{"id":"https://openalex.org/W2158541664","doi":"https://doi.org/10.1093/bioinformatics/btm107","title":"Cyclone: java-based querying and computing with Pathway/Genome databases","display_name":"Cyclone: java-based querying and computing with Pathway/Genome databases","publication_year":2007,"publication_date":"2007-03-28","ids":{"openalex":"https://openalex.org/W2158541664","doi":"https://doi.org/10.1093/bioinformatics/btm107","mag":"2158541664","pmid":"https://pubmed.ncbi.nlm.nih.gov/17392333"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/10/1299/501031/btm107.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/10/1299/501031/btm107.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019944621","display_name":"Fran\u00e7ois Le F\u00e8vre","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210115028","display_name":"Genoscope","ror":"https://ror.org/028pnqf58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210115028"]},{"id":"https://openalex.org/I4210101231","display_name":"Institut de Biologie syst\u00e9mique et synth\u00e9tique","ror":"https://ror.org/018r7pa17","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210101231","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fran\u00e7ois Le F\u00e8vre","raw_affiliation_strings":["Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France","institution_ids":["https://openalex.org/I4210101231","https://openalex.org/I4210115028","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067330761","display_name":"Serge Smidtas","orcid":null},"institutions":[{"id":"https://openalex.org/I4210115028","display_name":"Genoscope","ror":"https://ror.org/028pnqf58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210115028"]},{"id":"https://openalex.org/I4210101231","display_name":"Institut de Biologie syst\u00e9mique et synth\u00e9tique","ror":"https://ror.org/018r7pa17","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210101231","https://openalex.org/I88467170"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Serge Smidtas","raw_affiliation_strings":["Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France","institution_ids":["https://openalex.org/I4210101231","https://openalex.org/I4210115028","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032439096","display_name":"Vincent Sch\u00e4chter","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210115028","display_name":"Genoscope","ror":"https://ror.org/028pnqf58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210115028"]},{"id":"https://openalex.org/I4210101231","display_name":"Institut de Biologie syst\u00e9mique et synth\u00e9tique","ror":"https://ror.org/018r7pa17","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210101231","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Vincent Sch\u00e4chter","raw_affiliation_strings":["Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France","institution_ids":["https://openalex.org/I4210101231","https://openalex.org/I4210115028","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032439096"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210101231","https://openalex.org/I4210115028"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5236,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.65833174,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"10","first_page":"1299","last_page":"1300"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.991100013256073,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.78968346118927},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.7268399000167847},{"id":"https://openalex.org/keywords/cyclone","display_name":"Cyclone (programming language)","score":0.6216375827789307},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.589095950126648},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5531981587409973},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.526813268661499},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4009225368499756},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37301182746887207},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.18492141366004944},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13579201698303223}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.78968346118927},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7268399000167847},{"id":"https://openalex.org/C2777864850","wikidata":"https://www.wikidata.org/wiki/Q79598","display_name":"Cyclone (programming language)","level":3,"score":0.6216375827789307},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.589095950126648},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5531981587409973},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.526813268661499},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4009225368499756},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37301182746887207},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.18492141366004944},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13579201698303223},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/10/1299/501031/btm107.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17392333","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17392333","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/10/1299/501031/btm107.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158541664.pdf","grobid_xml":"https://content.openalex.org/works/W2158541664.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W69446631","https://openalex.org/W189489834","https://openalex.org/W1835571316","https://openalex.org/W2096144498","https://openalex.org/W2133298156","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2602753196","https://openalex.org/W6607706184"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2749690376","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W4281673905","https://openalex.org/W2121496884"],"abstract_inverted_index":{"For":[0],"download":[1],"and":[2,8],"installation":[3],"instructions,":[4],"tutorials,":[5],"use":[6],"cases":[7],"examples,":[9],"see":[10],"http://nemo-cyclone.sourceforge.net.":[11]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}