Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
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name
pubmed-database
description
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
PubMed is the U.S. National Library of Medicine's comprehensive database providing free access to MEDLINE and life sciences literature. Construct advanced queries with Boolean operators, MeSH terms, and field tags, access data programmatically via E-utilities API for systematic reviews and literature analysis.
When to Use This Skill
This skill should be used when:
Searching for biomedical or life sciences research articles
Constructing complex search queries with Boolean operators, field tags, or MeSH terms
Conducting systematic literature reviews or meta-analyses
Accessing PubMed data programmatically via the E-utilities API
Finding articles by specific criteria (author, journal, publication date, article type)
Retrieving citation information, abstracts, or full-text articles
Working with PMIDs (PubMed IDs) or DOIs
Creating automated workflows for literature monitoring or data extraction
Core Capabilities
1. Advanced Search Query Construction
Construct sophisticated PubMed queries using Boolean operators, field tags, and specialized syntax.
Basic Search Strategies:
Combine concepts with Boolean operators (AND, OR, NOT)
Use field tags to limit searches to specific record parts
Employ phrase searching with double quotes for exact matches
Apply wildcards for term variations
Use proximity searching for terms within specified distances
Example Queries:
# Recent systematic reviews on diabetes treatment
diabetes mellitus[mh] AND treatment[tiab] AND systematic review[pt] AND 2023:2024[dp]
# Clinical trials comparing two drugs
(metformin[nm] OR insulin[nm]) AND diabetes mellitus, type 2[mh] AND randomized controlled trial[pt]
# Author-specific research
smith ja[au] AND cancer[tiab] AND 2023[dp] AND english[la]
When to consult search_syntax.md:
Need comprehensive list of available field tags
Require detailed explanation of search operators
Constructing complex proximity searches
Understanding automatic term mapping behavior
Need specific syntax for date ranges, wildcards, or special characters
Grep pattern for field tags: \[au\]|\[ti\]|\[ab\]|\[mh\]|\[pt\]|\[dp\]
2. MeSH Terms and Controlled Vocabulary
Use Medical Subject Headings (MeSH) for precise, consistent searching across the biomedical literature.
MeSH Searching:
[mh] tag searches MeSH terms with automatic inclusion of narrower terms
[majr] tag limits to articles where the topic is the main focus
Combine MeSH terms with subheadings for specificity (e.g., diabetes mellitus/therapy[mh])
Common MeSH Subheadings:
/diagnosis - Diagnostic methods
/drug therapy - Pharmaceutical treatment
/epidemiology - Disease patterns and prevalence
/etiology - Disease causes
/prevention & control - Preventive measures
/therapy - Treatment approaches
Example:
# Diabetes therapy with specific focus
diabetes mellitus, type 2[mh]/drug therapy AND cardiovascular diseases[mh]/prevention & control
3. Article Type and Publication Filtering
Filter results by publication type, date, text availability, and other attributes.
Publication Types (use [pt] field tag):
Clinical Trial
Meta-Analysis
Randomized Controlled Trial
Review
Systematic Review
Case Reports
Guideline
Date Filtering:
Single year: 2024[dp]
Date range: 2020:2024[dp]
Specific date: 2024/03/15[dp]
Text Availability:
Free full text: Add AND free full text[sb] to query
Has abstract: Add AND hasabstract[text] to query
Example:
# Recent free full-text RCTs on hypertension
hypertension[mh] AND randomized controlled trial[pt] AND 2023:2024[dp] AND free full text[sb]
4. Programmatic Access via E-utilities API
Access PubMed data programmatically using the NCBI E-utilities REST API for automation and bulk operations.
# First author with year and topic
smith ja[1au] AND 2023[dp] AND cancer[tiab]
# Journal, volume, and page
nature[ta] AND 2024[dp] AND 456[vi] AND 123-130[pg]
6. Systematic Literature Reviews
Conduct comprehensive literature searches for systematic reviews and meta-analyses.
# Example: Diabetes treatment effectiveness
# P: diabetes mellitus, type 2[mh]
# I: metformin[nm]
# C: lifestyle modification[tiab]
# O: glycemic control[tiab]
diabetes mellitus, type 2[mh] AND
(metformin[nm] OR lifestyle modification[tiab]) AND
glycemic control[tiab] AND
randomized controlled trial[pt]
Comprehensive Search Strategy:
# Include multiple synonyms and MeSH terms
(disease name[tiab] OR disease name[mh] OR synonym[tiab]) AND
(treatment[tiab] OR therapy[tiab] OR intervention[tiab]) AND
(systematic review[pt] OR meta-analysis[pt] OR randomized controlled trial[pt]) AND
2020:2024[dp] AND
english[la]
Search Refinement:
Start broad, review results
Add specificity with field tags
Apply date and publication type filters
Use Advanced Search to view query translation
Combine search history for complex queries
When to consult common_queries.md:
Need example queries for specific disease types or research areas
Require templates for different study designs
Looking for population-specific query patterns (pediatric, geriatric, etc.)
Constructing methodology-specific searches
Need quality filters or best practice patterns
Grep pattern for query examples: diabetes|cancer|cardiovascular|clinical trial|systematic review
7. Search History and Saved Searches
Use PubMed's search history and My NCBI features for efficient research workflows.
Search History (via Advanced Search):
Maintains up to 100 searches
Expires after 8 hours of inactivity
Combine previous searches using # references
Preview result counts before executing
Example:
#1: diabetes mellitus[mh]
#2: cardiovascular diseases[mh]
#3: #1 AND #2 AND risk factors[tiab]
My NCBI Features:
Save searches indefinitely
Set up email alerts for new matching articles
Create collections of saved articles
Organize research by project or topic
RSS Feeds:
Create RSS feeds for any search to monitor new publications in your area of interest.
8. Related Articles and Citation Discovery
Find related research and explore citation networks.
Similar Articles Feature:
Every PubMed article includes pre-calculated related articles based on:
Title and abstract similarity
MeSH term overlap
Weighted algorithmic matching
ELink for Related Data:
# Find related articles programmatically
elink.fcgi?dbfrom=pubmed&db=pubmed&id=PMID&cmd=neighbor
Citation Links:
LinkOut to full text from publishers
Links to PubMed Central free articles
Connections to related NCBI databases (GenBank, ClinicalTrials.gov, etc.)
9. Export and Citation Management
Export search results in various formats for citation management and further analysis.
Export Formats:
.nbib files for reference managers (Zotero, Mendeley, EndNote)
AMA, MLA, APA, NLM citation styles
CSV for data analysis
XML for programmatic processing
Clipboard and Collections:
Clipboard: Temporary storage for up to 500 items (8-hour expiration)
Collections: Permanent storage via My NCBI account
Batch Export via API:
# Export citations in MEDLINE format
efetch.fcgi?db=pubmed&id=PMID1,PMID2&rettype=medline&retmode=text
Working with Reference Files
This skill includes three comprehensive reference files in the references/ directory:
references/api_reference.md
Complete E-utilities API documentation including all nine endpoints, parameters, response formats, and best practices. Consult when:
Implementing programmatic PubMed access
Constructing API requests
Understanding rate limits and authentication
Working with large datasets via history server
Troubleshooting API errors
references/search_syntax.md
Detailed guide to PubMed search syntax including field tags, Boolean operators, wildcards, and special characters. Consult when:
Constructing complex search queries
Understanding automatic term mapping
Using advanced search features (proximity, wildcards)
Applying filters and limits
Troubleshooting unexpected search results
references/common_queries.md
Extensive collection of example queries for various research scenarios, disease types, and methodologies. Consult when:
Starting a new literature search
Need templates for specific research areas
Looking for best practice query patterns
Conducting systematic reviews
Searching for specific study designs or populations
Reference Loading Strategy:
Load reference files into context as needed based on the specific task. For brief queries or basic searches, the information in this SKILL.md may be sufficient. For complex operations, consult the appropriate reference file.
Common Workflows
Workflow 1: Basic Literature Search
Identify key concepts and synonyms
Construct query with Boolean operators and field tags
Review initial results and refine query
Apply filters (date, article type, language)
Export results for analysis
Workflow 2: Systematic Review Search
Define research question using PICO framework
Identify all relevant MeSH terms and synonyms
Construct comprehensive search strategy
Search multiple databases (include PubMed)
Document search strategy and date
Export results for screening and review
Workflow 3: Programmatic Data Extraction
Design search query and test in web interface
Implement search using ESearch API
Use history server for large result sets
Retrieve detailed records with EFetch
Parse XML/JSON responses
Store data locally with caching
Implement rate limiting and error handling
Workflow 4: Citation Discovery
Start with known relevant article
Use Similar Articles to find related work
Check citing articles (when available)
Explore MeSH terms from relevant articles
Construct new searches based on discoveries
Use ELink to find related database entries
Workflow 5: Ongoing Literature Monitoring
Construct comprehensive search query
Test and refine query for precision
Save search to My NCBI account
Set up email alerts for new matches
Create RSS feed for feed reader monitoring
Review new articles regularly
Tips and Best Practices
Search Strategy
Start broad, then narrow with field tags and filters
Include synonyms and MeSH terms for comprehensive coverage
Use quotation marks for exact phrases
Check Search Details in Advanced Search to verify query translation
Combine multiple searches using search history
API Usage
Obtain API key for higher rate limits (10 req/sec vs 3 req/sec)
Use history server for result sets > 500 articles
Implement exponential backoff for rate limit handling
Cache results locally to minimize redundant requests
Always include descriptive User-Agent header
Quality Filtering
Prefer systematic reviews and meta-analyses for synthesized evidence
Use publication type filters to find specific study designs
Filter by date for most recent research
Apply language filters as appropriate
Use free full text filter for immediate access
Citation Management
Export early and often to avoid losing search results
Use .nbib format for compatibility with most reference managers
Create My NCBI account for permanent collections
Document search strategies for reproducibility
Use Collections to organize research by project
Limitations and Considerations
Database Coverage
Primarily biomedical and life sciences literature
Pre-1975 articles often lack abstracts
Full author names available from 2002 forward
Non-English abstracts available but may default to English display
Search Limitations
Display limited to 10,000 results maximum
Search history expires after 8 hours of inactivity
Clipboard holds max 500 items with 8-hour expiration
Automatic term mapping may produce unexpected results
API Considerations
Rate limits apply (3-10 requests/second)
Large queries may time out (use history server)
XML parsing required for detailed data extraction
API key recommended for production use
Access Limitations
PubMed provides citations and abstracts (not always full text)
Full text access depends on publisher, institutional access, or open access status
LinkOut availability varies by journal and institution
