Cyclone:: java']java-based querying and computing with Pathway/Genome databases

被引：5

作者：

Le Fevre, Francois ^{[1
]}

Smidtas, Serge ^{[1
]}

Schachter, Vincent ^{[1
]}

机构：

[1] Genoscope CNRS, UMR8030, Computat Syst Biol Grp, F-91057 Evry, France

来源：

BIOINFORMATICS | 2007年 / 23卷 / 10期

关键词：

D O I：

10.1093/bioinformatics/btm107

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization.

引用

页码：1299 / 1300

页数：2

共 7 条

[1]

Eliott J., 2004, HIBERNATE DEV NOTEBO

[2] KEGG: Kyoto Encyclopedia of Genes and Genomes [J].

Kanehisa, M ;

Goto, S .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :27-30

[3]

Karp PD, 1995, INT JOINT CONF ARTIF, P768

[4] Querying and computing with BioCyc databases [J].

Krummenacker, M ;

Paley, S ;

Mueller, L ;

Yan, T ;

Karp, PD .

BIOINFORMATICS, 2005, 21 (16) :3454-3455

[5] BioWarehouse: a bioinformatics database warehouse toolkit [J].

Lee, TJ ;

Pouliot, Y ;

Wagner, V ;

Gupta, P ;

Stringer-Calvert, DWJ ;

Tenenbaum, JD ;

Karp, PD .

BMC BIOINFORMATICS, 2006, 7 (1)

[6] Evaluation of computational metabolic-pathway predictions for Helicobacter pylori [J].

Paley, SM ;

Karp, PD .

BIOINFORMATICS, 2002, 18 (05) :715-724

[7] Cytoscape: A software environment for integrated models of biomolecular interaction networks [J].

Shannon, P ;

Markiel, A ;

Ozier, O ;

Baliga, NS ;

Wang, JT ;

Ramage, D ;

Amin, N ;

Schwikowski, B ;

Ideker, T .

GENOME RESEARCH, 2003, 13 (11) :2498-2504

← 1 →