1. Copyright OpenHelix. No use or reproduction without express written consent1

2. NCBI Entrez Overview Entrez: NCBI’s Universal Search and Retrieval System Materials prepared by: Cynthia Perreault-Micale, Ph.D. Karin Schinkmann, Ph.D. www.openhelix.com Updated: Q2 2010 Version 2

3. 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: http://www.ncbi.nlm.nih.gov/Entrez

4. 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

5. Copyright OpenHelix. No use or reproduction without express written consent5 Entrez Databases – An Interlinked Network http://www.ncbi.nlm.nih.gov/Database/datamodel/

6. Copyright OpenHelix. No use or reproduction without express written consent6 Help and Documentation Help documentation is available at: http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html  The NCBI Handbook: an overview and history of the development of Entrez, written by Jim Ostell: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.ch15 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.ch15  Entrez Tutorial, by Renata Geer and Eric Sayers: http://www.ncbi.nlm.nih.gov/Entrez/tutor.html

7. Copyright OpenHelix. No use or reproduction without express written consent7 Entrez Citation http://nar.oxfordjournals.org/cgi/reprint/37/suppl_1/D5

8. 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: http://www.ncbi.nlm.nih.gov/Entrez

9. Copyright OpenHelix. No use or reproduction without express written consent9 Entrez Global Search – Accessing Search Page http://www.ncbi.nlm.nih.gov/ click

10. 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

11. 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

12. 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

13. 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

14. Copyright OpenHelix. No use or reproduction without express written consent14 Basic Search: Displays Change Display

15. Copyright OpenHelix. No use or reproduction without express written consent15 Basic Search: Connectivity Change Display

16. Copyright OpenHelix. No use or reproduction without express written consent16 Clipboard Basic Search: Display Options

17. Copyright OpenHelix. No use or reproduction without express written consent17 Basic Search: Display Options - Saving Searches Save in My NCBI

18. Copyright OpenHelix. No use or reproduction without express written consent18 Basic Search: Report Links Blink Conserved Domains Links

19. 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

20. 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: http://www.ncbi.nlm.nih.gov/Entrez

21. 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

22. 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

23. Copyright OpenHelix. No use or reproduction without express written consent23 Entrez Advanced Search: Preview/Index Click

24. Copyright OpenHelix. No use or reproduction without express written consent24 Entrez Advanced Search: Results Click Search Results

25. 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: http://www.ncbi.nlm.nih.gov/Entrez

26. 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

27. 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 http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpentrez&part=EntrezHelp&rendertype=table&id=EntrezHelp.T6 http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpentrez&part=EntrezHelp&rendertype=table&id=EntrezHelp.T8

28. 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”

29. 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: http://www.ncbi.nlm.nih.gov/Entrez

30. 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 email Highlight search terms Order documents Sign In My NCBI: Sign In or Register

31. Copyright OpenHelix. No use or reproduction without express written consent31 My NCBI: Select Database

32. 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

33. Copyright OpenHelix. No use or reproduction without express written consent33 My NCBI: Example Go

34. Copyright OpenHelix. No use or reproduction without express written consent34 My NCBI: Display and Combine Subsets Go

35. Copyright OpenHelix. No use or reproduction without express written consent35 My NCBI: Display and Combine Subsets, cont. Save

36. Copyright OpenHelix. No use or reproduction without express written consent36 My NCBI: Saving Searches Search parameters Edit Name Save Set frequency Records format Email format Save Number

37. Copyright OpenHelix. No use or reproduction without express written consent37 My NCBI: Saving Searches, cont. Show What’s New

38. Copyright OpenHelix. No use or reproduction without express written consent38 My NCBI: Preferences Sign up for email Save Highlight search terms

39. Copyright OpenHelix. No use or reproduction without express written consent39 My NCBI: Preferences

40. Copyright OpenHelix. No use or reproduction without express written consent40 More Entrez Tools

41. 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: http://www.ncbi.nlm.nih.gov/Entrez

42. Copyright OpenHelix. No use or reproduction without express written consent42 Entrez: NCBI’s Search and Retrieval System http://www.ncbi.nlm.nih.gov/ More than 30 databases

43. 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

44. 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: http://www.ncbi.nlm.nih.gov/Entrez

45. Copyright OpenHelix. No use or reproduction without express written consent45