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

2. Classic Reactome Classic Reactome Legacy Site A Knowledgebase of Biological Processes Materials prepared by: Mary Mangan, Ph.D. Karin Schinkmann, Ph.D. www.openhelix.com Updated: Q2 2011 Version 1

3. Introduction and Credits Basic Keyword Search Selecting a Pathway Understanding Results Other Reactome Tools Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent3 Reactome Legacy Agenda Classic Reactome: http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1

4. Copyright OpenHelix. No use or reproduction without express written consent4 Introduction to Classic Reactome Reactome: a knowledgebase of biological processes Curated by scientists Pathways, reactions, participants, and chemical entities http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1

5. Copyright OpenHelix. No use or reproduction without express written consent5 Reactome Credits Overview Reactome Team Scientific Advisory Board http://www.reactome.org/about.html

6. Copyright OpenHelix. No use or reproduction without express written consent6 Curation Information Reactome editors and Board choose topics Expert scientists: bench biologists author “modules”; like a mini-review Reactome staff check, refine, add Data is reviewed by peer reviewers, and periodically re- examined and updated

7. Copyright OpenHelix. No use or reproduction without express written consent7 Data Content Curation emphasis = human pathways Non-human data may be used to infer reactions Computationally predicted from human  others

8. Copyright OpenHelix. No use or reproduction without express written consent8 Table of Contents Overview of the whole collection New modules are indicated

9. Copyright OpenHelix. No use or reproduction without express written consent9 Editorial Calendar Planned future content You can add your input!

10. Copyright OpenHelix. No use or reproduction without express written consent10 Schema Details Data model for verbal description Schema for the “blueprint”

11. Copyright OpenHelix. No use or reproduction without express written consent11 User Guide and Literature User Guide available Citing page has references, and guide to citing Reactome See the Reactome references for additional detail http://pid.nci.nih.gov/PID/2007/ 071211/full/pid.2007.3.shtml

12. Copyright OpenHelix. No use or reproduction without express written consent12 Reactome Legacy Agenda Classic Reactome: http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1 Introduction and Credits Basic Keyword Search Selecting a Pathway Understanding Results Other Reactome Tools Summary Exercises

13. Copyright OpenHelix. No use or reproduction without express written consent13 Classic Reactome Homepage Navigation options Useful information News Search Options keywords click maps click titles http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1

14. Copyright OpenHelix. No use or reproduction without express written consent14 Keyword Basic Searches Keywords to find data Make choices, send query to the database Sample query: cell cycle in Homo sapiens

15. Copyright OpenHelix. No use or reproduction without express written consent15 Results “cell cycle” query is displayed Keyword(s) highlighted Choices of data types to examine “Show” to view a specific results group Click to view record Results Categories “Show” a selected group of results Many pages Pathway

16. Copyright OpenHelix. No use or reproduction without express written consent16 Results - Reactions & Proteins Reactions Proteins Show

17. Copyright OpenHelix. No use or reproduction without express written consent17 Results - “Others” Others Complex Activation Literature

18. Copyright OpenHelix. No use or reproduction without express written consent18 Reactome Legacy Agenda Classic Reactome: http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1 Introduction and Credits Basic Keyword Search Selecting a Pathway Understanding Results Other Reactome Tools Summary Exercises

19. Copyright OpenHelix. No use or reproduction without express written consent19 Selecting a Pathway Click the Reaction Map or Click a topic in the table of pathways everything is clickable! Reaction Map Table of Pathways

20. Copyright OpenHelix. No use or reproduction without express written consent20 Gene Expression Pathway Details now zoomed event hierarchy event summary other species molecules involved

21. Copyright OpenHelix. No use or reproduction without express written consent21 Reactome Legacy Agenda Classic Reactome: http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1 Introduction and Credits Basic Keyword Search Selecting a Pathway Understanding Results Other Reactome Tools Summary Exercises

22. Copyright OpenHelix. No use or reproduction without express written consent22 Understanding Results: Pathways, Entities Pathways: more group details Entities: individual components and their details pathway page entity page

23. Copyright OpenHelix. No use or reproduction without express written consent23 Pathways Pages: Maps When you find a pathway page, what do you have?

24. Copyright OpenHelix. No use or reproduction without express written consent24 Pathways Pages: Tree of Events highest level single reactions = pathway = single step reaction When you find a pathway page, what do you have?

25. Copyright OpenHelix. No use or reproduction without express written consent25 Pathways Pages: Details UniProt Ensembl Entrez Gene BioGPS KEGG OMIM ChEBI Compound CTD EMBL dbSNP authors species location other species participating molecules stable identifier When you find a pathway page, what do you have? PubChem feedback summary process RefSeq HapMap UCSC PDB

26. Copyright OpenHelix. No use or reproduction without express written consent26 Entity Pages: Maps and Details Macromolecules or compounds can be entities names and IDs complexes

27. Copyright OpenHelix. No use or reproduction without express written consent27 Entity Pages: Maps and Details Macromolecules or compounds can be entities

28. Copyright OpenHelix. No use or reproduction without express written consent28 Reactome Legacy Agenda Classic Reactome: http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1 Introduction and Credits Basic Keyword Search Selecting a Pathway Understanding Results Other Reactome Tools Summary Exercises

29. Copyright OpenHelix. No use or reproduction without express written consent29 Other Reactome Tools PathFinder: illustrate connections between entities SkyPainter: upload IDs, find where they map (Now at URL http://www.reactome.org/cgi-bin/skypainter2) Downloads—and a textbook!

30. Copyright OpenHelix. No use or reproduction without express written consent30 PathFinder A sample start and end point shown

31. Copyright OpenHelix. No use or reproduction without express written consent31 PathFinder Results PathFinder presents items between two points start end paths found

32. Copyright OpenHelix. No use or reproduction without express written consent32 SkyPainter: http://www.reactome.org/cgi-bin/skypainter2 or upload a list Identifiers: color coded by number of times a path is hit Identifiers + values (a time course): ID time1 time2 time3 ID format varies; see examples on lower part of the page Sample data provided

33. Copyright OpenHelix. No use or reproduction without express written consent33 SkyPainter Results SkyPainter example, with their ID data set Hits are color-coded, then listed Try the other set to see a time course with multiple maps

34. Copyright OpenHelix. No use or reproduction without express written consent34 Downloads Reactome data and code can be downloaded and used Variety of formats—even a textbook! Can set up your own local copy textbook

35. Copyright OpenHelix. No use or reproduction without express written consent35 Reactome Legacy Agenda Classic Reactome: http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1 Introduction and Credits Basic Keyword Search Selecting a Pathway Understanding Results Other Reactome Tools Summary Exercises

36. http://www.reactome.org Pathway pages Copyright OpenHelix. No use or reproduction without express written consent36 Entity pages Summary Reactome: for pathways and entities Tools and views to find and visualize what you need SkyPainter

37. Copyright OpenHelix. No use or reproduction without express written consent37 Reactome Legacy Agenda Classic Reactome: http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1 Introduction and Credits Basic Keyword Search Selecting a Pathway Understanding Results Other Reactome Tools Summary Exercises

38. Copyright OpenHelix. No use or reproduction without express written consent38