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

2. PubMatrix PubMatrix: batch text mining of the PubMed literature database Materials prepared by: Cynthia Foote, Ph.D. www.openhelix.com Updated: Q3 2010 Version 1.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 PubMatrix Agenda Introduction and Credits PubMatrix Registration Entering Search Terms Viewing Search Results Visual Display of Results Summary Exercises PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Introduction List of Interesting Genes/Proteins (from high-throughput studies) GWAS Array Technology Large-scale proteomic studies Systems Biology Process and Function Information (from various public databases) Genome Browsers Species- or Taxa- Specific Databases Model Organism Databases Other repositories

5. Copyright OpenHelix. No use or reproduction without express written consent5 PubMed Search PubMed does have search feature Queries done individually Results are Lists of Publications

6. Copyright OpenHelix. No use or reproduction without express written consent6 PubMatrix Introduction Two keyword lists are compared through the PubMed database Interactive Reports show frequency of co-occurrence between any two keywords PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/ “…Lists of terms can be anything; gene names, diseases, gene functions, authors... pretty much anything. The user can then quickly sort or browse the frequency matrix table to do individual searches independently. ”

7. Copyright OpenHelix. No use or reproduction without express written consent7 PubMatrix Results Matrix Occurrence numbers are hyperlinked to show list of references

8. Copyright OpenHelix. No use or reproduction without express written consent8 Kevin G. Becker Tiffani J. Bright Chris Cheadle Douglas A. Hosack Glynn Dennis Jr. Richard A. Lempicki Jim Engel National Institute on Aging Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Fredrick, Inc. Gene Expression and Genomics Unit National Institutes of Health Credits PubMatrix Design and Development:

9. Copyright OpenHelix. No use or reproduction without express written consent9 Publications http://www.biomedcentral.com/content/pdf/1471-2105-4-61.pdf

10. Copyright OpenHelix. No use or reproduction without express written consent10 PubMatrix Agenda Introduction and Credits PubMatrix Registration Entering Search Terms Viewing Search Results Visual Display of Results Summary Exercises PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/

11. Copyright OpenHelix. No use or reproduction without express written consent11 User Registration Free to use But must register Click here

12. Copyright OpenHelix. No use or reproduction without express written consent12 Registration Window Need to enter email address to receive results and notifications via email Username Password Email

13. Copyright OpenHelix. No use or reproduction without express written consent13 Access Authenticated Site Authenticated site: http://pubmatrix.grc.nia.nih.gov/secure-bin/index.plhttp://pubmatrix.grc.nia.nih.gov/secure-bin/index.pl Click here Enter Username And Password Click here

14. Copyright OpenHelix. No use or reproduction without express written consent14 Top Navigation Bar

15. Copyright OpenHelix. No use or reproduction without express written consent15 Feedback Form Use to give developers feedback on tool Create Subject Heading Enter Feedback Comments Click Here

16. Copyright OpenHelix. No use or reproduction without express written consent16 Top Navigation Bar, cont.

17. Copyright OpenHelix. No use or reproduction without express written consent17 NIA DNA Array Unit Page Homepage for NIA- Gene Expression and Genomics Unit

18. Copyright OpenHelix. No use or reproduction without express written consent18 Top Navigation Bar, cont. 2

19. Copyright OpenHelix. No use or reproduction without express written consent19 Links Page Helpful Literature Mining Resources and Molecular/Genetic Databases Additional Literature Mining Resources Molecular/ Genetic Databases

20. Copyright OpenHelix. No use or reproduction without express written consent20 Top Navigation Bar, cont. 3

21. Copyright OpenHelix. No use or reproduction without express written consent21 Public Results Page Use to see possible search combinations Search and Modifier Term Combinations Re-run Search by Clicking Hyperlink

22. Copyright OpenHelix. No use or reproduction without express written consent22 Top Navigation Bar, cont. 4

23. Copyright OpenHelix. No use or reproduction without express written consent23 Past Results Page Shows last 50 searches run in PubMatrix. Use to archive searches

24. Copyright OpenHelix. No use or reproduction without express written consent24 PubMatrix Search Page

25. Copyright OpenHelix. No use or reproduction without express written consent25 PubMatrix Agenda Introduction and Credits PubMatrix Registration Entering Search Terms Viewing Search Results Visual Display of Results Summary Exercises PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/

26. Copyright OpenHelix. No use or reproduction without express written consent26 PubMatrix Search Click here to submit (scientist@openhelix.com)

27. Copyright OpenHelix. No use or reproduction without express written consent27 Enter Index Information 1) Enter index information about your search. Give your Search terms a title Give your Modifier terms a different title Y chromosome genes Y chromosome terms

28. Copyright OpenHelix. No use or reproduction without express written consent28 Enter Data 2) Upload or paste your delimited text file in the proper format.proper format Data is uploaded to PubMatrix in two separate.txt files, each must consist of one column of terms. SEARCH TERMS are the terms which will end up in the matrix on the left side, MODIFIER TERMS will end up across the top. Click Browse Choose file Terms entered into window must also be in single column

29. Copyright OpenHelix. No use or reproduction without express written consent29 Choose Notification Method 3) Choose if you want to be notified by email then press the "Submit to PubMatrix" button Searches will only be run from 5pm to 8am EST. Select Click here (scientist@openhelix.com)

30. Copyright OpenHelix. No use or reproduction without express written consent30 Results Pending Window will appear showing status of submission Gives important information: Run No., Date/Time Can choose to remove run

31. Copyright OpenHelix. No use or reproduction without express written consent31 Example Search Lists From “PubMatrix: a tool for multiplex literature mining” http://www.biomedcentral.com/content/pdf/1471-2105-4-61.pdf http://www.biomedcentral.com/content/pdf/1471-2105-4-61.pdf Useful examples of Search lists

32. Copyright OpenHelix. No use or reproduction without express written consent32 PubMatrix Agenda Introduction and Credits PubMatrix Registration Entering Search Terms Viewing Search Results Visual Display of Results Summary Exercises PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/

33. Copyright OpenHelix. No use or reproduction without express written consent33 Emailed Search Results Open attachment or Click on link provided to view PubMatrix results Open Attachment Click on Hyperlink scientist@openhelix.com

34. Copyright OpenHelix. No use or reproduction without express written consent34 View Past Results Click here

35. Copyright OpenHelix. No use or reproduction without express written consent35 Past Results Page Lists last 50 completed PubMatrix searches View results by clicking on link in Status column Click here For Results

36. Copyright OpenHelix. No use or reproduction without express written consent36 View Matrix Y chromosome genes in left column Y chromosome terms in top row Matrix numbers are hyperlinked to initiate de-novo search for that specific term combination Click here

37. Copyright OpenHelix. No use or reproduction without express written consent37 Literature Results PubMed lists the title and author for all publication matches

38. Copyright OpenHelix. No use or reproduction without express written consent38 User Options User can choose to Rerun or Remove Search.

39. Copyright OpenHelix. No use or reproduction without express written consent39 PubMatrix Agenda Introduction and Credits PubMatrix Registration Entering Search Terms Viewing Search Results Visual Display of Results Summary Exercises PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/

40. Copyright OpenHelix. No use or reproduction without express written consent40 Visualize Matrix Easily visualize results by creating a 3-D chart view Can use MS Excel, CLUSTER/TREE VIEW, or SPOTFIRE Copy all Data

41. Copyright OpenHelix. No use or reproduction without express written consent41 Data to MS Excel Paste copied matrix into MS Excel. Select entire matrix Select Chart Wizard Choose Column and 3-D chart Select Series in Rows Create title for Chart and X,Y and Z axis Create as a new sheet Chart Wizard Click here

42. Copyright OpenHelix. No use or reproduction without express written consent42 Excel 3-D Chart

43. Copyright OpenHelix. No use or reproduction without express written consent43 PubMatrix Agenda Introduction and Credits PubMatrix Registration Entering Search Terms Viewing Search Results Visual Display of Results Summary Exercises PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/

44. Copyright OpenHelix. No use or reproduction without express written consent44 (scientist@openhelix.com) PubMatrix Search Page

45. Copyright OpenHelix. No use or reproduction without express written consent45 Viewing Results Numbers are hyperlinked Search Terms Modifier Terms Number of Matches

46. Copyright OpenHelix. No use or reproduction without express written consent46 Visualization of Results Visualize matrix data with MS Excel, SPOTFIRE, or CLUSTER/TREEVIEW

47. Copyright OpenHelix. No use or reproduction without express written consent47 Medical Relevance http://physiolgenomics.physiology.org/cgi/content/full/23/2/192

48. Copyright OpenHelix. No use or reproduction without express written consent48 PubMatrix Summary

49. Copyright OpenHelix. No use or reproduction without express written consent49 PubMatrix Agenda PubMatrix: http://pubmatrix.grc.nia.nih.gov/http://pubmatrix.grc.nia.nih.gov/ Introduction and Credits PubMatrix Registration Entering Search Terms Viewing Search Results Visual Display of Results Summary Exercises

50. Copyright OpenHelix. No use or reproduction without express written consent50