PubMed Search

Get detailed information about a compound by PubChem CID. Args: cid: PubChem Compound ID Returns: JSON with compound details including formula, SMILES, properties

Get PubMed articles linked to a compound. Uses NCBI's curated compound-to-publication links. Args: cid: PubChem Compound ID limit: Maximum PubMed IDs to return (1-100) Returns: JSON with linked PubMed IDs

🔥 Enhanced multi-source fulltext retrieval. Automatically tries multiple sources to find the best fulltext: 1. Europe PMC (if PMC ID available) 2. Unpaywall (finds OA versions via DOI) 3. Institutional direct/EZproxy fetch (when DOI-backed and enabled) 4. CORE (open-access repository metadata and available text) With extended_sources=True, also searches: 5. CrossRef (publisher links) 6. DOAJ (Gold OA journals) 7. Zenodo (research repository) 8. PubMed LinkOut (external providers) 9. Semantic Scholar, OpenAlex, arXiv, bioRxiv, medRxiv ``source`` is a discriminated identifier object, so the …

Get detailed information about a gene by NCBI Gene ID. Args: gene_id: NCBI Gene ID (from search results or known) Returns: JSON with gene details including symbol, name, summary, location

Get PubMed articles linked to a gene. This uses NCBI's curated gene-to-publication links, which are more precise than keyword searches. Args: gene_id: NCBI Gene ID limit: Maximum PubMed IDs to return (1-100) Returns: JSON with linked PubMed IDs

Generate institutional access link (OpenURL) for an article. ═══════════════════════════════════════════════════════════════════════════════ 🔗 GET LIBRARY ACCESS LINK ═══════════════════════════════════════════════════════════════════════════════ Generate an OpenURL that will take you through your library's link resolver to access the full text of an article. PREREQUISITES: ───────────────── Must first call configure_institutional_access() to set up your resolver. USAGE: ───────────────── With PMID (easiest): get_institutional_link( source={"kind": "pmid", "value": "38353755"…

Get execution history for a saved pipeline. Shows past execution results with diff analysis: which articles are new compared to the previous run. Args: name: Name of the saved pipeline. limit: Maximum number of history entries to return (default: 5). Returns: Execution history with date, article count, new/removed articles, status.

Get text-mined annotations from Europe PMC. Returns entities extracted from the article text including genes, diseases, chemicals, organisms, and more. ``source`` is exactly one PMID or PMCID. Args: source: {"kind":"pmid","value":"12345678"} or {"kind":"pmcid","value":"PMC7096777"}. 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 typ…

List all saved pipeline configurations. Args: tag: Filter by tag (e.g., "sedation"). Empty = show all. scope: Filter by scope: "workspace", "global", or "" (show all). Returns: Table of saved pipelines with name, scope, description, tags.

List available institutional link resolver presets. ═══════════════════════════════════════════════════════════════════════════════ 📚 AVAILABLE RESOLVER PRESETS ═══════════════════════════════════════════════════════════════════════════════ These presets contain pre-configured URLs for common institutions. Use them with configure_institutional_access(preset="name"). Returns: List of available presets with URLs

Load a pipeline configuration for review or editing. Loads from either source: - Saved name: "weekly_remimazolam" or "saved:weekly_remimazolam" - Local-only file: "file:path/to/pipeline.yaml" (disabled for authenticated service callers) The returned YAML can be reviewed, modified, and then: - Executed directly: unified_search(pipeline="<yaml>") - Saved with changes: save_pipeline(name="...", config="<yaml>") Args: source: Pipeline source identifier (see above). Returns: Full pipeline YAML content + metadata.

Export citations to reference manager formats. ╔═══════════════════════════════════════════════════════════════════╗ ║ RECOMMENDED: Use source="official" (default) for best quality ║ ╚═══════════════════════════════════════════════════════════════════╝ ## When to Use - Exporting references to EndNote, Zotero, Mendeley - Creating BibTeX for LaTeX documents - Generating citation lists for manuscripts ## Source Options | Source | Formats | Quality | Speed | |------------|--------------------|------------|--------| | official | ris, medline, csl | ★★★★★ | Fast | |…

Analyze a scientific figure or image for literature search. ═══════════════════════════════════════════════════════════════════════ 🔬 VISION-TO-LITERATURE SEARCH (Experimental) ═══════════════════════════════════════════════════════════════════════ This tool enables searching for scientific literature based on images. WORKFLOW (the host agent performs the analysis and search): ───────────────────────────────────────────────────────── 1. Provide an image (URL or base64-encoded) 2. This tool returns the image using MCP ImageContent protocol 3. YOU (the Agent) analyze the image using your vis…

Read corpus records using numeric transport IDs returned by search.

Read stored Research Chronicles: load, list, diff, narrate, analyze, compare. This is the read facade over chronicles created by `build_research_chronicle`. Chronicles persist across sessions, so you can revisit a topic weeks later and see precisely what moved. Because the evidence is already stored, analysis and comparison are instant and do not re-run any search. Actions: - "load": read one revision (defaults to latest) in any output format - "list": list stored chronicles, most recently updated first - "diff": compare two revisions — added, not observed/removed from the later view, and …

Read session data through one schema-exact discriminated request. Actions: - pmids: return PMIDs for one recorded search - article: return one cached article payload - summary: return current session summary and optional history - list_artifacts: list persistent MCP output artifact manifests - artifact: read one persistent artifact by artifact_id or artifact_uri - search_runs: list durable unified_search run envelopes - search_run: read one run by stable run_id - replay_search: return credential-free unified_search replay arguments Each action accepts only its own fields. For remote artifact…

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 ## …

Save a pipeline configuration for later reuse. The config format is identical to unified_search's pipeline parameter (YAML or JSON). Saved pipelines can be loaded later by name: unified_search(pipeline="saved:weekly_remimazolam") Args: name: Unique identifier (alphanumeric + hyphens/underscores, max 64 chars). Overwrites if name already exists (upsert semantics). config: Pipeline YAML/JSON string. Same format as unified_search pipeline param. tags: Bounded array of canonical tags (e.g., ["anesthesia", "sedation"]). description: Human-readable description of the …

Schedule a saved pipeline for periodic execution. Args: name: Saved pipeline name. cron: Required 5-field cron expression. Example: "0 9 * * 1" (Mon 9am). diff_mode: When True, store diff-mode preference with the schedule. notify: When True, store notify preference with the schedule. Returns: Schedule confirmation or removal result.

Search title/abstract text with plain lexical terms. Supports iterative queries.

🖼️ Search biomedical images from NLM Open-i. Searches medical/scientific images from Open-i and returns image URLs with metadata (caption, article info, MeSH terms). ═══════════════════════════════════════════════════════════════ ⚠️ CRITICAL - LANGUAGE REQUIREMENT: ═══════════════════════════════════════════════════════════ Open-i ONLY supports English queries. If the user queries in non-English (Chinese, Japanese, Korean, etc.), you MUST: 1. Translate the query to English medical terminology first 2. Then call this tool with the English query Example: "喉頭水腫" → "laryngeal edema" …

Search ClinVar for clinical variants. ═══════════════════════════════════════════════════════════════ USE CASES: ═══════════════════════════════════════════════════════════════ - Look up clinical significance of genetic variants - Find variants associated with diseases - Research gene-disease associations - Get variant pathogenicity classifications Args: query: Gene name, variant, or disease condition limit: Maximum results (1-50) Returns: JSON with variant records including significance and conditions

Search PubChem for chemical compounds. ═══════════════════════════════════════════════════════════════ USE CASES: ═══════════════════════════════════════════════════════════════ - Look up drug/compound information - Find molecular formula and structure - Get compound synonyms and identifiers - Research chemical properties Args: query: Compound name or description limit: Maximum results (1-50) Returns: JSON with compound records including names, formulas, properties

Search NCBI Gene database for gene information. ═══════════════════════════════════════════════════════════════ USE CASES: ═══════════════════════════════════════════════════════════════ - Look up gene function and description - Find gene aliases and official symbols - Get chromosome location - Find genes by name or function Args: query: Gene name, symbol, or function keyword organism: Filter by organism (e.g., "human", "Homo sapiens", "mouse") limit: Maximum results (1-50) Returns: JSON with gene records including symbols, names, locations

Test your institutional link resolver configuration. ═══════════════════════════════════════════════════════════════════════════════ 🧪 TEST INSTITUTIONAL ACCESS ═══════════════════════════════════════════════════════════════════════════════ Tests if your configured link resolver is: 1. Properly configured 2. Reachable (network connection) 3. Returns a valid response NOTE: This only tests if the resolver endpoint is reachable. Actual full-text access depends on your institution's subscriptions. ═══════════════════════════════════════════════════════════════════════════════ FREE TEST OPTION…

🔍 Unified Search - Single entry point for multi-source academic search. Automatically analyzes your query and searches the best sources. No need to choose between PubMed, OpenAlex, CrossRef, etc. ═══════════════════════════════════════════════════════════════════ WHAT IT DOES: ═══════════════════════════════════════════════════════════════════ 1. Analyzes your query (complexity, intent, PICO elements) 2. Automatically selects best sources based on query type 3. Searches multiple sources in parallel 4. Deduplicates and merges results 5. Ranks by configurable criteria 6. Enriches with OA link…

Remove the active schedule for a saved pipeline. Args: name: Saved pipeline name whose schedule will be removed. Returns: Removed schedule metadata, or a native MCP error when none exists.

Validate agent-provided P/I/C/O and return a runnable PICO pipeline. ``question_type`` and ``profile`` are closed enums. ``sources`` is an explicit array of supported unified-search providers; malformed values fail instead of being silently replaced. When ``question_type`` is omitted, the application service infers it from the clinical question.

Verify a plain-text reference list against PubMed evidence. First version scope: - Reference-list verification only - Client supplies the extracted reference list text - Backend parses entries and resolves them via PMID / DOI / ECitMatch Second version scope: - Adds unresolved review workflow for ``partial_match`` and ``unresolved`` rows - Returns a manual-review queue with retry queries and review checklist - Supports human-in-the-loop acceptance/rejection in client-side workflows Args: reference_text: Plain-text references, ideally one per line or a num…