Description
Complete reference for all 46 MCP tools, including parameter descriptions and usage examples.
For capability-oriented usage, please first see docs/TOOLS_USAGE_GUIDE.zh-TW.md。
⚠️ Note: This document was automatically generated by
scripts/count_mcp_tools.py --update-docs. Manual modifications will be overwritten on the next run.
Condensed Understanding Model
There are currently 46 tools exposed externally, but it is recommended to first understand them through 8 capability families.
- Theoretical minimum lower bound: 6 multiplexed meta-tools
- Practical understandable lower bound: 8 capability families
- Recommendation: first learn the capability families, then consult the complete tool table
The capability families are as follows: Search, Query Planning, Article Exploration, Full Text and Retrieval, Visual and Context, Entities and Terminology, Results and Memory, Automation and Preservation.
Tool Category Overview
| Category | Number of Tools | Main Use |
|---|---|---|
| Search Tools | 1 | Unified multi-source literature search gateway |
| Query Intelligence | 3 | MeSH expansion, agent-provided PICO handoff, and query analysis |
| Article Exploration | 5 | Related articles, citation network |
| Full Text Tools | 2 | Full text retrieval and text mining |
| NCBI Extensions | 7 | Gene, PubChem, ClinVar |
| Citation Network | 1 | Citation tree construction and exploration |
| Export Tools | 2 | Citation format export and local literature note preservation |
| Session Management | 5 | PMID caching and history |
| Institutional Subscription | 5 | OpenURL Link Resolver |
| Visual Search | 1 | Image analysis and search (experimental) |
| ICD Conversion | 1 | ICD-10 and MeSH conversion |
| Research Timeline | 3 | Research evolution tracking and milestone detection |
| Citation Validation | 1 | Reference list verification with PubMed evidence |
| Figure Extraction | 1 | Article figures and visual data extraction |
| Image Search | 1 | Biomedical image search |
| Pipeline Management | 7 | Pipeline persistence, loading, scheduling |
Search Tools
Unified multi-source literature search gateway
| Tool | Description |
|---|---|
unified_search |
Unified Search - Single entry point for multi-source academic search. |
Query Intelligence
MeSH expansion, agent-provided PICO handoff, and query analysis
| Tool | Description |
|---|---|
parse_pico |
Validate agent-provided PICO elements and return a runnable search plan. |
generate_search_queries |
Gather search intelligence for a topic - returns RAW MATERIALS for Agent to decide. |
analyze_search_query |
Analyze a search query without executing the search. |
Article Exploration
Related articles, citation network
| Tool | Description |
|---|---|
fetch_article_details |
Fetch detailed information for one or more PubMed articles. |
find_related_articles |
Find articles related to a given PubMed article. |
find_citing_articles |
Find articles that cite a given PubMed article. |
get_article_references |
Get the references (bibliography) of a PubMed article. |
get_citation_metrics |
Get citation metrics from NIH iCite for articles. |
Full Text Tools
Full text retrieval and text mining
| Tool | Description |
|---|---|
get_fulltext |
Enhanced multi-source fulltext retrieval. |
get_text_mined_terms |
Get text-mined annotations from Europe PMC. |
NCBI Extensions
Gene, PubChem, ClinVar
| Tool | Description |
|---|---|
search_gene |
Search NCBI Gene database for gene information. |
get_gene_details |
Get detailed information about a gene by NCBI Gene ID. |
get_gene_literature |
Get PubMed articles linked to a gene. |
search_compound |
Search PubChem for chemical compounds. |
get_compound_details |
Get detailed information about a compound by PubChem CID. |
get_compound_literature |
Get PubMed articles linked to a compound. |
search_clinvar |
Search ClinVar for clinical variants. |
Citation Network
Citation tree construction and exploration
| Tool | Description |
|---|---|
build_citation_tree |
Build a citation tree (network) from a single article. |
Export Tools
Citation format export and local literature note preservation
| Tool | Description |
|---|---|
prepare_export |
Export citations to reference manager formats. |
save_literature_notes |
Save searched articles as guided local wiki/Foam/Markdown notes. |
Session Management
PMID caching and history
| Tool | Description |
|---|---|
read_session |
Read session data through a single facade. |
get_session_pmids |
Get the list of PMIDs cached in the session. |
get_cached_article |
Get article details from the session cache. |
get_session_summary |
Get summary information for the current session. |
get_session_log |
Get the activity log and search history summary for the current session. |
Institutional subscription
OpenURL Link Resolver
| Tools | Description |
|---|---|
configure_institutional_access |
Configure your institution's link resolver for full-text access. |
get_institutional_link |
Generate institutional access link (OpenURL) for an article. |
list_resolver_presets |
List available institutional link resolver presets. |
test_institutional_access |
Test your institutional link resolver configuration. |
diagnose_institutional_access |
Diagnose why institutional fulltext access succeeds or fails for an article. |
Visual search
Image analysis and search (experimental)
| Tools | Description |
|---|---|
analyze_figure_for_search |
Analyze a scientific figure or image for literature search. |
ICD conversion
ICD-10 and MeSH conversion
| Tools | Description |
|---|---|
convert_icd_mesh |
Convert between ICD codes and MeSH terms (bidirectional). |
Research timeline
Research evolution tracking and milestone detection
| Tools | Description |
|---|---|
build_research_timeline |
Build a research timeline for a topic OR specific PMIDs. |
analyze_timeline_milestones |
Analyze milestone distribution for a research topic. |
compare_timelines |
Compare research timelines of multiple topics. |
Citation verification
Reference list verification with PubMed evidence
| Tools | Description |
|---|---|
verify_reference_list |
Verify a plain-text reference list against PubMed evidence. |
Figure extraction
Article figure and visual data extraction
| Tools | Description |
|---|---|
get_article_figures |
Get structured figure metadata (label, caption, image URL) and PDF links from a PMC Open Access arti |
Image search
Biomedical image search
| Tools | Description |
|---|---|
search_biomedical_images |
Search biomedical images across Open-i and Europe PMC. |
Pipeline management
Pipeline persistence, loading, scheduling
| Tools | Description |
|---|---|
manage_pipeline |
Manage saved pipelines through a single facade. |
save_pipeline |
Save a pipeline configuration for later reuse. |
list_pipelines |
List all saved pipeline configurations. |
load_pipeline |
Load a pipeline configuration for review or editing. |
delete_pipeline |
Delete a saved pipeline configuration and its execution history. |
get_pipeline_history |
Get execution history for a saved pipeline. |
schedule_pipeline |
Schedule a saved pipeline for periodic execution. |
Common workflows
Quick search
unified_search → fetch_article_details → prepare_export
Systematic search
generate_search_queries → Boolean query → analyze_search_query → unified_search
PICO search
Agent P/I/C/O -> parse_pico handoff -> unified_search(template:pico) / expanded Boolean
Paper exploration
fetch_article_details → find_related_articles + find_citing_articles + build_citation_tree
Full-text retrieval
get_fulltext → get_article_figures / get_text_mined_terms / get_institutional_link
Total: 46 tools in 16 categories
Auto-generated by scripts/count_mcp_tools.py --update-docs