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NCBI Entrez Overview Entrez: NCBI’s Universal Search and Retrieval System Materials prepared by: Cynthia Perreault-Micale, Ph.D. Karin Schinkmann, Ph.D. Updated: Q Version 2
Copyright OpenHelix. No use or reproduction without express written consent3 Entrez Overview Agenda Introduction and Credits Basic Search Advanced Search Complex Boolean Search My NCBI and Other Entrez Tools Summary Exercises NCBI Entrez:
Copyright OpenHelix. No use or reproduction without express written consent4 Entrez: NCBI’s Search and Retrieval System More than 30 databases Results displayed in organized reports Use My NCBI options to customize searches across databases
Copyright OpenHelix. No use or reproduction without express written consent5 Entrez Databases – An Interlinked Network
Copyright OpenHelix. No use or reproduction without express written consent6 Help and Documentation Help documentation is available at: The NCBI Handbook: an overview and history of the development of Entrez, written by Jim Ostell: Entrez Tutorial, by Renata Geer and Eric Sayers:
Copyright OpenHelix. No use or reproduction without express written consent7 Entrez Citation
Copyright OpenHelix. No use or reproduction without express written consent8 Entrez Overview Agenda Introduction and Credits Basic Search Advanced Search Complex Boolean Search My NCBI and Other Entrez Tools Summary Exercises NCBI Entrez:
Copyright OpenHelix. No use or reproduction without express written consent9 Entrez Global Search – Accessing Search Page click
Copyright OpenHelix. No use or reproduction without express written consent10 Literature databases Molecular databases NCBI services Search Function Back to NCBI Entrez Cross-database Search Page
Copyright OpenHelix. No use or reproduction without express written consent11 Entrez: Global Search Example Enter your search term Click “GO” Parkinson’s disease Help Links
Copyright OpenHelix. No use or reproduction without express written consent12 Entrez: Basic Search Overview No hits Incomplete hit Number of hits Click here Explanation OMIA See Details Click here
Copyright OpenHelix. No use or reproduction without express written consent13 Basic Search: Common Elements Entrez Database Results Search Results, Common Elements (Nucleotide vs. Protein) Database specific banner My NCBI Sign In Area Entrez Search Window and Filter Tabs Database Display Options and default database specific filter tabs Results
Copyright OpenHelix. No use or reproduction without express written consent14 Basic Search: Displays Change Display
Copyright OpenHelix. No use or reproduction without express written consent15 Basic Search: Connectivity Change Display
Copyright OpenHelix. No use or reproduction without express written consent16 Clipboard Basic Search: Display Options
Copyright OpenHelix. No use or reproduction without express written consent17 Basic Search: Display Options - Saving Searches Save in My NCBI
Copyright OpenHelix. No use or reproduction without express written consent18 Basic Search: Report Links Blink Conserved Domains Links
Copyright OpenHelix. No use or reproduction without express written consent19 Basic Search: Individual Reports - Controls Report Change region Change view Tools & structure Display links Recent history Report Controls
Copyright OpenHelix. No use or reproduction without express written consent20 Entrez Overview Agenda Introduction and Credits Basic Search Advanced Search Complex Boolean Search My NCBI and Other Entrez Tools Summary Exercises NCBI Entrez:
Copyright OpenHelix. No use or reproduction without express written consent21 Entrez: Advanced Search Functions Entrez search tabs: LIMITS: exclude or include specific types of records PREVIEW / INDEX: select field, indexed terms HISTORY: Combine searches using “AND, OR, and NOT” DETAILS: view search details CLIPBOARD: save searches temporarily
Copyright OpenHelix. No use or reproduction without express written consent22 Entrez Advanced Search: Limits Go Limits can be set to filter your results for exactly what you want! Date
Copyright OpenHelix. No use or reproduction without express written consent23 Entrez Advanced Search: Preview/Index Click
Copyright OpenHelix. No use or reproduction without express written consent24 Entrez Advanced Search: Results Click Search Results
Copyright OpenHelix. No use or reproduction without express written consent25 Entrez Overview Agenda Introduction and Credits Basic Search Advanced Search Complex Boolean Search My NCBI and Other Entrez Tools Summary Exercises NCBI Entrez:
Copyright OpenHelix. No use or reproduction without express written consent26 “Parkinson’s disease” AND “human”[Organism] NOT isoform Complex Boolean Search: Syntax Boolean Operators (AND, NOT, OR) Field qualifier Wildcard: Parkin* Quotes: “Parkinson’s disease” “Parkinson’s disease” AND conserved domain OR kinase “Parkinson’s disease” AND (conserved domain OR kinase) Parenthesis
Copyright OpenHelix. No use or reproduction without express written consent27 Field Qualifiers – Availability, Formats and Help Several formats may be accepted for the same field qualifier For example, [Organism] or [ORGN], [AUTH] or [AUTHOR] Availability varies between databases
Copyright OpenHelix. No use or reproduction without express written consent28 Complex Boolean Search: Example “Parkinson’s disease” AND (Cell[Journal] OR kinase) No field qualifier - search of “All Fields”
Copyright OpenHelix. No use or reproduction without express written consent29 Entrez Overview Agenda Introduction and Credits Basic Search Advanced Search Complex Boolean Search My NCBI and Other Entrez Tools Summary Exercises NCBI Entrez:
Copyright OpenHelix. No use or reproduction without express written consent30 My NCBI allows you to: Select filters Save searches Automatically send search results to your Highlight search terms Order documents Sign In My NCBI: Sign In or Register
Copyright OpenHelix. No use or reproduction without express written consent31 My NCBI: Select Database
Copyright OpenHelix. No use or reproduction without express written consent32 My NCBI: Select Filters Leave Add Remove Add Filters will now be Bacteria, DDBL/EMBL/GenBank, Eukaryotes and Links to Protein Structures
Copyright OpenHelix. No use or reproduction without express written consent33 My NCBI: Example Go
Copyright OpenHelix. No use or reproduction without express written consent34 My NCBI: Display and Combine Subsets Go
Copyright OpenHelix. No use or reproduction without express written consent35 My NCBI: Display and Combine Subsets, cont. Save
Copyright OpenHelix. No use or reproduction without express written consent36 My NCBI: Saving Searches Search parameters Edit Name Save Set frequency Records format format Save Number
Copyright OpenHelix. No use or reproduction without express written consent37 My NCBI: Saving Searches, cont. Show What’s New
Copyright OpenHelix. No use or reproduction without express written consent38 My NCBI: Preferences Sign up for Save Highlight search terms
Copyright OpenHelix. No use or reproduction without express written consent39 My NCBI: Preferences
Copyright OpenHelix. No use or reproduction without express written consent40 More Entrez Tools
Copyright OpenHelix. No use or reproduction without express written consent41 Entrez Overview Agenda Introduction and Credits Basic Search Advanced Search Complex Boolean Search My NCBI and Other Entrez Tools Summary Exercises NCBI Entrez:
Copyright OpenHelix. No use or reproduction without express written consent42 Entrez: NCBI’s Search and Retrieval System More than 30 databases
Copyright OpenHelix. No use or reproduction without express written consent43 Entrez: Detailed Results, An Interlinked Network Results offer many options Internal and external links Internal External
Copyright OpenHelix. No use or reproduction without express written consent44 Entrez Overview Agenda Introduction and Credits Basic Search Advanced Search Complex Boolean Search My NCBI and Other Entrez Tools Summary Exercises NCBI Entrez:
Copyright OpenHelix. No use or reproduction without express written consent45