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musharna

plant-genomics-mcp

locus_literature

Search Europe PMC for literature mentioning a plant locus. Returns title, authors, journal, year, DOI, PMID, open-access status, citation count, and abstract. For non-Arabidopsis species, appends common name to disambiguate locus IDs.

Instructions

Search Europe PMC for literature mentioning a plant locus. Free, no API key. Returns up to size results (default 10, capped at 25) with title, authors, journal, year, DOI, PMID, open-access status, citation count, and abstract. For non-Arabidopsis species the species common name is appended to the query to disambiguate locus IDs (rice, maize, ...). Pair with resolve_locus_to_uniprot or ensembl_plants_lookup_locus to ground the locus before fanning out to the literature.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYese.g. AT1G01010 (Arabidopsis), Os01g0100100 (rice)
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana
sizeNoMax results (1–25, default 10)

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYes
organismYes
queryYesFinal query string sent to Europe PMC
hitCountYesTotal hits available upstream (may exceed returned)
returnedYesNumber of hits actually in hits[]
hitsYes
Behavior5/5

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

No annotations are provided, so the description fully bears the burden. It discloses the free usage, result limits (default 10, capped 25), returned fields (title, authors, journal, year, DOI, PMID, open-access, citation count, abstract), and the automatic disambiguation for non-Arabidopsis species. No contradictions.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single dense paragraph with no fluff. Every sentence adds value: purpose, free usage, result limits, returned fields, disambiguation, and pairing suggestions. It is front-loaded with the main action.

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?

Given an output schema exists (not shown but flagged), the description need not detail return values. It already lists key fields, explains result limits, disambiguation, and suggests complementary tools. For a literature search tool with these parameters, it covers all essential context.

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% (baseline 3). The description adds significant value by explaining that 'locus' expects IDs like AT1G01010, 'organism' accepts various formats, 'size' has a default and cap. It also clarifies the disambiguation behavior, which is not evident from the schema alone.

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 clearly states 'Search Europe PMC for literature mentioning a plant locus.' It identifies the resource, verb, and specific entity. It distinguishes from siblings by suggesting pairing with resolve_locus_to_uniprot or ensembl_plants_lookup_locus.

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 mentions it is free and requires no API key, and explains disambiguation behavior for non-Arabidopsis species. It implicitly suggests when to use (for literature search) and even recommends complementary tools. However, it does not explicitly state when not to use this tool.

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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