{"id":"https://openalex.org/W2997551827","doi":"https://doi.org/10.1093/bioinformatics/btz968","title":"Bringing data from curated pathway resources to Cytoscape with OmniPath","display_name":"Bringing data from curated pathway resources to Cytoscape with OmniPath","publication_year":2019,"publication_date":"2019-12-28","ids":{"openalex":"https://openalex.org/W2997551827","doi":"https://doi.org/10.1093/bioinformatics/btz968","mag":"2997551827","pmid":"https://pubmed.ncbi.nlm.nih.gov/31886476"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz968","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz968","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083316438","display_name":"Francesco Ceccarelli","orcid":"https://orcid.org/0000-0002-5995-5077"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE","GB"],"is_corresponding":false,"raw_author_name":"Francesco Ceccarelli","raw_affiliation_strings":["Computer Laboratory, University of Cambridge , CB3 0FD, Cambridge, UK","Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge , CB3 0FD, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany","institution_ids":["https://openalex.org/I887968799","https://openalex.org/I4210133948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028302173","display_name":"D\u00e9nes T\u00fcrei","orcid":"https://orcid.org/0000-0002-7249-9379"},"institutions":[{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Denes Turei","raw_affiliation_strings":["European Molecular Biology Laboratory (EMBL)","Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory (EMBL)","institution_ids":[]},{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany","institution_ids":["https://openalex.org/I887968799","https://openalex.org/I4210133948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050239570","display_name":"Attila G\u00e1bor","orcid":"https://orcid.org/0000-0002-0776-1182"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Attila Gabor","raw_affiliation_strings":["Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany","Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Bioquant, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany","institution_ids":["https://openalex.org/I887968799","https://openalex.org/I4210133948"]},{"raw_affiliation_string":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Bioquant, Heidelberg, Germany","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"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/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany","Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Bioquant, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany","institution_ids":["https://openalex.org/I887968799","https://openalex.org/I4210133948"]},{"raw_affiliation_string":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Bioquant, Heidelberg, Germany","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005499510"],"corresponding_institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210133948","https://openalex.org/I887968799"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2215,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.88876174,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"36","issue":"8","first_page":"2632","last_page":"2633"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8716999888420105,"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":0.8716999888420105,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.042100001126527786,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10492","display_name":"Microtubule and mitosis dynamics","score":0.013399999588727951,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/plug-in","display_name":"Plug-in","score":0.8364949822425842},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7885136604309082},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6721221804618835},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.529065728187561},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.438265323638916},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4121881425380707},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34660351276397705},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.34186118841171265},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3368135988712311},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33496177196502686},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22434327006340027},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09584754705429077}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8364949822425842},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7885136604309082},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6721221804618835},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.529065728187561},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.438265323638916},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4121881425380707},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34660351276397705},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.34186118841171265},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3368135988712311},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33496177196502686},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22434327006340027},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09584754705429077},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz968","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz968","pdf_url":null,"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:31886476","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31886476","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":null,"sustainable_development_goals":[{"score":0.5299999713897705,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307771","display_name":"Bayer","ror":"https://ror.org/04hmn8g73"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2003003919","https://openalex.org/W2027319259","https://openalex.org/W2050200982","https://openalex.org/W2138862823","https://openalex.org/W2155142785","https://openalex.org/W2159675211","https://openalex.org/W2164298117","https://openalex.org/W2557833574","https://openalex.org/W2767490506","https://openalex.org/W2964315448","https://openalex.org/W6663326725"],"related_works":["https://openalex.org/W4287378204","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W2981957539","https://openalex.org/W1494668222","https://openalex.org/W2924735795","https://openalex.org/W2381929017","https://openalex.org/W2369108811","https://openalex.org/W3011348691"],"abstract_inverted_index":{"SUMMARY:":[0],"Multiple":[1],"databases":[2],"provide":[3],"valuable":[4],"information":[5],"about":[6],"curated":[7],"pathways":[8],"and":[9,18,56,79,106,114],"other":[10,83],"resources":[11,28],"that":[12],"can":[13,109],"be":[14,110],"used":[15],"to":[16,47,63],"build":[17],"analyze":[19],"networks.":[20],"OmniPath":[21,42,52,74,89],"combines":[22],"61":[23],"(and":[24],"continuously":[25],"growing)":[26],"network":[27],"into":[29],"a":[30,44,54],"comprehensive":[31],"collection,":[32],"with":[33,82],"over":[34],"120":[35],"000":[36],"interactions.":[37],"We":[38],"present":[39],"here":[40],"the":[41,66,98,107],"App,":[43],"Cytoscape":[45,76,95],"plugin":[46,108],"flexibly":[48],"import":[49],"data":[50,120],"from":[51],"via":[53],"simple":[55],"intuitive":[57],"interface.":[58],"Thus,":[59],"it":[60],"makes":[61],"possible":[62],"directly":[64],"access":[65],"large":[67],"body":[68],"of":[69],"high-quality":[70],"knowledge":[71],"provided":[72],"by":[73],"within":[75],"for":[77,94],"inspection":[78],"further":[80],"use":[81],"tools.":[84],"AVAILABILITY":[85],"AND":[86],"IMPLEMENTATION:":[87],"The":[88,102],"App":[90],"has":[91],"been":[92],"developed":[93],"3":[96],"in":[97],"Java":[99],"programing":[100],"language.":[101],"latest":[103],"source":[104],"code":[105],"found":[111],"at:":[112],"https://github.com/saezlab/Omnipath_Cytoscape":[113],"http://apps.cytoscape.org/apps/omnipath,":[115],"respectively.":[116],"SUPPLEMENTARY":[117],"INFORMATION:":[118],"Supplementary":[119],"are":[121],"available":[122],"at":[123],"Bioinformatics":[124],"online.":[125]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
