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					  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



      caBIG™ is an initiative of the National Cancer Institute, NIH, DHHS
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.
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
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
Lesson 1: Introduction to Reactome

 In this Lesson, we will introduce:
   –   What Reactome is
   –   Reactome web site
   –   Reactome data model
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
Lesson 1: Introduction to Reactome

 Reactome Web Site: Front Page (http://www.reactome.org)

                                                       Menu bar
                                                       Search Box



                                                       Reaction
                                                       Map




                                                       Topic
                                                       Table
   Lesson 1: Introduction to Reactome

    Reactome Web Site: Pathway Page (Human Apoptosis)




Hierarchical
       Tree

                                                         Summation




                                                         Figure
Lesson 1: Introduction to Reactome

 Reactome Web Site: Pathway Page (Human Apoptosis) (continued)


                                                             Figure




                                                             Detailed
                                                             Properties
Lesson 1: Introduction to Reactome

 Reactome Web Site: Reaction Page (FASL Binds FAS Receptor)



                                                       Reaction
                                                       Diagram




                                                       Detailed
                                                       Properties
Lesson 1: Introduction to Reactome

 Reactome Data Model
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
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/caBIOServic
          e?wsdl
      •   BioPAXExporter:
          http://www.reactome.org:8080/caBIOWebApp/services/BioPAXExpo
          rter?wsdl
Lesson 2: Simple Queries with the Reactome WS API

 Initialize Class:
   –   Create a TestCase:



   –   Create a method to initialize a Call object:

                                                      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 (continued):
   –   Register Types:

                                                                           Register
                                                                           InstanceNot-
                                                                           FoundException

                                                                           Reactome-
                                                                           Remote-
                                                                           Exception

                                                                           Register
                                                                           Catalyst-
                                                                           Activity


                                                                           Register
                                                                           Complex


                                                                           ……
   –   See complete code at:
       http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/reactomedata/WEB-
       INF/src/unitTest/WSUnitTest.java
Lesson 2: Simple Queries with the Reactome WS API

 Query pathways using UniProt identifiers:
  –   Query pathways with three uniprot accession numbers:

                                                       Set up query
                                                       parameter
                                                       Create a call

                                                       Handle the result
Lesson 2: Simple Queries with the Reactome WS API

 Query pathways using UniProt identifiers:
  –   Display the query result:

                                              Output an
                                              Object Array




                                              Output JavaBean
                                              properties with
                                              Java reflection
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
  ……
Lesson 2: Simple Queries with the Reactome WS API

 Generate a SVG diagram for a pathway:
  –   Generate a SVG diagram for a pathway:

                                              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:
  –   Open the SVG diagram in Adobe SVG plug-in (partial display):
Lesson 2: Simple Queries with the Reactome WS API

 Output pathway into BioPAX level 2 format:
  –   Output pathway into BioPAX level 2 format:



                                                   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:
  –   Download BioPAX plug-in from:
      http://cbio.mskcc.org/cytoscape/plugins/biopax/
  –   Open BioPAX output in Cytoscape (partial display):
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
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.ht
      ml
                                             Dedicated BioPAX output endpoint
  –   API List:

                                             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

 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.
Lesson 3: A Comprehensive Example with Reactome WS API

 Comprehensive Example:
  –   Set up:
                                           Create a dummy method


                                           An array of 11 MGD
                                           identifiers


                                           Initialize three Call
                                           objects to be used
                                           later

  –   Query ReferenceProteins:
                                           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:
  –   Query EventEntities:
                                        Set to hold EventEntities

                                        Iterate each
                                        ReferenceProtein


                                        Push the returned
                                        results into the set


  –   Query Pathways:

                                                         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 pathway participants:

                                                              Iterate Pathways

                                                              Invoke the call


                                                              Output
                                                              participants
                                                              Close for loop
                                                              and method

  –   All example source code is available at:
      http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/reactomedata/WE
      B-INF/src/unitTest/WSUnitTest.java
Lesson 3: A Comprehensive Example with Reactome WS API

 Comprehensive Example:
  –   Query results:
       ID: NM_01057 8
       Collage n adhesio n via alpha 2 beta 1 glyco prote in: 6
           180988: Homolog ues of Collage n alpha 1(I) chain precurs or [extrac ellul ar region]
           180997: Homolog ues of Collage n alpha 1(I) chain precurs or [plasma membran e]
           114632: Magnesi um [extrac ellul ar region]
           140344: Magnesi um [plasma membran e]
           180993: P09055 [plasma membran e]
           180991: Q8CB84 [plasma membran e]
       ID: NM_00821 2
       mitocho ndria l fatty acid beta-ox idati on of saturat ed fatty acids: 44
           77251: (S)-3-H ydrox ybuta noyl- CoA [mitoch ondri al matrix]
           77252: (S)-3-H ydrox ydode canoy l-CoA [mitoch ondri al matrix]
           77300: (S)-3-H ydrox yhexa decan oyl-C oA [mitoch ondri al matrix]
           77276: (S)-3-H ydrox ytetr adeca noyl- CoA [mitoch ondri al matrix]
           77341: (S)-Hyd roxyd ecano yl-Co A [mitoch ondri al matrix]
           77322: (S)-Hydroxyh exano yl-Co A [mitoch ondri al matrix]
           77330: (S)-Hyd roxyo ctano yl-Co A [mitoch ondri al matrix]
           77255: 2-trans -Dode cenoy l-CoA [mitoch ondri al matrix]
           77339: 3-Oxode canoy l-CoA [mitoch ondri al matrix]
           77253: 3-Oxodo decan oyl-C oA [mitoch ondri al matrix]
              ……
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
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/doc
     s/caBIG_Reactome_User_Guide.pdf

				
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