BioCyc is a collection of 205 organism-specific Pathway/Genome Databases (PGDBs) developed at SRI, together with the MetaCyc database,
which is made of nonredundant, experimentally elucidated metabolic pathways from various organisms.
 PGDBs range from highly curated (EcoCyc) to automatically reconstructed from genome annotations. Their contents can be queried and visualized
using a web interface or a dedicated software called 'Pathways Tools' (see references).
Although curated BioCyc databases include very high quality data, their contents are not easy to access or manipulate for external developers. Cyclone aims at facilitating the use of BioCyc
for computational biologists and bioinformaticians, by providing a fully extensible Java Object API that goes beyond the native Lisp API and its derivatives (PerlCyc, JavaCyc).
Cyclone maps the Frame Representation System (FRS) model onto the Cyclone object representation which mirrors the BioCyc data model.
Cyclone can read and write BioCyc PGDBs, and can write its own data in the CycloneML format, which is defined by an XML schema (XSD). The latter is automatically generated from the Pathway-Tools
ontologies by Cyclone itself, ensuring continued compatibility between both storage standards. Since Cyclone objects can also be stored in a relational database, CycloneDB,
queries can be written in SQL, and, more interestingly, in Hibernate Query Language (HQL), an object oriented query language, an intuitive and concise query language. In addition, Cyclone interfaces easily with :
JaxFront for data edition, Jung API for graph handling, Cytoscape for graph visualization.
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