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 Database Overview 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 : 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 : 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 : 4. Programmatic Access via E utilities API Access PubMed data programmatically using the NCBI E utilities REST API for automation and bulk operations. Core API Endpoints : 1. ESearch Search database and retrieve PMIDs 2. EFetch Download full records in various formats 3. ESummary Get document summaries 4. EPost Upload UIDs for batch processing 5. ELink Find related articles and linked data Basic Workflow : Rate Limits : Without API key: 3 requests/second With API key: 10 requests/second Always include User Agent header Best Practices : Use history server (usehistory=y) for large result sets Implement batch operations via EPost for multiple UIDs Cache results locally to minimize redundant calls Respect rate limits to avoid service disruption When to consult api reference.md : Need detailed endpoint documentation Require parameter specifications for each E utility Constructing batch operations or history server workflows Understanding response formats (XML, JSON, text) Troubleshooting API errors or rate limit issues Grep pattern for API endpoints: esearch efetch esummary epost elink einfo 5. Citation Matching and Article Retrieval Find articles using partial citation information or specific identifiers. By Identifier : Citation Matching (via ECitMatch API): Use journal name, year, volume, page, and author to find PMIDs: By Author and Metadata : 6. Systematic Literature Reviews Conduct comprehensive literature searches for systematic reviews and meta analyses. PICO Framework (Population, Intervention, Comparison, Outcome): Structure clinical research questions systematically: Comprehensive Search Strategy : Search Refinement : 1. Start broad, review results 2. Add specificity with field tags 3. Apply date and publication type filters 4. Use Advanced Search to view query translation 5. 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 : 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 : 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 : 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 1. Identify key concepts and synonyms 2. Construct query with Boolean operators and field tags 3. Review initial results and refine query 4. Apply filters (date, article type, language) 5. Export results for analysis Workflow 2: Systematic Review Search 1. Define research question using PICO framework 2. Identify all relevant MeSH terms and synonyms 3. Construct comprehensive search strategy 4. Search multiple databases (include PubMed) 5. Document search strategy and date 6. Export results for screening and review Workflow 3: Programmatic Data Extraction 1. Design search query and test in web interface 2. Implement search using ESearch API 3. Use history server for large result sets 4. Retrieve detailed records with EFetch 5. Parse XML/JSON responses 6. Store data locally with caching 7. Implement rate limiting and error handling Workflow 4: Citation Discovery 1. Start with known relevant article 2. Use Similar Articles to find related work 3. Check citing articles (when available) 4. Explore MeSH terms from relevant articles 5. Construct new searches based on discoveries 6. Use ELink to find related database entries Workflow 5: Ongoing Literature Monitoring 1. Construct comprehensive search query 2. Test and refine query for precision 3. Save search to My NCBI account 4. Set up email alerts for new matches 5. Create RSS feed for feed reader monitoring 6. 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,

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