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get_text_mined_terms

Extract text-mined entities from PubMed articles via Europe PMC. Identify genes, diseases, chemicals, and other key concepts with counts and sections.

Instructions

Get text-mined annotations from Europe PMC.

Returns entities extracted from the article text including genes, diseases, chemicals, organisms, and more. Useful for identifying key concepts.

Args: pmid: PubMed ID of the article (accepts: "12345678", 12345678). pmcid: PMC ID (alternative to PMID, accepts: "PMC7096777", "7096777"). semantic_type: Filter by entity type. Options: - "GENE_PROTEIN": Genes and proteins - "DISEASE": Diseases and conditions - "CHEMICAL": Drugs and chemicals - "ORGANISM": Species and organisms - "GO_TERM": Gene Ontology terms - None: Return all types (default)

Returns: List of text-mined entities with counts and sections.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidNo
pmcidNo
semantic_typeNo
output_formatNomarkdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

With no annotations, the description carries the full burden. It discloses that the tool returns a list of entities with counts and sections, and explains parameter behaviors (e.g., accepted formats for IDs). However, it does not mention potential limitations (e.g., article accessibility, rate limits) or side effects.

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 well-structured with a summary line, an Args section, and Returns. It is clear and informative, though slightly long. Every sentence serves a purpose, and the formatting aids readability.

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

Completeness3/5

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

Given no annotation coverage, the description covers the tool's purpose, main parameters, and return type. However, it omits the output_format parameter and does not mention pagination or data volume. The presence of an output schema partially mitigates the need for return format details, but the missing parameter is a gap.

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

Parameters3/5

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

Schema coverage is 0%, so the description must compensate. It adds detailed semantics for pmid, pmcid, and semantic_type, including accepted formats and options. However, it fails to document the output_format parameter, which has an enum (markdown, json, toon) in the schema but is completely omitted from the description.

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 states the tool 'gets text-mined annotations from Europe PMC' and lists specific entity types (genes, diseases, chemicals, organisms), clearly distinguishing it from sibling tools that fetch article details or gene-specific data.

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 mentions it is 'useful for identifying key concepts', implying a usage context, but does not provide explicit guidance on when to use this tool versus alternatives like get_gene_details or fetch_article_details. No exclusions or alternatives are named.

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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