{"id":"https://openalex.org/W4360619191","doi":"https://doi.org/10.3389/fbinf.2023.1125949","title":"Translating desktop success to the web in the cytoscape project","display_name":"Translating desktop success to the web in the cytoscape project","publication_year":2023,"publication_date":"2023-03-23","ids":{"openalex":"https://openalex.org/W4360619191","doi":"https://doi.org/10.3389/fbinf.2023.1125949","pmid":"https://pubmed.ncbi.nlm.nih.gov/37035036"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1125949","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1125949","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1125949/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1125949/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038117263","display_name":"Dexter Pratt","orcid":"https://orcid.org/0000-0002-1471-9513"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dexter Pratt","raw_affiliation_strings":["Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, United States"],"affiliations":[{"raw_affiliation_string":"Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091233369","display_name":"Rudolf Pillich","orcid":"https://orcid.org/0000-0001-8682-0568"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rudolf T. Pillich","raw_affiliation_strings":["Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, United States"],"affiliations":[{"raw_affiliation_string":"Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054399637","display_name":"John H. Morris","orcid":"https://orcid.org/0000-0003-0290-7979"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John H. Morris","raw_affiliation_strings":["Resource on Biocomputing, Visualization, and Informatics, University of California San Francisco, San Francisco, CA, United States"],"affiliations":[{"raw_affiliation_string":"Resource on Biocomputing, Visualization, and Informatics, University of California San Francisco, San Francisco, CA, United States","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038117263"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.4568,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.65942113,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"3","issue":null,"first_page":"1125949","last_page":"1125949"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9945999979972839,"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":0.9945999979972839,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.98580002784729,"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":0.6633257269859314},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6120513081550598},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6036064624786377},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4785338342189789},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46475186944007874},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.43335962295532227},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.42038023471832275},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3334243893623352},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.1425037682056427},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12187665700912476}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6633257269859314},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6120513081550598},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6036064624786377},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4785338342189789},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46475186944007874},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.43335962295532227},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.42038023471832275},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3334243893623352},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.1425037682056427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12187665700912476},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.3389/fbinf.2023.1125949","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1125949","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1125949/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37035036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37035036","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt0rh108b7","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/0rh108b7","pdf_url":"https://escholarship.org/content/qt0rh108b7/qt0rh108b7.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10076771","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10076771","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10076771/pdf/fbinf-03-1125949.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"},{"id":"pmh:ark:/13030/qt0rh108b7","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:edbb24b9786640bfb61d4db22b10740e","is_oa":true,"landing_page_url":"https://doaj.org/article/edbb24b9786640bfb61d4db22b10740e","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 3 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1125949","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1125949","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1125949/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1605731393","display_name":null,"funder_award_id":"CA209891","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1863333649","display_name":null,"funder_award_id":"CA184427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1875211201","display_name":null,"funder_award_id":"2019-207395","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"},{"id":"https://openalex.org/G2065419579","display_name":null,"funder_award_id":"R01 HG009979","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4412323338","display_name":null,"funder_award_id":"GM103504","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5180836318","display_name":null,"funder_award_id":"GM10350","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5190646370","display_name":null,"funder_award_id":"P41 GM103504 R01 HG009979 U19AI135990 U54CA209891 U24CA184427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5298496832","display_name":null,"funder_award_id":"P41 GM103504","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8798940694","display_name":null,"funder_award_id":"U19AI135990","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8841462186","display_name":null,"funder_award_id":"U54CA209891","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G919333870","display_name":null,"funder_award_id":"U24CA184427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320315474","display_name":"Chan Zuckerberg Initiative","ror":"https://ror.org/02qenvm24"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4360619191.pdf"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1871096589","https://openalex.org/W1956024495","https://openalex.org/W1989277387","https://openalex.org/W2097508475","https://openalex.org/W2101725042","https://openalex.org/W2103912979","https://openalex.org/W2152026276","https://openalex.org/W2155142785","https://openalex.org/W2159675211","https://openalex.org/W2166542841","https://openalex.org/W2169589032","https://openalex.org/W2171030481","https://openalex.org/W2537623931","https://openalex.org/W2597175664","https://openalex.org/W2766352310","https://openalex.org/W2809000676","https://openalex.org/W2950764390","https://openalex.org/W3090217015","https://openalex.org/W3102147110","https://openalex.org/W3203161883","https://openalex.org/W3212342036","https://openalex.org/W4231254854"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2156434174","https://openalex.org/W2121496884","https://openalex.org/W2387910809","https://openalex.org/W2130094614"],"abstract_inverted_index":{"Cytoscape":[0,27,71],"is":[1],"an":[2],"open-source":[3],"bioinformatics":[4,44,53],"environment":[5],"for":[6],"the":[7,26,31,43,58,75],"analysis,":[8],"integration,":[9],"visualization,":[10],"and":[11,49,60,62],"query":[12],"of":[13],"biological":[14],"networks.":[15],"In":[16],"this":[17],"perspective":[18],"piece,":[19],"we":[20,63],"describe":[21,64],"our":[22,35,65,79],"project":[23],"to":[24,30,40,68],"bring":[25],"desktop":[28,59],"application":[29],"web":[32,72],"while":[33],"explaining":[34],"strategy":[36],"in":[37,42,51],"ways":[38],"relevant":[39],"others":[41],"community.":[45],"We":[46],"examine":[47],"opportunities":[48],"challenges":[50],"developing":[52],"software":[54],"that":[55,77],"spans":[56],"both":[57],"web,":[61],"ongoing":[66],"efforts":[67],"build":[69],"a":[70],"application,":[73],"highlighting":[74],"principles":[76],"guide":[78],"development.":[80]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}