Cyclone

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Architecture

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

Pipeline

The BioCyc schema is queried by Cyclone through Javacyc and converted into a XML schema (XSD). This XSD schema is used by JaxB to define 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).

The data themselves are then queried by Cyclone using JavaCyc, and written to an XML file.

Pipeline:
0-Using an extended version of Javacyc,
1-we query PathwayTools to generate the XSD file.
2-we query PathwayTools to generate the XML files.
3-From the XML schema (XSD) using HiperJaxB, JaxB and Hibernate, we build java objects
4-persisted into the database.

From Frames (FRS) to Java Objects

Frame Representation System (FRS) is the BioCyc's standard to define its schema. Cyclone provides a method to translate this schema into an xsd schema, which is used in order to define java classes definition.

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.

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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