Reactome RESTful API

The following lists the Reactome RESTful API. To use this API efficiently, the user needs to understand the Reactome data model. The returned result can be specified as either XML or JSON. The user can view the HTML source of this document to see some examples on how to use this API.

• BioPAX Exporter: biopaxExporter/{dbId: \\d+}

  Pass an Event database identifier, and get the BioPAX exported in either XML or JSON. The passed Id has to be an Event Id. If there is no matching ID in the database, it will return an empty string.

  Request Type:

  GET

  Parameters:

  Integer - Event database identifier

  Output:

  String - BioPAX RDF document

  Example:

  To get the BioPAX level 2 export for Apoptosis, use biopaxExporter/109581

• FrontPageItems: frontPageItems

  Get the list of front page items listed in the Reactome pathway browser. In the current implementation, only human pathways are returned.

  Request Type:

  GET

  Output:

  list of fully encoded Pathway objects in JSON or XML

  Example:

  To get a list of front page items for human pathways, use frontPageItems

• ListByQuery: listByQuery/{className}

  This API lets you query the Reactome Database for a list of objects by using Key Value pairs based on an object's attributes. The format of the HTTP POST body should structured as a Key=Value pair. First there must be a key "key", and a value "value" inside the body of the HTTP POST request. For example, to query pathways with names as "Apoptosis", post "name=Apoptosis" to the server.

  Request Type:

  POST

  Parameters:

  String - class name

  String - attribute values encoded in key-value pair in the POST body

  Output:

  encoded objects in JSON or XML

  Example:

  To query a list of pathways with names as "Apoptosis", try XML or JSON result

• PathwayDiagram: pathwayDiagram/{dbId : \\d+}/{format: .+}

  This API lets you retrieve a pathway diagram by passing the database identifier of the pathway and the format of the pathway diagram returned. The available format choices are PDF, PNG and XML.

  Request Type:

  GET

  Parameters:

  Integer - Pathway database identifier

  String - image format: PNG, PDF, or XML.

  Output:

  String - Base64 encoded pathway diagram for PNG or PDF. XML text for the XML file type.

  Example:

  To get the pathway diagram in XML for Apoptosis, use pathwayDiagram/109581/XML

• PathwayParticipants: pathwayParticipants/{dbId : \\d+}

  This API lets you query for a list of pathway participants for a pathway using a Pathway database identifier. It returns a list of all PhysicalEntity objects that participate in the Pathway.

  Request Type:

  GET

  Parameters:

  Integer - Pathway database identifier

  Output:

  list of fully encoded PhysicalEntity objects in JSON or XML

  Example:

  To get a list of PhysicalEntity objects participating in Apoptosis, use pathwayParticipants/109581

• QueryById: queryById/{className}/{dbId: \\d+}

  This API lets you query the Reactome Database for a specific object. It requires passing class name of the object, as well as the database identifier or the stable identifier of the object. The class name is required. It returns a full object, including full class information about all the attributes of the returned object. For example, if the object has one PublicationSource attribute, it will return a full PublicationSource object within the returned object.

  Request Type:

  GET

  Parameters:

  String - class name

  Integer - instance database identifier or stable identifier if available

  Output:

  encoded object in JSON or XML

  Example:

  To get a Pathway object for Apoptosis, use queryById/Pathway/109581

• QueryByIds: queryByIds/{className}

  This API lets you query the Reactome Database for a list of objects. It requires passing the object class as the first parameter in the URL, and a list of database identifiers or stable identifiers as the second parameter. The Identifiers are passed inside the body of the HTTP Post request. The Id's format should be structured as a Key=Value pair. First a key "ID", and a value of comma separated list inside the body of the HTTP POST request.

  Request Type:

  POST

  Parameters:

  String - class name

  Integer - database identifiers or stable identifiers if available in the POST body

  Output:

  encoded objects in JSON or XML

  Example:

  To get the sub-pathway objects for Apoptosis, try XML or JSON result

• QueryPathwayForEntities: pathwaysForEntities

  Query for pathway objects by specifying an array of PhysicalEntity database identifiers. The returned Pathways should contain the passed EventEntity objects. All passed EventEntity database identifiers should be in the database.

  Request Type:

  POST

  Parameters:

  Integer - PhysicalEntity database identifiers delimited by comma

  Output:

  list of fully encoded Pathways objects in JSON or XML

  Example:

  To get a list of pathways containing CDC2, HUS1, and MCM2, try XML or JSON result