{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T05:29:40Z","timestamp":1791091780605,"version":"4.1.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: 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.<\/jats:p><jats:p>Availability: Cyclone is freely available under an open source license at: http:\/\/sourceforge.net\/projects\/nemo-cyclone<\/jats:p><jats:p>Contact: \u00a0cyclone@genoscope.cns.fr<\/jats:p><jats:p>Supplementary information: For download and installation instructions, tutorials, use cases and examples, see http:\/\/nemo-cyclone.sourceforge.net<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm107","type":"journal-article","created":{"date-parts":[[2007,3,29]],"date-time":"2007-03-29T00:32:41Z","timestamp":1175128361000},"page":"1299-1300","source":"Crossref","is-referenced-by-count":11,"title":["Cyclone: java-based querying and computing with Pathway\/Genome databases"],"prefix":"10.1093","volume":"23","author":[{"given":"Fran\u00e7ois Le","family":"F\u00e8vre","sequence":"first","affiliation":[{"name":"Computational Systems Biology Group, Genoscope\/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serge","family":"Smidtas","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Group, Genoscope\/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Sch\u00e4chter","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Group, Genoscope\/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2007,3,28]]},"reference":[{"key":"2023041104481618700_","volume-title":"Hibernate: a developer's notebook","author":"Eliott","year":"2004"},{"key":"2023041104481618700_","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-7-170","article-title":"BioWarehouse: a bioinformatics database warehouse toolkit","volume":"7","author":"Lee","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023041104481618700_","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/27.1.29","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"27","author":"Kanehisa","year":"1999","journal-title":"Nucleic Acid Res."},{"key":"2023041104481618700_","doi-asserted-by":"crossref","first-page":"3454","DOI":"10.1093\/bioinformatics\/bti546","article-title":"Querying and computing with BioCyc databases","volume":"16","author":"Krummenacker","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041104481618700_","first-page":"768","article-title":"The Generic Frame Protocol","volume-title":"Proceedings of the 1995 International Joint Conference on Artificial Intelligence","author":"Karp","year":"1995"},{"key":"2023041104481618700_","doi-asserted-by":"crossref","first-page":"S225","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225","article-title":"The pathway tools software","volume":"18","author":"Karp","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041104481618700_","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/10\/1299\/49813072\/bioinformatics_23_10_1299.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/10\/1299\/49813072\/bioinformatics_23_10_1299.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T05:54:27Z","timestamp":1683784467000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/10\/1299\/198057"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3,28]]},"references-count":7,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2007,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm107","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,5,15]]},"published":{"date-parts":[[2007,3,28]]}}}