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skills/pubmed-database/references/search_syntax.md
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skills/pubmed-database/references/search_syntax.md
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# PubMed Search Syntax and Field Tags
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## Boolean Operators
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PubMed supports standard Boolean operators to combine search terms:
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### AND
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Retrieves results containing all search terms. PubMed automatically applies AND between separate concepts.
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**Example**:
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```
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diabetes AND hypertension
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```
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### OR
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Retrieves results containing at least one of the search terms. Useful for synonyms or related concepts.
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**Example**:
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```
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heart attack OR myocardial infarction
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```
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### NOT
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Excludes results containing the specified term. Use cautiously as it may eliminate relevant results.
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**Example**:
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```
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cancer NOT lung
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```
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**Precedence**: Operations are processed left to right. Use parentheses to control evaluation order:
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```
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(heart attack OR myocardial infarction) AND treatment
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```
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## Phrase Searching
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### Double Quotes
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Enclose exact phrases in double quotes to search for terms in specific order:
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```
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"kidney allograft"
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"machine learning"
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"systematic review"
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```
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### Field Tags
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Alternative method using field tags:
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```
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kidney allograft[Title]
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```
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## Wildcards
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Use asterisk (*) to substitute for zero or more characters:
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**Rules**:
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- Minimum 4 characters before first wildcard
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- Matches word variations and plurals
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**Examples**:
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```
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vaccin* → matches vaccine, vaccination, vaccines, vaccinate
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pediatr* → matches pediatric, pediatrics, pediatrician
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colo*r → matches color, colour
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```
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**Limitations**:
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- Cannot use at beginning of search term
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- May retrieve unexpected variations
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## Proximity Searching
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Search for terms within a specified distance from each other. Only available in Title, Title/Abstract, and Affiliation fields.
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**Syntax**: `"search terms"[field:~N]`
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- N = maximum number of words between terms
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**Examples**:
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```
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"vitamin C"[Title:~3] → vitamin within 3 words of C in title
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"breast cancer screening"[TIAB:~5] → terms within 5 words in title/abstract
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```
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## Search Field Tags
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Field tags limit searches to specific parts of PubMed records. Format: `term[tag]`
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### Author Searching
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| Tag | Field | Example |
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|-----|-------|---------|
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| [au] | Author | smith j[au] |
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| [1au] | First Author | jones m[1au] |
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| [lastau] | Last Author | wilson k[lastau] |
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| [fau] | Full Author Name | smith john a[fau] |
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**Author Search Notes**:
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- Full author names searchable from 2002 forward
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- Format: last name + initials (e.g., `smith ja[au]`)
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- Can search without field tag, but [au] ensures accuracy
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**Corporate Authors**:
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Search organizations as authors:
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```
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world health organization[au]
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```
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### Title and Abstract
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| Tag | Field | Example |
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|-----|-------|---------|
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| [ti] | Title | diabetes[ti] |
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| [ab] | Abstract | treatment[ab] |
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| [tiab] | Title/Abstract | cancer screening[tiab] |
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| [tw] | Text Word | cardiovascular[tw] |
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**Notes**:
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- [tw] searches title, abstract, and other text fields
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- [tiab] is most commonly used for comprehensive searching
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### Journal Information
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| Tag | Field | Example |
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|-----|-------|---------|
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| [ta] | Journal Title Abbreviation | Science[ta] |
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| [jour] | Journal | New England Journal of Medicine[jour] |
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| [issn] | ISSN | 0028-4793[issn] |
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### Date Fields
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| Tag | Field | Format | Example |
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|-----|-------|--------|---------|
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| [dp] | Publication Date | YYYY/MM/DD | 2023[dp] |
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| [edat] | Entrez Date | YYYY/MM/DD | 2023/01/15[edat] |
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| [crdt] | Create Date | YYYY/MM/DD | 2023[crdt] |
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| [mhda] | MeSH Date | YYYY/MM/DD | 2023[mhda] |
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**Date Ranges**:
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Use colon to specify ranges:
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```
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2020:2023[dp] → publications from 2020 to 2023
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2023/01/01:2023/06/30[dp] → first half of 2023
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```
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**Relative Dates**:
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PubMed filters provide common ranges:
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- Last 1 year
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- Last 5 years
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- Last 10 years
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- Custom date range
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### MeSH and Subject Headings
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| Tag | Field | Example |
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|-----|-------|---------|
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| [mh] | MeSH Terms | diabetes mellitus[mh] |
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| [majr] | MeSH Major Topic | hypertension[majr] |
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| [mesh] | MeSH Terms | cancer[mesh] |
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| [sh] | MeSH Subheading | therapy[sh] |
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**MeSH Searching**:
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- Medical Subject Headings provide controlled vocabulary
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- [mh] includes narrower terms automatically
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- [majr] limits to articles where topic is main focus
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- Combine with subheadings: `diabetes mellitus/therapy[mh]`
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**Common MeSH Subheadings**:
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- /diagnosis
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- /drug therapy
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- /epidemiology
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- /etiology
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- /prevention & control
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- /therapy
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### Publication Types
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| Tag | Field | Example |
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|-----|-------|---------|
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| [pt] | Publication Type | clinical trial[pt] |
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| [ptyp] | Publication Type | review[ptyp] |
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**Common Publication Types**:
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- Clinical Trial
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- Meta-Analysis
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- Randomized Controlled Trial
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- Review
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- Systematic Review
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- Case Reports
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- Letter
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- Editorial
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- Guideline
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**Example**:
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```
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cancer AND systematic review[pt]
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```
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### Other Useful Fields
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| Tag | Field | Example |
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|-----|-------|---------|
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| [la] | Language | english[la] |
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| [affil] | Affiliation | harvard[affil] |
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| [pmid] | PubMed ID | 12345678[pmid] |
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| [pmc] | PMC ID | PMC123456[pmc] |
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| [doi] | DOI | 10.1234/example[doi] |
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| [gr] | Grant Number | R01CA123456[gr] |
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| [isbn] | ISBN | 9780123456789[isbn] |
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| [pg] | Pagination | 123-145[pg] |
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| [vi] | Volume | 45[vi] |
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| [ip] | Issue | 3[ip] |
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### Supplemental Concepts
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| Tag | Field | Example |
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|-----|-------|---------|
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| [nm] | Substance Name | aspirin[nm] |
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| [ps] | Personal Name | darwin charles[ps] |
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## Automatic Term Mapping (ATM)
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When searching without field tags, PubMed automatically:
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1. **Searches MeSH translation table** for matching MeSH terms
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2. **Searches journal translation table** for journal names
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3. **Searches author index** for author names
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4. **Searches full text** for remaining terms
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**Bypass ATM**:
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- Use double quotes: `"breast cancer"`
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- Use field tags: `breast cancer[tiab]`
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**View Translation**:
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Use Advanced Search to see how PubMed translated your query in the Search Details box.
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## Filters and Limits
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### Article Types
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- Clinical Trial
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- Meta-Analysis
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- Randomized Controlled Trial
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- Review
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- Systematic Review
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### Text Availability
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- Free full text
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- Full text
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- Abstract
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### Publication Date
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- Last 1 year
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- Last 5 years
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- Last 10 years
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- Custom date range
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### Species
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- Humans
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- Animals (specific species available)
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### Sex
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- Female
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- Male
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### Age Groups
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- Child (0-18 years)
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- Infant (birth-23 months)
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- Child, Preschool (2-5 years)
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- Child (6-12 years)
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- Adolescent (13-18 years)
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- Adult (19+ years)
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- Aged (65+ years)
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- 80 and over
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### Languages
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- English
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- Spanish
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- French
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- German
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- Chinese
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- And many others
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### Other Filters
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- Journal categories
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- Subject area
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- Article attributes (e.g., has abstract, free PMC article)
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## Advanced Search Strategies
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### Clinical Queries
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PubMed provides specialized filters for clinical research:
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**Study Categories**:
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- Therapy (narrow/broad)
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- Diagnosis (narrow/broad)
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- Etiology (narrow/broad)
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- Prognosis (narrow/broad)
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- Clinical prediction guides
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**Medical Genetics**:
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- Diagnosis
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- Differential diagnosis
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- Clinical description
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- Management
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- Genetic counseling
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### Hedges and Filters
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Pre-built search strategies for specific purposes:
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- Systematic review filters
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- Quality filters for study types
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- Geographic filters
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### Combining Searches
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Use Advanced Search to combine previous queries:
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```
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#1 AND #2
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#3 OR #4
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#5 NOT #6
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```
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### Search History
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- Saves up to 100 searches
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- Expires after 8 hours of inactivity
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- Access via Advanced Search page
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- Combine using # references
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## Best Practices
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### 1. Start Broad, Then Narrow
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Begin with general terms and add specificity:
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```
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diabetes → too broad
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diabetes mellitus type 2 → better
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diabetes mellitus type 2[mh] AND treatment[tiab] → more specific
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```
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### 2. Use Synonyms with OR
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Include alternative terms:
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```
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heart attack OR myocardial infarction OR MI
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```
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### 3. Combine Concepts with AND
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Link different aspects of your research question:
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```
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(heart attack OR myocardial infarction) AND (aspirin OR acetylsalicylic acid) AND prevention
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```
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### 4. Leverage MeSH Terms
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Use MeSH for consistent indexing:
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```
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diabetes mellitus[mh] AND hypertension[mh]
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```
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### 5. Use Filters Strategically
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Apply filters to refine results:
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- Publication date for recent research
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- Article type for specific study designs
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- Free full text for accessible articles
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### 6. Review Search Details
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Check how PubMed interpreted your search in Advanced Search to ensure accuracy.
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### 7. Save Effective Searches
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Create My NCBI account to:
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- Save searches
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- Set up email alerts
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- Create collections
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## Common Search Patterns
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### Systematic Review Search
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```
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(breast cancer[tiab] OR breast neoplasm[mh]) AND (screening[tiab] OR early detection[tiab]) AND systematic review[pt]
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```
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### Clinical Trial Search
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```
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diabetes mellitus type 2[mh] AND metformin[nm] AND randomized controlled trial[pt] AND 2020:2024[dp]
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```
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### Recent Research by Author
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```
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smith ja[au] AND cancer[tiab] AND 2023:2024[dp] AND english[la]
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```
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### Drug Treatment Studies
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```
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hypertension[mh] AND (amlodipine[nm] OR losartan[nm]) AND drug therapy[sh] AND humans[mh]
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```
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### Geographic-Specific Research
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```
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malaria[tiab] AND (africa[affil] OR african[tiab]) AND 2020:2024[dp]
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```
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## Special Characters
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| Character | Purpose | Example |
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|-----------|---------|---------|
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| * | Wildcard | colo*r |
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| " " | Phrase search | "breast cancer" |
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| ( ) | Group terms | (A OR B) AND C |
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| : | Range | 2020:2023[dp] |
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| - | Hyphenated terms | COVID-19 |
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| / | MeSH subheading | diabetes/therapy[mh] |
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## Troubleshooting
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### Too Many Results
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- Add more specific terms
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- Use field tags to limit search scope
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- Apply date restrictions
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- Use filters for article type
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- Add additional concepts with AND
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### Too Few Results
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- Remove restrictive terms
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- Use OR to add synonyms
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- Check spelling and terminology
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- Remove field tags for broader search
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- Expand date range
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- Remove filters
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### No Results
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- Check spelling using ESpell
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- Try alternative terminology
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- Remove field tags
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- Verify correct database (PubMed vs. PMC)
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- Broaden search terms
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### Unexpected Results
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- Review Search Details to see query translation
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- Use field tags to prevent automatic term mapping
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- Check for common synonyms that may be included
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- Refine with additional limiting terms
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Reference in New Issue
Block a user