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NCBI PubMed NCBI PubMed: Finding the Literature You Need Materials prepared by: Cynthia Perreault-Micale, Ph.D. Jennifer Williams, Ph.D. Updated: Q2 2012
Copyright OpenHelix. No use or reproduction without express written consent3 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Copyright OpenHelix. No use or reproduction without express written consent4 PubMed Overview contains millions of abstracts from thousands of journals covers diverse topics within the biomedical field citations come mostly from MEDLINE allows efficient searching of the biomedical literature is linked to many other databases
Copyright OpenHelix. No use or reproduction without express written consent5 PubMed Homepage: Features Help Search Function Tools Additional Links My NCBI Help More Resources
Copyright OpenHelix. No use or reproduction without express written consent PubMed Homepage: More Features & Help 6 Help NCBI Help Other NCBI Resources
Copyright OpenHelix. No use or reproduction without express written consent7 PubMed: Reference and Citation
Copyright OpenHelix. No use or reproduction without express written consent8 PubMed: Member of Entrez Interlinked Network Over 40 molecular and literature databases in Entrez system Enter Search term Click
Copyright OpenHelix. No use or reproduction without express written consent9 Global Query: Results in All Databases PubMed Results across all Entrez databases Click ? for database description One query Click database, icon, or # of results to view
Copyright OpenHelix. No use or reproduction without express written consent10 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Copyright OpenHelix. No use or reproduction without express written consent11 Beginning a Basic Search: NCBI Homepage Enter search term & then click Search OR click Search to go to PubMed’s homepage PubMed
Copyright OpenHelix. No use or reproduction without express written consent12 Beginning a Basic Search: PubMed Homepage Our search example will be nerve regeneration auto-complete menu takes you to results Turn off Enter Search term
matches Basic Search: Results header 13Copyright OpenHelix. No use or reproduction without express written consent # of Results Display Settings Click here
Copyright OpenHelix. No use or reproduction without express written consent14 Formatting Options Basic information - authors, title, journal, citation status Summary Format
Copyright OpenHelix. No use or reproduction without express written consent15 More Formatting Options Summary (text) Abstract PMID List Abstract (text) MEDLINE XML
Copyright OpenHelix. No use or reproduction without express written consent16 Outputting Results Also saves search in My NCBI Send to
Copyright OpenHelix. No use or reproduction without express written consent17 Results Filters All Manage Filters Filters: click to view subsets of results Review Full Text Select confirm
Copyright OpenHelix. No use or reproduction without express written consent18 More Information Related Titles Free full-text Find data Search details Recent activity
Copyright OpenHelix. No use or reproduction without express written consent19 Article Report Also MeSH Terms for older papers
Copyright OpenHelix. No use or reproduction without express written consent20 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Advanced search click Help tip Copyright OpenHelix. No use or reproduction without express written consent21 Advanced Search Builder
Copyright OpenHelix. No use or reproduction without express written consent22 Advanced Search Builder, cont. count
Copyright OpenHelix. No use or reproduction without express written consent23 Advanced Search Builder: Edit & Results Either Build area or Edit area is active, Not both Search Builder area is now gone Manually add search criteria
click Copyright OpenHelix. No use or reproduction without express written consent24 Specialized Queries - MeSH MeSH terms can improve searches Not immediately available upon publication heart attack click
Copyright OpenHelix. No use or reproduction without express written consent25 MeSH Query Results entry terms hierarchy MeSH term subheadings Search options
Copyright OpenHelix. No use or reproduction without express written consent26 MeSH Query PubMed Results Search = myocardial infarction AND (diet therapy OR drug therapy OR economics) AND genetics Results = 90 hits (vs 183,000+ for “heart attack”)
Copyright OpenHelix. No use or reproduction without express written consent27 Journal & Single Citation Searches A tool to find a PubMed article
Copyright OpenHelix. No use or reproduction without express written consent28 Clinical Queries Search for “pancreatic cancer” Focused clinical results
Copyright OpenHelix. No use or reproduction without express written consent29 Topic-Specific Queries Queries for many topics in PubMed
Copyright OpenHelix. No use or reproduction without express written consent30 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Copyright OpenHelix. No use or reproduction without express written consent31 (lee hk[AU] AND "Journal of Neurochemistry"[TA]) AND “nerve regeneration” Complex Boolean Search: Syntax Boolean Operators (AND, NOT, OR) Field Qualifiers: Author = [AU], Journal Title = [TA] Parenthesis Quotes: “nerve regeneration” Wildcard: regen* = regenerate or regeneration No Field Qualifier = All Fields or [ALL] See Search details
Copyright OpenHelix. No use or reproduction without express written consent32 Complex Boolean Search: Field Qualifiers Common field qualifiers: Author = [AU] Journal Title = [TA] Title = [TI] Text Words = [TW] Qualifier Tags Field Descriptions
Search: (Rapoport t[AU] AND cell[TA]) AND Harvard[AD] Copyright OpenHelix. No use or reproduction without express written consent33 Complex Boolean Search: Example Edit your query here and click on Search
Copyright OpenHelix. No use or reproduction without express written consent34 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Copyright OpenHelix. No use or reproduction without express written consent35 username My NCBI: Sign In or Register password
Copyright OpenHelix. No use or reproduction without express written consent36 My NCBI includes: Search databases My Bibliography Recent Activity Save Searches Collections Filters Customization options My NCBI
Copyright OpenHelix. No use or reproduction without express written consent37 Customization Basic search My Bibliography Recent Activity Collections Saved Searches Filters NCBI Search BLAST
Copyright OpenHelix. No use or reproduction without express written consent38 Bibliography Build bibliography from PubMed results Bibliography help:
Copyright OpenHelix. No use or reproduction without express written consent39 Saved Searches BioSystem saved searches PubMed saved searches
Copyright OpenHelix. No use or reproduction without express written consent40 Collections Permanent collections, by default Created collections, Send to option Collections include: My Bibliography Favorites Other Citations User-created Collections
Copyright OpenHelix. No use or reproduction without express written consent41 Collections Basic PubMed Filters
Chemical Info Molecular DB Gender Clinical queries Books links Gene links Copyright OpenHelix. No use or reproduction without express written consent42 Filters My NCBI: Adding Power to Your NCBI & PubMed Searches bioinformatics education Counts
Copyright OpenHelix. No use or reproduction without express written consent43 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Copyright OpenHelix. No use or reproduction without express written consent44 PubMed Homepage Services: New & Noteworthy For further info on versioning also see:
Copyright OpenHelix. No use or reproduction without express written consent45 PubMed Homepage Services: Batch Matcher upload PubMed or PubMed Central enter
Copyright OpenHelix. No use or reproduction without express written consent46 PubMed Homepage Services: E-Utilities Next slide
Copyright OpenHelix. No use or reproduction without express written consent47 PubMed Homepage Services: LinkOut More info Single Citations, Abstract display
Copyright OpenHelix. No use or reproduction without express written consent48 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Copyright OpenHelix. No use or reproduction without express written consent49 PubMed Summary PubMed: contains millions of abstracts covers diverse topics within the biomedical field is linked to many other databases allows basic, advanced and specialized search strategies can be customized using My NCBI
Copyright OpenHelix. No use or reproduction without express written consent50 Sophisticated Search & Display Options Display Settings Output Options Basic Search Results Advanced Searches Specialized Searches Additional Information
Copyright OpenHelix. No use or reproduction without express written consent51 Powerful Additional Features E-Utilities For programmers My NCBI accounts Bibliography
Copyright OpenHelix. No use or reproduction without express written consent52 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : or
Copyright OpenHelix. No use or reproduction without express written consent53