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Cyclone is a Java based application that uses BioCyc as its primary source of data through Pathway Tools.
The storage backend is composed of Relational Database Management Systems (RDBMS) such as mySQL or Oracle.
The database records are mapped onto the object model using XML and Hibernate.

Information flow

Object model and database generation

1-Using an extension of Javacyc, Cyclone is able to extract from Pathway Tools the BioCyc data model and convert it into an XML Schema (XSD) defining the Cyclone object representation model.

2-This schema is then used by JaxB to define the corresponding Java classes. It is also used by HyperJaxB to define adequate mappings in Hibernate, which is responsible for the persistence of the classes in RDBMS (Relational DataBase Management System).

Data translation and manipulation

3-The data themselves are then queried by Cyclone using JavaCyc, and written to an XML file (CycloneML) which is then translated into Java objects by Jaxb in order to be manipulated by Cyclone Core functions or to be stored in CycloneDB by Hibernate.

4-Query, compute and visualize the loaded Pathway Genome DataBase. Export data into SIF for Cytoscape, GraphML for Jung or ClusterML.

5-All changes made to your organism can be commited back into BioCyc.

From BioCyc's Frame Representation System (FRS) to Cyclone Object Model

General mapping concepts
Each frame is made of slots, with their attached annots. These concepts are translated into complexType, a structure of Xml schema. JaxB then follows this schema to define adequate Java classes (see Jaxb).

Mapping of an entire Pathway Genome DataBase
Each biocyc PGDB is a frame composed of root classes such as Enzymatic-reactions, Evidences, Generalized-Reactions. Inregards Cyclone PGDB contains a sequence of complexType such as EnzymaticReactions, Evidences, GeneralizedReactions.

Mapping of a particular frame : Generalized-Reactions
Each root biocyc classes is composed of slot and annots. They are translate into complexType containing simple element .

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