{"id":"https://openalex.org/W1973242626","doi":"https://doi.org/10.1186/1471-2105-14-17","title":"CySBGN: A Cytoscape plug-in to integrate SBGN maps","display_name":"CySBGN: A Cytoscape plug-in to integrate SBGN maps","publication_year":2013,"publication_date":"2013-01-16","ids":{"openalex":"https://openalex.org/W1973242626","doi":"https://doi.org/10.1186/1471-2105-14-17","mag":"1973242626","pmid":"https://pubmed.ncbi.nlm.nih.gov/23324051"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-17","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-17","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-17","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065746791","display_name":"Emanuel Gon\u00e7alves","orcid":"https://orcid.org/0000-0002-9967-5205"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Emanuel Gon\u00e7alves","raw_affiliation_strings":["EMBL - European Bioinformatics Institute, Cambridge, UK","EMBL- European Bioinformatics Institute, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"EMBL - European Bioinformatics Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL- European Bioinformatics Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058353197","display_name":"Martijn van Iersel","orcid":"https://orcid.org/0000-0002-5877-4338"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Martijn van Iersel","raw_affiliation_strings":["EMBL - European Bioinformatics Institute, Cambridge, UK","EMBL- European Bioinformatics Institute, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"EMBL - European Bioinformatics Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL- European Bioinformatics Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["EMBL - European Bioinformatics Institute, Cambridge, UK","EMBL- European Bioinformatics Institute, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"EMBL - European Bioinformatics Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL- European Bioinformatics Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065746791"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1959,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.77615541,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"14","issue":"1","first_page":"17","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9988999962806702,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.998199999332428,"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/sbml","display_name":"SBML","score":0.9281661510467529},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7492060661315918},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.6617271304130554},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.48836156725883484},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4564892649650574},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35970431566238403},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.33656740188598633},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3012528419494629},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.17252102494239807},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.16344347596168518}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9281661510467529},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7492060661315918},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.6617271304130554},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.48836156725883484},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4564892649650574},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35970431566238403},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.33656740188598633},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3012528419494629},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.17252102494239807},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.16344347596168518}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","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":3,"locations":[{"id":"doi:10.1186/1471-2105-14-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-17","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-17","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23324051","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23324051","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2598197","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3599859","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-17","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-17","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320338366","display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1973242626.pdf","grobid_xml":"https://content.openalex.org/works/W1973242626.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1702766678","https://openalex.org/W1946371345","https://openalex.org/W1969709265","https://openalex.org/W1970594207","https://openalex.org/W2000860171","https://openalex.org/W2038264484","https://openalex.org/W2041396547","https://openalex.org/W2045478141","https://openalex.org/W2064885721","https://openalex.org/W2068146784","https://openalex.org/W2069157810","https://openalex.org/W2069435157","https://openalex.org/W2075495945","https://openalex.org/W2080130499","https://openalex.org/W2082099821","https://openalex.org/W2082621456","https://openalex.org/W2102057828","https://openalex.org/W2114124738","https://openalex.org/W2134185611","https://openalex.org/W2135857985","https://openalex.org/W2138326194","https://openalex.org/W2155142785","https://openalex.org/W2159675211","https://openalex.org/W2163993275","https://openalex.org/W2184417913"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W1546010648","https://openalex.org/W2890725831"],"abstract_inverted_index":{"CySBGN":[0],"imports,":[1],"modifies":[2],"and":[3,9,20,27],"analyzes":[4],"SBGN":[5,30],"diagrams":[6],"in":[7,22,29],"Cytoscape,":[8],"thus":[10],"allows":[11],"the":[12,15],"application":[13],"of":[14,18],"large":[16],"palette":[17],"tools":[19],"plug-ins":[21],"this":[23],"platform":[24],"to":[25],"networks":[26],"pathways":[28],"format.":[31]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
