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skills/pubmed-database/references/api_reference.md
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skills/pubmed-database/references/api_reference.md
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# PubMed E-utilities API Reference
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## Overview
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The NCBI E-utilities provide programmatic access to PubMed and other Entrez databases through a REST API. The base URL for all E-utilities is:
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```
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
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```
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## API Key Requirements
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As of December 1, 2018, NCBI enforces API key usage for E-utility calls. API keys increase rate limits from 3 requests/second to 10 requests/second. To obtain an API key, register for an NCBI account and generate a key from your account settings.
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Include the API key in requests using the `&api_key` parameter:
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```
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esearch.fcgi?db=pubmed&term=cancer&api_key=YOUR_API_KEY
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```
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## Rate Limits
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- **Without API key**: 3 requests per second
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- **With API key**: 10 requests per second
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- Always include a User-Agent header in requests
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## Core E-utility Tools
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### 1. ESearch - Query Databases
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**Endpoint**: `esearch.fcgi`
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**Purpose**: Search an Entrez database and retrieve a list of UIDs (e.g., PMIDs for PubMed)
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**Required Parameters**:
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- `db` - Database to search (e.g., pubmed, gene, protein)
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- `term` - Search query
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**Optional Parameters**:
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- `retmax` - Maximum records to return (default: 20, max: 10000)
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- `retstart` - Index of first record to return (default: 0)
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- `usehistory=y` - Store results on history server for large result sets
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- `retmode` - Return format (xml, json)
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- `sort` - Sort order (relevance, pub_date, first_author, last_author, journal)
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- `field` - Limit search to specific field
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- `datetype` - Type of date to use for filtering (pdat for publication date)
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- `mindate` - Minimum date (YYYY/MM/DD format)
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- `maxdate` - Maximum date (YYYY/MM/DD format)
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**Example Request**:
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```
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esearch.fcgi?db=pubmed&term=breast+cancer&retmax=100&retmode=json&api_key=YOUR_API_KEY
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```
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**Response Elements**:
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- `Count` - Total number of records matching query
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- `RetMax` - Number of records returned in this response
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- `RetStart` - Index of first returned record
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- `IdList` - List of UIDs (PMIDs)
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- `WebEnv` - History server environment string (when usehistory=y)
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- `QueryKey` - Query key for history server (when usehistory=y)
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### 2. EFetch - Download Records
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**Endpoint**: `efetch.fcgi`
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**Purpose**: Retrieve full records from a database in various formats
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**Required Parameters**:
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- `db` - Database name
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- `id` - Comma-separated list of UIDs, or use WebEnv/query_key from ESearch
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**Optional Parameters**:
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- `rettype` - Record type (abstract, medline, xml, uilist)
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- `retmode` - Return mode (text, xml)
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- `retstart` - Starting record index
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- `retmax` - Maximum records per request
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**Example Request**:
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```
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efetch.fcgi?db=pubmed&id=123456,234567&rettype=abstract&retmode=text&api_key=YOUR_API_KEY
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```
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**Common rettype Values for PubMed**:
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- `abstract` - Abstract text
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- `medline` - Full MEDLINE format
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- `xml` - PubMed XML format
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- `uilist` - List of UIDs only
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### 3. ESummary - Retrieve Document Summaries
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**Endpoint**: `esummary.fcgi`
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**Purpose**: Get document summaries (DocSum) for a list of UIDs
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**Required Parameters**:
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- `db` - Database name
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- `id` - Comma-separated UIDs or WebEnv/query_key
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**Optional Parameters**:
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- `retmode` - Return format (xml, json)
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- `version` - DocSum version (1.0 or 2.0, default is 1.0)
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**Example Request**:
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```
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esummary.fcgi?db=pubmed&id=123456,234567&retmode=json&version=2.0&api_key=YOUR_API_KEY
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```
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**DocSum Fields** (vary by database, common PubMed fields):
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- Title
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- Authors
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- Source (journal)
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- PubDate
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- Volume, Issue, Pages
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- DOI
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- PmcRefCount (citations in PMC)
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### 4. EPost - Upload UIDs
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**Endpoint**: `epost.fcgi`
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**Purpose**: Upload a list of UIDs to the history server for use in subsequent requests
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**Required Parameters**:
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- `db` - Database name
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- `id` - Comma-separated list of UIDs
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**Example Request**:
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```
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epost.fcgi?db=pubmed&id=123456,234567,345678&api_key=YOUR_API_KEY
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```
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**Response**:
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Returns WebEnv and QueryKey for use in subsequent requests
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### 5. ELink - Find Related Data
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**Endpoint**: `elink.fcgi`
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**Purpose**: Find related records within the same database or in different databases
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**Required Parameters**:
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- `dbfrom` - Source database
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- `db` - Target database (can be same as dbfrom)
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- `id` - UID(s) from source database
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**Optional Parameters**:
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- `cmd` - Link command (neighbor, neighbor_history, prlinks, llinks, etc.)
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- `linkname` - Specific link type to retrieve
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- `term` - Filter results with search query
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- `holding` - Filter by library holdings
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**Example Request**:
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```
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elink.fcgi?dbfrom=pubmed&db=pubmed&id=123456&cmd=neighbor&api_key=YOUR_API_KEY
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```
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**Common Link Commands**:
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- `neighbor` - Return related records
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- `neighbor_history` - Post related records to history server
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- `prlinks` - Return provider URLs
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- `llinks` - Return LinkOut URLs
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### 6. EInfo - Database Information
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**Endpoint**: `einfo.fcgi`
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**Purpose**: Get information about available Entrez databases or specific database fields
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**Parameters**:
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- `db` - Database name (optional; omit to list all databases)
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- `retmode` - Return format (xml, json)
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**Example Request**:
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```
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einfo.fcgi?db=pubmed&retmode=json&api_key=YOUR_API_KEY
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```
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**Returns**:
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- Database description
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- Record count
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- Last update date
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- Available search fields with descriptions
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### 7. EGQuery - Global Query
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**Endpoint**: `egquery.fcgi`
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**Purpose**: Search term counts across all Entrez databases
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**Required Parameters**:
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- `term` - Search query
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**Example Request**:
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```
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egquery.fcgi?term=cancer&api_key=YOUR_API_KEY
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```
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### 8. ESpell - Spelling Suggestions
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**Endpoint**: `espell.fcgi`
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**Purpose**: Get spelling suggestions for queries
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**Required Parameters**:
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- `db` - Database name
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- `term` - Search term with potential misspelling
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**Example Request**:
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```
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espell.fcgi?db=pubmed&term=cancre&api_key=YOUR_API_KEY
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```
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### 9. ECitMatch - Citation Matching
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**Endpoint**: `ecitmatch.cgi`
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**Purpose**: Search PubMed citations using journal, year, volume, page, author information
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**Request Format**: POST request with citation strings
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**Citation String Format**:
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```
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journal|year|volume|page|author|key|
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```
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**Example**:
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```
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Science|2008|320|5880|1185|key1|
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Nature|2010|463|7279|318|key2|
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```
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**Rate Limit**: 3 requests per second with User-Agent header required
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## Best Practices
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### Use History Server for Large Result Sets
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For queries returning more than 500 records, use the history server:
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1. **Initial Search with History**:
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```
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esearch.fcgi?db=pubmed&term=cancer&usehistory=y&retmode=json&api_key=YOUR_API_KEY
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```
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2. **Retrieve Records in Batches**:
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```
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efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_12345&retstart=0&retmax=500&rettype=xml&api_key=YOUR_API_KEY
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efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_12345&retstart=500&retmax=500&rettype=xml&api_key=YOUR_API_KEY
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```
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### Batch Operations
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Use EPost to upload large lists of UIDs before fetching:
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```
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# Step 1: Post UIDs
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epost.fcgi?db=pubmed&id=123,456,789,...&api_key=YOUR_API_KEY
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# Step 2: Fetch using WebEnv/query_key
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efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_12345&rettype=xml&api_key=YOUR_API_KEY
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```
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### Error Handling
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Common HTTP status codes:
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- `200` - Success
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- `400` - Bad request (check parameters)
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- `414` - URI too long (use POST or history server)
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- `429` - Rate limit exceeded
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### Caching
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Implement local caching to:
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- Reduce redundant API calls
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- Stay within rate limits
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- Improve response times
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- Respect NCBI resources
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## Response Formats
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### XML (Default)
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Most detailed format with full structured data. Each database has its own DTD (Document Type Definition).
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### JSON
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Available for most utilities with `retmode=json`. Easier to parse in modern applications.
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### Text
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Plain text format, useful for abstracts and simple data retrieval.
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## Support and Resources
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- **API Documentation**: https://www.ncbi.nlm.nih.gov/books/NBK25501/
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- **Mailing List**: utilities-announce@ncbi.nlm.nih.gov
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- **Support**: vog.hin.mln.ibcn@seitilitue
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- **NLM Help Desk**: 1-888-FIND-NLM (1-888-346-3656)
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453
skills/pubmed-database/references/common_queries.md
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skills/pubmed-database/references/common_queries.md
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# Common PubMed Query Patterns
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This reference provides practical examples of common PubMed search patterns for various research scenarios.
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## General Research Queries
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### Finding Recent Research on a Topic
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```
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breast cancer[tiab] AND 2023:2024[dp]
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```
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### Systematic Reviews on a Topic
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```
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(diabetes[tiab] OR diabetes mellitus[mh]) AND systematic review[pt]
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```
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### Meta-Analyses
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```
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hypertension[tiab] AND meta-analysis[pt] AND 2020:2024[dp]
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```
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### Clinical Trials
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```
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alzheimer disease[mh] AND randomized controlled trial[pt]
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```
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### Finding Guidelines
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```
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asthma[tiab] AND (guideline[pt] OR practice guideline[pt])
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```
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## Disease-Specific Queries
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### Cancer Research
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```
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# General cancer screening
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cancer screening[tiab] AND systematic review[pt] AND 2020:2024[dp]
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# Specific cancer type with treatment
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lung cancer[tiab] AND immunotherapy[tiab] AND clinical trial[pt]
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# Cancer genetics
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breast neoplasms[mh] AND BRCA1[tiab] AND genetic testing[tiab]
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```
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### Cardiovascular Disease
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```
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# Heart disease prevention
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(heart disease[tiab] OR cardiovascular disease[mh]) AND prevention[tiab] AND 2022:2024[dp]
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# Stroke treatment
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stroke[mh] AND (thrombectomy[tiab] OR thrombolysis[tiab]) AND randomized controlled trial[pt]
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# Hypertension management
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hypertension[mh]/drug therapy AND comparative effectiveness[tiab]
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```
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### Infectious Diseases
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```
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# COVID-19 research
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COVID-19[tiab] AND (vaccine[tiab] OR vaccination[tiab]) AND 2023:2024[dp]
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# Antibiotic resistance
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(antibiotic resistance[tiab] OR drug resistance, bacterial[mh]) AND systematic review[pt]
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# Tuberculosis treatment
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tuberculosis[mh]/drug therapy AND (multidrug-resistant[tiab] OR MDR-TB[tiab])
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```
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### Neurological Disorders
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```
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# Alzheimer's disease
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alzheimer disease[mh] AND (diagnosis[sh] OR biomarkers[tiab]) AND 2020:2024[dp]
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# Parkinson's disease treatment
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parkinson disease[mh] AND treatment[tiab] AND clinical trial[pt]
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# Multiple sclerosis
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multiple sclerosis[mh] AND disease modifying[tiab] AND review[pt]
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```
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### Diabetes
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```
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# Type 2 diabetes management
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diabetes mellitus, type 2[mh] AND (lifestyle[tiab] OR diet[tiab]) AND randomized controlled trial[pt]
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# Diabetes complications
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diabetes mellitus[mh] AND (complications[sh] OR diabetic neuropathy[mh])
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# New diabetes drugs
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diabetes mellitus, type 2[mh] AND (GLP-1[tiab] OR SGLT2[tiab]) AND 2022:2024[dp]
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```
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## Drug and Treatment Research
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### Drug Efficacy Studies
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```
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# Compare two drugs
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(drug A[nm] OR drug B[nm]) AND condition[mh] AND comparative effectiveness[tiab]
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# Drug side effects
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medication name[nm] AND (adverse effects[sh] OR side effects[tiab])
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# Drug combination therapy
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(aspirin[nm] AND clopidogrel[nm]) AND acute coronary syndrome[mh]
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```
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### Treatment Comparisons
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```
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# Surgery vs medication
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condition[mh] AND (surgery[tiab] OR surgical[tiab]) AND (medication[tiab] OR drug therapy[sh]) AND comparative study[pt]
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# Different surgical approaches
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procedure[tiab] AND (laparoscopic[tiab] OR open surgery[tiab]) AND outcomes[tiab]
|
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```
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### Alternative Medicine
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```
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# Herbal supplements
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(herbal medicine[mh] OR phytotherapy[mh]) AND condition[tiab] AND clinical trial[pt]
|
||||
|
||||
# Acupuncture
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||||
acupuncture[mh] AND pain[tiab] AND randomized controlled trial[pt]
|
||||
```
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## Diagnostic Research
|
||||
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### Diagnostic Tests
|
||||
```
|
||||
# Sensitivity and specificity
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test name[tiab] AND condition[tiab] AND (sensitivity[tiab] AND specificity[tiab])
|
||||
|
||||
# Diagnostic imaging
|
||||
(MRI[tiab] OR magnetic resonance imaging[tiab]) AND brain tumor[tiab] AND diagnosis[sh]
|
||||
|
||||
# Lab test evaluation
|
||||
biomarker name[tiab] AND disease[tiab] AND (diagnostic[tiab] OR screening[tiab])
|
||||
```
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||||
|
||||
### Screening Programs
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||||
```
|
||||
# Cancer screening
|
||||
cancer type[tiab] AND screening[tiab] AND (cost effectiveness[tiab] OR benefit[tiab])
|
||||
|
||||
# Population screening
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||||
condition[tiab] AND mass screening[mh] AND public health[tiab]
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||||
```
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||||
|
||||
## Population-Specific Queries
|
||||
|
||||
### Pediatric Research
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||||
```
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||||
# Children with specific condition
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||||
condition[tiab] AND (child[mh] OR pediatric[tiab]) AND treatment[tiab]
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||||
# Age-specific
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||||
disease[tiab] AND (infant[mh] OR child, preschool[mh])
|
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|
||||
# Pediatric dosing
|
||||
drug name[nm] AND pediatric[tiab] AND (dosing[tiab] OR dose[tiab])
|
||||
```
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||||
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||||
### Geriatric Research
|
||||
```
|
||||
# Elderly population
|
||||
condition[tiab] AND (aged[mh] OR elderly[tiab] OR geriatric[tiab])
|
||||
|
||||
# Aging and disease
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||||
aging[mh] AND disease[tiab] AND mechanism[tiab]
|
||||
|
||||
# Polypharmacy
|
||||
polypharmacy[tiab] AND elderly[tiab] AND adverse effects[tiab]
|
||||
```
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||||
|
||||
### Pregnant Women
|
||||
```
|
||||
# Pregnancy and medications
|
||||
drug name[nm] AND (pregnancy[mh] OR pregnant women[tiab]) AND safety[tiab]
|
||||
|
||||
# Pregnancy complications
|
||||
pregnancy complication[tiab] AND management[tiab]
|
||||
```
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||||
|
||||
### Sex-Specific Research
|
||||
```
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||||
# Female-specific
|
||||
condition[tiab] AND female[mh] AND hormones[tiab]
|
||||
|
||||
# Male-specific
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||||
disease[tiab] AND male[mh] AND risk factors[tiab]
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||||
|
||||
# Sex differences
|
||||
condition[tiab] AND (sex factors[mh] OR gender differences[tiab])
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||||
```
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||||
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||||
## Epidemiology and Public Health
|
||||
|
||||
### Prevalence Studies
|
||||
```
|
||||
disease[tiab] AND (prevalence[tiab] OR epidemiology[sh]) AND country/region[tiab]
|
||||
```
|
||||
|
||||
### Incidence Studies
|
||||
```
|
||||
condition[tiab] AND incidence[tiab] AND population[tiab] AND 2020:2024[dp]
|
||||
```
|
||||
|
||||
### Risk Factors
|
||||
```
|
||||
disease[mh] AND (risk factors[mh] OR etiology[sh]) AND cohort study[tiab]
|
||||
```
|
||||
|
||||
### Global Health
|
||||
```
|
||||
disease[tiab] AND (developing countries[mh] OR low income[tiab]) AND burden[tiab]
|
||||
```
|
||||
|
||||
### Health Disparities
|
||||
```
|
||||
condition[tiab] AND (health disparities[tiab] OR health equity[tiab]) AND minority groups[tiab]
|
||||
```
|
||||
|
||||
## Methodology-Specific Queries
|
||||
|
||||
### Research Methodology
|
||||
|
||||
#### Cohort Studies
|
||||
```
|
||||
condition[tiab] AND cohort study[tiab] AND prospective[tiab]
|
||||
```
|
||||
|
||||
#### Case-Control Studies
|
||||
```
|
||||
disease[tiab] AND case-control studies[mh] AND risk factors[tiab]
|
||||
```
|
||||
|
||||
#### Cross-Sectional Studies
|
||||
```
|
||||
condition[tiab] AND cross-sectional studies[mh] AND prevalence[tiab]
|
||||
```
|
||||
|
||||
### Statistical Methods
|
||||
```
|
||||
# Machine learning in medicine
|
||||
(machine learning[tiab] OR artificial intelligence[tiab]) AND diagnosis[tiab] AND validation[tiab]
|
||||
|
||||
# Bayesian analysis
|
||||
condition[tiab] AND bayes theorem[mh] AND clinical decision[tiab]
|
||||
```
|
||||
|
||||
### Genetic and Molecular Research
|
||||
```
|
||||
# GWAS studies
|
||||
disease[tiab] AND (genome-wide association study[tiab] OR GWAS[tiab])
|
||||
|
||||
# Gene expression
|
||||
gene name[tiab] AND (gene expression[mh] OR mRNA[tiab]) AND disease[tiab]
|
||||
|
||||
# Proteomics
|
||||
condition[tiab] AND proteomics[mh] AND biomarkers[tiab]
|
||||
|
||||
# CRISPR research
|
||||
CRISPR[tiab] AND (gene editing[tiab] OR genome editing[tiab]) AND 2020:2024[dp]
|
||||
```
|
||||
|
||||
## Author and Institution Queries
|
||||
|
||||
### Finding Work by Specific Author
|
||||
```
|
||||
# Single author
|
||||
smith ja[au] AND cancer[tiab] AND 2023:2024[dp]
|
||||
|
||||
# First author only
|
||||
jones m[1au] AND cardiology[tiab]
|
||||
|
||||
# Multiple authors from same group
|
||||
(smith ja[au] OR jones m[au] OR wilson k[au]) AND research topic[tiab]
|
||||
```
|
||||
|
||||
### Institution-Specific Research
|
||||
```
|
||||
# University affiliation
|
||||
harvard[affil] AND cancer research[tiab] AND 2023:2024[dp]
|
||||
|
||||
# Hospital research
|
||||
"mayo clinic"[affil] AND clinical trial[pt]
|
||||
|
||||
# Country-specific
|
||||
japan[affil] AND robotics[tiab] AND surgery[tiab]
|
||||
```
|
||||
|
||||
## Journal-Specific Queries
|
||||
|
||||
### High-Impact Journals
|
||||
```
|
||||
# Specific journal
|
||||
nature[ta] AND genetics[tiab] AND 2024[dp]
|
||||
|
||||
# Multiple journals
|
||||
(nature[ta] OR science[ta] OR cell[ta]) AND immunology[tiab]
|
||||
|
||||
# Journal with ISSN
|
||||
0028-4793[issn] AND clinical trial[pt]
|
||||
```
|
||||
|
||||
## Citation and Reference Queries
|
||||
|
||||
### Finding Specific Articles
|
||||
```
|
||||
# By PMID
|
||||
12345678[pmid]
|
||||
|
||||
# By DOI
|
||||
10.1056/NEJMoa123456[doi]
|
||||
|
||||
# By first author and year
|
||||
smith ja[1au] AND 2023[dp] AND cancer[tiab]
|
||||
```
|
||||
|
||||
### Finding Cited Work
|
||||
```
|
||||
# Related articles
|
||||
Similar Articles feature from any PubMed result
|
||||
|
||||
# By keyword in references
|
||||
Use "Cited by" links when available
|
||||
```
|
||||
|
||||
## Advanced Combination Queries
|
||||
|
||||
### Comprehensive Literature Review
|
||||
```
|
||||
(disease name[tiab] OR disease name[mh]) AND
|
||||
((treatment[tiab] OR therapy[tiab] OR management[tiab]) OR
|
||||
(diagnosis[tiab] OR screening[tiab]) OR
|
||||
(epidemiology[tiab] OR prevalence[tiab])) AND
|
||||
(systematic review[pt] OR meta-analysis[pt] OR review[pt]) AND
|
||||
2019:2024[dp] AND english[la]
|
||||
```
|
||||
|
||||
### Precision Medicine Query
|
||||
```
|
||||
(precision medicine[tiab] OR personalized medicine[tiab] OR pharmacogenomics[mh]) AND
|
||||
cancer[tiab] AND
|
||||
(biomarkers[tiab] OR genetic testing[tiab]) AND
|
||||
clinical application[tiab] AND
|
||||
2020:2024[dp]
|
||||
```
|
||||
|
||||
### Translational Research
|
||||
```
|
||||
(basic science[tiab] OR bench to bedside[tiab] OR translational medical research[mh]) AND
|
||||
disease[tiab] AND
|
||||
(clinical trial[pt] OR clinical application[tiab]) AND
|
||||
2020:2024[dp]
|
||||
```
|
||||
|
||||
## Quality Filters
|
||||
|
||||
### High-Quality Evidence
|
||||
```
|
||||
condition[tiab] AND
|
||||
(randomized controlled trial[pt] OR systematic review[pt] OR meta-analysis[pt]) AND
|
||||
humans[mh] AND
|
||||
english[la] AND
|
||||
2020:2024[dp]
|
||||
```
|
||||
|
||||
### Free Full Text Articles
|
||||
```
|
||||
topic[tiab] AND free full text[sb] AND 2023:2024[dp]
|
||||
```
|
||||
|
||||
### Articles with Abstracts
|
||||
```
|
||||
condition[tiab] AND hasabstract[text] AND review[pt]
|
||||
```
|
||||
|
||||
## Staying Current
|
||||
|
||||
### Latest Publications
|
||||
```
|
||||
topic[tiab] AND 2024[dp] AND english[la]
|
||||
```
|
||||
|
||||
### Preprints and Early Access
|
||||
```
|
||||
topic[tiab] AND (epub ahead of print[tiab] OR publisher[sb])
|
||||
```
|
||||
|
||||
### Setting Up Alerts
|
||||
```
|
||||
# Create search and save to My NCBI
|
||||
# Enable email alerts for new matching articles
|
||||
topic[tiab] AND (randomized controlled trial[pt] OR systematic review[pt])
|
||||
```
|
||||
|
||||
## COVID-19 Specific Queries
|
||||
|
||||
### Vaccine Research
|
||||
```
|
||||
(COVID-19[tiab] OR SARS-CoV-2[tiab]) AND
|
||||
(vaccine[tiab] OR vaccination[tiab]) AND
|
||||
(efficacy[tiab] OR effectiveness[tiab]) AND
|
||||
2023:2024[dp]
|
||||
```
|
||||
|
||||
### Long COVID
|
||||
```
|
||||
(long covid[tiab] OR post-acute covid[tiab] OR PASC[tiab]) AND
|
||||
(symptoms[tiab] OR treatment[tiab])
|
||||
```
|
||||
|
||||
### COVID Treatment
|
||||
```
|
||||
COVID-19[tiab] AND
|
||||
(antiviral[tiab] OR monoclonal antibody[tiab] OR treatment[tiab]) AND
|
||||
randomized controlled trial[pt]
|
||||
```
|
||||
|
||||
## Tips for Constructing Queries
|
||||
|
||||
### 1. PICO Framework
|
||||
Use PICO (Population, Intervention, Comparison, Outcome) to structure clinical queries:
|
||||
|
||||
```
|
||||
P: diabetes mellitus, type 2[mh]
|
||||
I: metformin[nm]
|
||||
C: lifestyle modification[tiab]
|
||||
O: glycemic control[tiab]
|
||||
|
||||
Query: diabetes mellitus, type 2[mh] AND (metformin[nm] OR lifestyle modification[tiab]) AND glycemic control[tiab]
|
||||
```
|
||||
|
||||
### 2. Iterative Refinement
|
||||
Start broad, review results, refine:
|
||||
```
|
||||
1. diabetes → too broad
|
||||
2. diabetes mellitus type 2 → better
|
||||
3. diabetes mellitus, type 2[mh] AND metformin[nm] → more specific
|
||||
4. diabetes mellitus, type 2[mh] AND metformin[nm] AND randomized controlled trial[pt] → focused
|
||||
```
|
||||
|
||||
### 3. Use Search History
|
||||
Combine previous searches in Advanced Search:
|
||||
```
|
||||
#1: diabetes mellitus, type 2[mh]
|
||||
#2: cardiovascular disease[mh]
|
||||
#3: #1 AND #2 AND risk factors[tiab]
|
||||
```
|
||||
|
||||
### 4. Save Effective Searches
|
||||
Create My NCBI account to save successful queries for future use and set up automatic alerts.
|
||||
436
skills/pubmed-database/references/search_syntax.md
Normal file
436
skills/pubmed-database/references/search_syntax.md
Normal file
@@ -0,0 +1,436 @@
|
||||
# PubMed Search Syntax and Field Tags
|
||||
|
||||
## Boolean Operators
|
||||
|
||||
PubMed supports standard Boolean operators to combine search terms:
|
||||
|
||||
### AND
|
||||
Retrieves results containing all search terms. PubMed automatically applies AND between separate concepts.
|
||||
|
||||
**Example**:
|
||||
```
|
||||
diabetes AND hypertension
|
||||
```
|
||||
|
||||
### OR
|
||||
Retrieves results containing at least one of the search terms. Useful for synonyms or related concepts.
|
||||
|
||||
**Example**:
|
||||
```
|
||||
heart attack OR myocardial infarction
|
||||
```
|
||||
|
||||
### NOT
|
||||
Excludes results containing the specified term. Use cautiously as it may eliminate relevant results.
|
||||
|
||||
**Example**:
|
||||
```
|
||||
cancer NOT lung
|
||||
```
|
||||
|
||||
**Precedence**: Operations are processed left to right. Use parentheses to control evaluation order:
|
||||
```
|
||||
(heart attack OR myocardial infarction) AND treatment
|
||||
```
|
||||
|
||||
## Phrase Searching
|
||||
|
||||
### Double Quotes
|
||||
Enclose exact phrases in double quotes to search for terms in specific order:
|
||||
|
||||
```
|
||||
"kidney allograft"
|
||||
"machine learning"
|
||||
"systematic review"
|
||||
```
|
||||
|
||||
### Field Tags
|
||||
Alternative method using field tags:
|
||||
```
|
||||
kidney allograft[Title]
|
||||
```
|
||||
|
||||
## Wildcards
|
||||
|
||||
Use asterisk (*) to substitute for zero or more characters:
|
||||
|
||||
**Rules**:
|
||||
- Minimum 4 characters before first wildcard
|
||||
- Matches word variations and plurals
|
||||
|
||||
**Examples**:
|
||||
```
|
||||
vaccin* → matches vaccine, vaccination, vaccines, vaccinate
|
||||
pediatr* → matches pediatric, pediatrics, pediatrician
|
||||
colo*r → matches color, colour
|
||||
```
|
||||
|
||||
**Limitations**:
|
||||
- Cannot use at beginning of search term
|
||||
- May retrieve unexpected variations
|
||||
|
||||
## Proximity Searching
|
||||
|
||||
Search for terms within a specified distance from each other. Only available in Title, Title/Abstract, and Affiliation fields.
|
||||
|
||||
**Syntax**: `"search terms"[field:~N]`
|
||||
- N = maximum number of words between terms
|
||||
|
||||
**Examples**:
|
||||
```
|
||||
"vitamin C"[Title:~3] → vitamin within 3 words of C in title
|
||||
"breast cancer screening"[TIAB:~5] → terms within 5 words in title/abstract
|
||||
```
|
||||
|
||||
## Search Field Tags
|
||||
|
||||
Field tags limit searches to specific parts of PubMed records. Format: `term[tag]`
|
||||
|
||||
### Author Searching
|
||||
|
||||
| Tag | Field | Example |
|
||||
|-----|-------|---------|
|
||||
| [au] | Author | smith j[au] |
|
||||
| [1au] | First Author | jones m[1au] |
|
||||
| [lastau] | Last Author | wilson k[lastau] |
|
||||
| [fau] | Full Author Name | smith john a[fau] |
|
||||
|
||||
**Author Search Notes**:
|
||||
- Full author names searchable from 2002 forward
|
||||
- Format: last name + initials (e.g., `smith ja[au]`)
|
||||
- Can search without field tag, but [au] ensures accuracy
|
||||
|
||||
**Corporate Authors**:
|
||||
Search organizations as authors:
|
||||
```
|
||||
world health organization[au]
|
||||
```
|
||||
|
||||
### Title and Abstract
|
||||
|
||||
| Tag | Field | Example |
|
||||
|-----|-------|---------|
|
||||
| [ti] | Title | diabetes[ti] |
|
||||
| [ab] | Abstract | treatment[ab] |
|
||||
| [tiab] | Title/Abstract | cancer screening[tiab] |
|
||||
| [tw] | Text Word | cardiovascular[tw] |
|
||||
|
||||
**Notes**:
|
||||
- [tw] searches title, abstract, and other text fields
|
||||
- [tiab] is most commonly used for comprehensive searching
|
||||
|
||||
### Journal Information
|
||||
|
||||
| Tag | Field | Example |
|
||||
|-----|-------|---------|
|
||||
| [ta] | Journal Title Abbreviation | Science[ta] |
|
||||
| [jour] | Journal | New England Journal of Medicine[jour] |
|
||||
| [issn] | ISSN | 0028-4793[issn] |
|
||||
|
||||
### Date Fields
|
||||
|
||||
| Tag | Field | Format | Example |
|
||||
|-----|-------|--------|---------|
|
||||
| [dp] | Publication Date | YYYY/MM/DD | 2023[dp] |
|
||||
| [edat] | Entrez Date | YYYY/MM/DD | 2023/01/15[edat] |
|
||||
| [crdt] | Create Date | YYYY/MM/DD | 2023[crdt] |
|
||||
| [mhda] | MeSH Date | YYYY/MM/DD | 2023[mhda] |
|
||||
|
||||
**Date Ranges**:
|
||||
Use colon to specify ranges:
|
||||
```
|
||||
2020:2023[dp] → publications from 2020 to 2023
|
||||
2023/01/01:2023/06/30[dp] → first half of 2023
|
||||
```
|
||||
|
||||
**Relative Dates**:
|
||||
PubMed filters provide common ranges:
|
||||
- Last 1 year
|
||||
- Last 5 years
|
||||
- Last 10 years
|
||||
- Custom date range
|
||||
|
||||
### MeSH and Subject Headings
|
||||
|
||||
| Tag | Field | Example |
|
||||
|-----|-------|---------|
|
||||
| [mh] | MeSH Terms | diabetes mellitus[mh] |
|
||||
| [majr] | MeSH Major Topic | hypertension[majr] |
|
||||
| [mesh] | MeSH Terms | cancer[mesh] |
|
||||
| [sh] | MeSH Subheading | therapy[sh] |
|
||||
|
||||
**MeSH Searching**:
|
||||
- Medical Subject Headings provide controlled vocabulary
|
||||
- [mh] includes narrower terms automatically
|
||||
- [majr] limits to articles where topic is main focus
|
||||
- Combine with subheadings: `diabetes mellitus/therapy[mh]`
|
||||
|
||||
**Common MeSH Subheadings**:
|
||||
- /diagnosis
|
||||
- /drug therapy
|
||||
- /epidemiology
|
||||
- /etiology
|
||||
- /prevention & control
|
||||
- /therapy
|
||||
|
||||
### Publication Types
|
||||
|
||||
| Tag | Field | Example |
|
||||
|-----|-------|---------|
|
||||
| [pt] | Publication Type | clinical trial[pt] |
|
||||
| [ptyp] | Publication Type | review[ptyp] |
|
||||
|
||||
**Common Publication Types**:
|
||||
- Clinical Trial
|
||||
- Meta-Analysis
|
||||
- Randomized Controlled Trial
|
||||
- Review
|
||||
- Systematic Review
|
||||
- Case Reports
|
||||
- Letter
|
||||
- Editorial
|
||||
- Guideline
|
||||
|
||||
**Example**:
|
||||
```
|
||||
cancer AND systematic review[pt]
|
||||
```
|
||||
|
||||
### Other Useful Fields
|
||||
|
||||
| Tag | Field | Example |
|
||||
|-----|-------|---------|
|
||||
| [la] | Language | english[la] |
|
||||
| [affil] | Affiliation | harvard[affil] |
|
||||
| [pmid] | PubMed ID | 12345678[pmid] |
|
||||
| [pmc] | PMC ID | PMC123456[pmc] |
|
||||
| [doi] | DOI | 10.1234/example[doi] |
|
||||
| [gr] | Grant Number | R01CA123456[gr] |
|
||||
| [isbn] | ISBN | 9780123456789[isbn] |
|
||||
| [pg] | Pagination | 123-145[pg] |
|
||||
| [vi] | Volume | 45[vi] |
|
||||
| [ip] | Issue | 3[ip] |
|
||||
|
||||
### Supplemental Concepts
|
||||
|
||||
| Tag | Field | Example |
|
||||
|-----|-------|---------|
|
||||
| [nm] | Substance Name | aspirin[nm] |
|
||||
| [ps] | Personal Name | darwin charles[ps] |
|
||||
|
||||
## Automatic Term Mapping (ATM)
|
||||
|
||||
When searching without field tags, PubMed automatically:
|
||||
|
||||
1. **Searches MeSH translation table** for matching MeSH terms
|
||||
2. **Searches journal translation table** for journal names
|
||||
3. **Searches author index** for author names
|
||||
4. **Searches full text** for remaining terms
|
||||
|
||||
**Bypass ATM**:
|
||||
- Use double quotes: `"breast cancer"`
|
||||
- Use field tags: `breast cancer[tiab]`
|
||||
|
||||
**View Translation**:
|
||||
Use Advanced Search to see how PubMed translated your query in the Search Details box.
|
||||
|
||||
## Filters and Limits
|
||||
|
||||
### Article Types
|
||||
- Clinical Trial
|
||||
- Meta-Analysis
|
||||
- Randomized Controlled Trial
|
||||
- Review
|
||||
- Systematic Review
|
||||
|
||||
### Text Availability
|
||||
- Free full text
|
||||
- Full text
|
||||
- Abstract
|
||||
|
||||
### Publication Date
|
||||
- Last 1 year
|
||||
- Last 5 years
|
||||
- Last 10 years
|
||||
- Custom date range
|
||||
|
||||
### Species
|
||||
- Humans
|
||||
- Animals (specific species available)
|
||||
|
||||
### Sex
|
||||
- Female
|
||||
- Male
|
||||
|
||||
### Age Groups
|
||||
- Child (0-18 years)
|
||||
- Infant (birth-23 months)
|
||||
- Child, Preschool (2-5 years)
|
||||
- Child (6-12 years)
|
||||
- Adolescent (13-18 years)
|
||||
- Adult (19+ years)
|
||||
- Aged (65+ years)
|
||||
- 80 and over
|
||||
|
||||
### Languages
|
||||
- English
|
||||
- Spanish
|
||||
- French
|
||||
- German
|
||||
- Chinese
|
||||
- And many others
|
||||
|
||||
### Other Filters
|
||||
- Journal categories
|
||||
- Subject area
|
||||
- Article attributes (e.g., has abstract, free PMC article)
|
||||
|
||||
## Advanced Search Strategies
|
||||
|
||||
### Clinical Queries
|
||||
PubMed provides specialized filters for clinical research:
|
||||
|
||||
**Study Categories**:
|
||||
- Therapy (narrow/broad)
|
||||
- Diagnosis (narrow/broad)
|
||||
- Etiology (narrow/broad)
|
||||
- Prognosis (narrow/broad)
|
||||
- Clinical prediction guides
|
||||
|
||||
**Medical Genetics**:
|
||||
- Diagnosis
|
||||
- Differential diagnosis
|
||||
- Clinical description
|
||||
- Management
|
||||
- Genetic counseling
|
||||
|
||||
### Hedges and Filters
|
||||
Pre-built search strategies for specific purposes:
|
||||
- Systematic review filters
|
||||
- Quality filters for study types
|
||||
- Geographic filters
|
||||
|
||||
### Combining Searches
|
||||
Use Advanced Search to combine previous queries:
|
||||
```
|
||||
#1 AND #2
|
||||
#3 OR #4
|
||||
#5 NOT #6
|
||||
```
|
||||
|
||||
### Search History
|
||||
- Saves up to 100 searches
|
||||
- Expires after 8 hours of inactivity
|
||||
- Access via Advanced Search page
|
||||
- Combine using # references
|
||||
|
||||
## Best Practices
|
||||
|
||||
### 1. Start Broad, Then Narrow
|
||||
Begin with general terms and add specificity:
|
||||
```
|
||||
diabetes → too broad
|
||||
diabetes mellitus type 2 → better
|
||||
diabetes mellitus type 2[mh] AND treatment[tiab] → more specific
|
||||
```
|
||||
|
||||
### 2. Use Synonyms with OR
|
||||
Include alternative terms:
|
||||
```
|
||||
heart attack OR myocardial infarction OR MI
|
||||
```
|
||||
|
||||
### 3. Combine Concepts with AND
|
||||
Link different aspects of your research question:
|
||||
```
|
||||
(heart attack OR myocardial infarction) AND (aspirin OR acetylsalicylic acid) AND prevention
|
||||
```
|
||||
|
||||
### 4. Leverage MeSH Terms
|
||||
Use MeSH for consistent indexing:
|
||||
```
|
||||
diabetes mellitus[mh] AND hypertension[mh]
|
||||
```
|
||||
|
||||
### 5. Use Filters Strategically
|
||||
Apply filters to refine results:
|
||||
- Publication date for recent research
|
||||
- Article type for specific study designs
|
||||
- Free full text for accessible articles
|
||||
|
||||
### 6. Review Search Details
|
||||
Check how PubMed interpreted your search in Advanced Search to ensure accuracy.
|
||||
|
||||
### 7. Save Effective Searches
|
||||
Create My NCBI account to:
|
||||
- Save searches
|
||||
- Set up email alerts
|
||||
- Create collections
|
||||
|
||||
## Common Search Patterns
|
||||
|
||||
### Systematic Review Search
|
||||
```
|
||||
(breast cancer[tiab] OR breast neoplasm[mh]) AND (screening[tiab] OR early detection[tiab]) AND systematic review[pt]
|
||||
```
|
||||
|
||||
### Clinical Trial Search
|
||||
```
|
||||
diabetes mellitus type 2[mh] AND metformin[nm] AND randomized controlled trial[pt] AND 2020:2024[dp]
|
||||
```
|
||||
|
||||
### Recent Research by Author
|
||||
```
|
||||
smith ja[au] AND cancer[tiab] AND 2023:2024[dp] AND english[la]
|
||||
```
|
||||
|
||||
### Drug Treatment Studies
|
||||
```
|
||||
hypertension[mh] AND (amlodipine[nm] OR losartan[nm]) AND drug therapy[sh] AND humans[mh]
|
||||
```
|
||||
|
||||
### Geographic-Specific Research
|
||||
```
|
||||
malaria[tiab] AND (africa[affil] OR african[tiab]) AND 2020:2024[dp]
|
||||
```
|
||||
|
||||
## Special Characters
|
||||
|
||||
| Character | Purpose | Example |
|
||||
|-----------|---------|---------|
|
||||
| * | Wildcard | colo*r |
|
||||
| " " | Phrase search | "breast cancer" |
|
||||
| ( ) | Group terms | (A OR B) AND C |
|
||||
| : | Range | 2020:2023[dp] |
|
||||
| - | Hyphenated terms | COVID-19 |
|
||||
| / | MeSH subheading | diabetes/therapy[mh] |
|
||||
|
||||
## Troubleshooting
|
||||
|
||||
### Too Many Results
|
||||
- Add more specific terms
|
||||
- Use field tags to limit search scope
|
||||
- Apply date restrictions
|
||||
- Use filters for article type
|
||||
- Add additional concepts with AND
|
||||
|
||||
### Too Few Results
|
||||
- Remove restrictive terms
|
||||
- Use OR to add synonyms
|
||||
- Check spelling and terminology
|
||||
- Remove field tags for broader search
|
||||
- Expand date range
|
||||
- Remove filters
|
||||
|
||||
### No Results
|
||||
- Check spelling using ESpell
|
||||
- Try alternative terminology
|
||||
- Remove field tags
|
||||
- Verify correct database (PubMed vs. PMC)
|
||||
- Broaden search terms
|
||||
|
||||
### Unexpected Results
|
||||
- Review Search Details to see query translation
|
||||
- Use field tags to prevent automatic term mapping
|
||||
- Check for common synonyms that may be included
|
||||
- Refine with additional limiting terms
|
||||
Reference in New Issue
Block a user