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save_literature_notes

Save PubMed search results as structured local wiki or Markdown notes with wikilinks and frontmatter for knowledge management.

Instructions

Save searched articles as guided local wiki/Foam/Markdown notes.

When to Use

  • After unified_search, persist the selected literature into a local note library.

  • Give agents a structured alternative to generic write_file calls.

  • Create wiki notes with Foam-compatible wikilinks, MedPaper-like reference notes, and frontmatter.

  • Use stable wiki/Foam link targets and return wiki_validation for unresolved-link checks.

Local Directory Resolution

  1. output_dir argument, if provided

  2. PUBMED_NOTES_DIR environment variable

  3. PUBMED_WORKSPACE_DIR/references

  4. PUBMED_DATA_DIR/references

Args: pmids: Articles to save. Accepts "last", comma-separated PMIDs, list, or int. output_dir: Optional target folder for notes. note_format: "wiki" (default, Foam-compatible), "foam", "markdown", or "medpaper". include_abstract: Include abstracts in article notes. overwrite: Overwrite existing per-article notes when filenames collide. create_index: Create a collection index note linking saved articles. collection_name: Optional title/file stem for the index note. template_file: Optional Markdown template with placeholders like {title}, {pmid}, {citation_key}. include_csl_json: Write references.csl.json beside notes for citation-manager handoff.

Returns: JSON with output_dir, written files, skipped files, index path, and wiki_validation.

Examples: save_literature_notes(pmids="last") save_literature_notes(pmids="last", note_format="medpaper", output_dir="./references") save_literature_notes(pmids="12345678,87654321", template_file="./ref-template.md")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidsNolast
output_dirNo
note_formatNowiki
include_abstractNo
overwriteNo
create_indexNo
collection_nameNo
template_fileNo
include_csl_jsonNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior5/5

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

With no annotations, the description fully discloses behavior: directory resolution priority, overwrite control, index creation, and return value including written and skipped files. It also mentions wiki_validation for unresolved-link checks, covering important behavioral details.

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 well-structured with sections (When to Use, Directory Resolution, Args, Returns, Examples). It is efficient, front-loaded with purpose, and every sentence provides value without redundancy.

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?

The description covers purpose, usage, parameters, return values, and examples. It is comprehensive given the complexity and lack of annotations. Minor gaps like error handling or edge cases are not covered, but overall it is very complete.

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?

Schema coverage is 0%, so the description must explain parameters. It does so comprehensively: pmids (accepts 'last', list, etc.), output_dir (optional), note_format (defaults to wiki, lists options), and template_file (placeholders). This adds significant meaning beyond the schema.

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 it saves searched articles as guided local wiki/Foam/Markdown notes, specifying the resource (articles) and verb (save). It distinguishes from siblings by mentioning 'structured alternative to generic write_file calls' and focuses on Foam-compatible wikilinks and MedPaper-like reference notes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The 'When to Use' section explicitly states to use after unified_search, provides a structured alternative to write_file, and describes the purpose of creating wiki notes. It also indicates when to use (after search) and provides context for 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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