguments are validated once and results are returned per locus with individual errors.

Instructions

Run one locus-keyed tool over up to 50 loci in one call (#131). 'tool' names any tool whose only required argument is 'locus' (interpro_domains, alphafold_structure, panther_family, orthodb_orthologs, gene_report, ...); 'args' holds that tool's other arguments, shared by every locus and checked against its schema once before any call. Returns the standard batch envelope: results keyed by locus, each exactly what the single tool returns, and per-locus errors. The dedicated batch_* tools remain.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
argsNoThe tool's arguments other than 'locus' (and not 'cursor'), e.g. {"organism": "oryza_sativa"}
lociYesLocus identifiers (max 50)
toolYes

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. Changed1 schema field changedv1.26.0
    • changedInput schema / properties / tool / enum
      Previous value: -[
-  "alphafold_structure",
-  "analyze_locus_synth",
-  "arabidopsis_natural_variation",
-  "aragwas_associations",
-  "atted_coexpression",
-  "bar_aiv_interactions",
-  "bar_efp_expression",
-  "bar_gene_summary",
-  "biological_context_synth",
-  "consensus_homologs",
-  "ensembl_plants_lookup_locus",
-  "experimental_interactions",
-  "experimental_structures",
-  "gene_report",
-  "get_gene_xrefs",
-  "get_sequence",
-  "gramene_homologs",
-  "interpro_domains",
-  "kegg_pathways",
-  "locus_gene_rifs",
-  "locus_go_annotations",
-  "locus_literature",
-  "locus_plant_ontology",
-  "locus_variants",
-  "orthodb_orthologs",
-  "panther_family",
-  "phytozome_lookup_locus",
-  "plantcyc_locus_info",
-  "resolve_locus_to_uniprot",
-  "string_interactions",
-  "tair_locus_info",
-  "tf_binding_motifs"
-]New value: +[
+  "alphafold_structure",
+  "analyze_locus_synth",
+  "arabidopsis_natural_variation",
+  "aragwas_associations",
+  "atted_coexpression",
+  "bar_aiv_interactions",
+  "bar_efp_expression",
+  "bar_gene_summary",
+  "biological_context_synth",
+  "consensus_homologs",
+  "ensembl_plants_lookup_locus",
+  "ensembl_plants_paralogs",
+  "experimental_interactions",
+  "experimental_structures",
+  "gene_report",
+  "get_gene_xrefs",
+  "get_sequence",
+  "gramene_homologs",
+  "interpro_domains",
+  "kegg_pathways",
+  "locus_gene_rifs",
+  "locus_go_annotations",
+  "locus_literature",
+  "locus_plant_ontology",
+  "locus_variants",
+  "orthodb_orthologs",
+  "panther_family",
+  "phytozome_lookup_locus",
+  "plantcyc_locus_info",
+  "resolve_locus_to_uniprot",
+  "string_interactions",
+  "tair_locus_info",
+  "tf_binding_motifs"
+]
  2. Addedv1.22.0

TDQS

A4.3/5.0
Behavior5/5

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

The description substantially enriches the annotations by disclosing that args are shared across loci and validated once against the target tool's schema, that the response is a standard batch envelope keyed by locus, that each result matches the single-tool output, and that per-locus errors are included. This is exactly the behavioral nuance an agent needs beyond readOnly/idempotent hints.

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 compact and front-loaded, with the core action, limit, examples, behavior, and relationship to dedicated batch tools all conveyed in three sentences. The only minor drag is the issue-number reference (#131), which is noise for an agent selecting the tool.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the output schema exists and the annotations already carry the safety profile, the description covers what an agent needs: eligibility, argument handling, limits, and the response envelope. It could be slightly more explicit about when the generic batch path should be chosen over dedicated batch tools, but nothing required for a correct call 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 description coverage is 67%, so the description must compensate, and it does. It explains the meaning of 'tool' beyond the enum, defines 'args' as the target tool's non-locus arguments, and states that args are shared and schema-checked. It adds real semantic value over the bare schema, though the schema already covers the 'loci' array limit and basic args shape.

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: 'Run one locus-keyed tool over up to 50 loci in one call'. It further clarifies the exact class of tools eligible ('any tool whose only required argument is "locus"') with concrete examples, making it easy to distinguish from the single-locus tools and the dedicated batch_* siblings.

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 states the eligibility condition for the 'tool' argument and notes that 'dedicated batch_* tools remain', but it does not explicitly say when to prefer this generic batch tool over a dedicated batch_* sibling. The use case is implied (batch many loci through one locus-keyed tool) rather than directly contrasted with alternatives.

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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