Reactome Web Services Overview

1. Reactome Web Services Overview Session Length: approx 20 minutes Target Audience: application developers Trainer: self-paced Developer Subject Matter Expert : Lincoln Stein (lstein@cshl.edu) Guanming Wu (wugm@cshl.edu) Creation Date: July 2006

2. Session Details • Target Audience: Application developers that need to access data from within Reactome • Prerequisites: Java programming knowledge Web Services practical experience Basic UML knowledge • Note: Some slides have notes attached. To see these notes, please select the “Normal” option under the View menu on your toolbar.

3. Session Details:Session Objectives • By the end of this session, you should be able to • Describe what Reactome is • Use its Web Services API to access its datasets

4. Session Details:Lesson Plan • Lesson 1: Introduction to Reactome • Lesson 2: Simple Queries with the Reactome WS API • Lesson 3: A Comprehensive Example with the Reactome WS API

5. Lesson 1: Introduction to Reactome • In this Lesson, we will introduce: • What Reactome is • Reactome web site • Reactome data model

6. Lesson 1: Introduction to Reactome • What is Reactome? • An open, on-line, human-curated knowledgebase of biological pathways and reactions in humans • Pathways and reactions in other species are predicated based on protein orthologies • Data in the Reactome is interconnected with other databases: pubmed, Gene Ontology, NCBI, Ensembl, UniProt, OMIM, etc. • Authored and created by experts

7. Menu bar Search Box Reaction Map Lesson 1: Introduction to Reactome • Reactome Web Site: Front Page (http://www.reactome.org) Topic Table

8. Hierarchical Tree Summation Figure Lesson 1: Introduction to Reactome • Reactome Web Site: Pathway Page (Human Apoptosis)

9. Figure Detailed Properties Lesson 1: Introduction to Reactome • Reactome Web Site: Pathway Page (Human Apoptosis) (continued)

10. Reaction Diagram Detailed Properties Lesson 1: Introduction to Reactome • Reactome Web Site: Reaction Page (FASL Binds FAS Receptor)

11. Lesson 1: Introduction to Reactome • Reactome Data Model

12. Lesson 2: Simple Queries with the Reactome WS API • In this lesson, we will introduce how to use the Reactome SOAP API for some simple queries in Java. You will learn how to: • Set up the working environment • Query pathways using a list of UniProt identifiers • Generate a SVG diagram for a pathway • Output a pathway into the BioPAX level 2 format • Open the returned BioPAX file in CytoScape

13. Lesson 2: Simple Queries with the Reactome WS API • Set up the working environment: • Eclipse used as Java IDE • Required third-party libraries: client.jar from caBIO, axis.jar, axis-ant.jar, axis-schema.jar, wsdl4j.jar, jaxrpc.jar, saaj.jar, commons-discovery.jar, commons-logging.jar, junit.jar • Reactome domain classes: reactome.jar • URLs for WSDL files: • caBIOService: http://www.reactome.org:8080/caBIOWebApp/services/caBIOService?wsdl • BioPAXExporter: http://www.reactome.org:8080/caBIOWebApp/services/BioPAXExporter?wsdl

14. Initialize caBIOService if it is not initialize Create a Call from the service and register type mappings Lesson 2: Simple Queries with the Reactome WS API • Initialize Class: • Create a TestCase: • Create a method to initialize a Call object:

15. Register InstanceNot- FoundException Reactome-Remote-Exception Register Catalyst- Activity Register Complex …… Lesson 2: Simple Queries with the Reactome WS API • Initialize Class (continued): • Register Types: • See complete code at: http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/reactomedata/WEB-INF/src/unitTest/WSUnitTest.java

16. Set up query parameter Create a call Handle the result Lesson 2: Simple Queries with the Reactome WS API • Query pathways using UniProt identifiers: • Query pathways with three uniprot accession numbers:

17. Output an Object Array Output JavaBean properties with Java reflection Lesson 2: Simple Queries with the Reactome WS API • Query pathways using UniProt identifiers: • Display the query result:

18. Lesson 2: Simple Queries with the Reactome WS API • Query pathways using UniProt identifiers: • Query result: Pathway for a list of identifiers: 2 class org.reactome.cabig.domain.Pathway -> 69278: Cell Cycle, Mitotic hasComponent: …… compartment: null literatureReference: null species: 48887: Homo sapiens summation: [69280: null] goBiologicalProcess: 4802: mitotic cell cycle inferredFrom: null orthologousEvent: …… precedingEvent: null evidenceType: Cell Cycle, Mitotic name: Cell Cycle, Mitotic id: 69278 class: class org.reactome.cabig.domain.Pathway class org.reactome.cabig.domain.Pathway -> 74159: Transcription ……

19. Initialize a pathway as parameter Create and invoke a call Output the returned SVG to an external file Lesson 2: Simple Queries with the Reactome WS API • Generate a SVG diagram for a pathway: • Generate a SVG diagram for a pathway:

20. Lesson 2: Simple Queries with the Reactome WS API • Generate a SVG diagram for a pathway: • Open the SVG diagram in Adobe SVG plug-in (partial display):

21. Set up a SOAP Call With Axis Client ToolSet. Invoke the call Output the returned BioPAX into a local file. Lesson 2: Simple Queries with the Reactome WS API • Output pathway into BioPAX level 2 format: • Output pathway into BioPAX level 2 format:

22. Lesson 2: Simple Queries with the Reactome WS API • Output pathway into BioPAX level 2 format: • Download BioPAX plug-in from: http://cbio.mskcc.org/cytoscape/plugins/biopax/ • Open BioPAX output in Cytoscape (partial display):

23. Lesson 3: A Comprehensive Example With Reactome WS API • In this lesson, we will introduce: • The whole list of Reactome WS API • A comprehensive example to use this WS API

24. Dedicated BioPAX output endpoint Generate pathway diagram in SVG List methods return proxy objects Load methods return recursively loaded pathways Query methods return fully loaded objects Lesson 3: A Comprehensive Example with Reactome WS API • The whole list of Reactome WS API: • On-line document: http://www.reactome.org:8080/caBIOWebApp/docs/services.html • API List:

25. Lesson 3: A Comprehensive Example with Reactome WS API • Comprehensive Example: • Requirement description: • Given a list of identifiers in MGD, find ReferenceProtein objects using these identifiers • Query EventEntities using these ReferenceProteins as values of referenceEntity attribute • Query Pathways with these EventEntities participating • Get a list of EventEntity participants for each Pathway object.

26. Create a dummy method An array of 11 MGD identifiers Initialize three Call objects to be used later Loop through all MGD identifiers Query for ReferenceProtein using identifiers in its relatedIdentifiers attribute Lesson 3: A Comprehensive Example with Reactome WS API • Comprehensive Example: • Set up: • Query ReferenceProteins:

27. Set to hold EventEntities Iterate each ReferenceProtein Push the returned results into the set Use Ids as a call argument to speed up deserialization Invoke the call Lesson 3: A Comprehensive Example with Reactome WS API • Comprehensive Example: • Query EventEntities: • Query Pathways:

28. Iterate Pathways Invoke the call Output participants Close for loop and method Lesson 3: A Comprehensive Example with Reactome WS API • Comprehensive Example: • Query pathway participants: • All example source code is available at: http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/reactomedata/WEB-INF/src/unitTest/WSUnitTest.java

29. Lesson 3: A Comprehensive Example with Reactome WS API • Comprehensive Example: • Query results: ……

30. Session Review • Now that you have successfully completed this training, you should be able to • Describe what Reactome is • Use its Web Services API to access its datasets

31. Session Review:Questions? • We would love to hear from you: please send us your questions and/or suggestions at wugm@cshl.edu or lstein@cshl.edu • You can also refer to the user’s guide for Reactome Web Services API at http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/reactomedata/docs/caBIG_Reactome_User_Guide.pdf