{"id":"https://openalex.org/W2155142785","doi":"https://doi.org/10.1093/bioinformatics/btq675","title":"Cytoscape 2.8: new features for data integration and network visualization","display_name":"Cytoscape 2.8: new features for data integration and network visualization","publication_year":2010,"publication_date":"2010-12-12","ids":{"openalex":"https://openalex.org/W2155142785","doi":"https://doi.org/10.1093/bioinformatics/btq675","mag":"2155142785","pmid":"https://pubmed.ncbi.nlm.nih.gov/21149340"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq675","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq675","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/431/917014/btq675.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/431/917014/btq675.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068272466","display_name":"Michael Smoot","orcid":"https://orcid.org/0000-0002-0584-6537"},"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":"Michael E. Smoot","raw_affiliation_strings":["1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057223513","display_name":"Keiichiro Ono","orcid":"https://orcid.org/0000-0003-4042-3748"},"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":"Keiichiro Ono","raw_affiliation_strings":["1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083584145","display_name":"Johannes Ruscheinski","orcid":null},"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":"Johannes Ruscheinski","raw_affiliation_strings":["1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080024036","display_name":"Pengliang Wang","orcid":"https://orcid.org/0000-0002-9792-3586"},"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":"Peng-Liang Wang","raw_affiliation_strings":["1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089373684","display_name":"Trey Ideker","orcid":"https://orcid.org/0000-0002-1708-8454"},"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":"Trey Ideker","raw_affiliation_strings":["1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine and 2Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5068272466"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":114.3765,"has_fulltext":true,"cited_by_count":5039,"citation_normalized_percentile":{"value":0.99993159,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"27","issue":"3","first_page":"431","last_page":"432"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6664999723434448,"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":0.6664999723434448,"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":0.156700000166893,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.019099999219179153,"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":0.7864351272583008},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7788195610046387},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6149318218231201},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5834840536117554},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.581075131893158},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5734180808067322},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5111239552497864},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4815114438533783},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4633086025714874},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.4584893584251404},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4573383629322052},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.451738178730011},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34029871225357056},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.30800849199295044},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20252281427383423},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12120974063873291}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7864351272583008},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7788195610046387},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6149318218231201},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5834840536117554},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.581075131893158},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5734180808067322},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5111239552497864},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4815114438533783},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4633086025714874},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.4584893584251404},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4573383629322052},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.451738178730011},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34029871225357056},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.30800849199295044},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20252281427383423},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12120974063873291},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"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":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq675","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq675","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/431/917014/btq675.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21149340","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21149340","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},{"id":"pmh:oai:pubmedcentral.nih.gov:3031041","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3031041","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq675","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq675","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/431/917014/btq675.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1625404758","display_name":null,"funder_award_id":"P01HG005062","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G179655095","display_name":null,"funder_award_id":"R01 GM070743","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5291345379","display_name":null,"funder_award_id":"GM070743","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G574326724","display_name":null,"funder_award_id":"P30 MH062261","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G8292457432","display_name":null,"funder_award_id":"P01 HG005062","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155142785.pdf","grobid_xml":"https://content.openalex.org/works/W2155142785.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2080569341","https://openalex.org/W2137531873","https://openalex.org/W2146243727","https://openalex.org/W2159675211"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W4384009753","https://openalex.org/W4309247532","https://openalex.org/W2791776396","https://openalex.org/W4286531993","https://openalex.org/W2964820744"],"abstract_inverted_index":{"UNLABELLED:":[0],"Cytoscape":[1,62,88,109],"is":[2,73,89],"a":[3,49,77,90],"popular":[4],"bioinformatics":[5],"package":[6],"for":[7,108,113],"biological":[8],"network":[9,83],"visualization":[10,37],"and":[11,23,36,82,105],"data":[12,34],"integration.":[13],"Version":[14],"2.8":[15,110],"introduces":[16],"two":[17],"powerful":[18],"new":[19],"features--Custom":[20],"Node":[21,40],"Graphics":[22,41],"Attribute":[24,59],"Equations--which":[25],"can":[26],"be":[27,46],"used":[28],"jointly":[29],"to":[30,45],"greatly":[31],"enhance":[32],"Cytoscape's":[33],"integration":[35],"capabilities.":[38],"Custom":[39],"allow":[42],"an":[43,71],"image":[44],"projected":[47],"onto":[48],"node,":[50],"including":[51],"images":[52],"generated":[53],"dynamically":[54,75],"or":[55],"at":[56],"remote":[57],"locations.":[58],"Equations":[60],"provide":[61],"with":[63],"spreadsheet-like":[64],"functionality":[65],"in":[66],"which":[67],"the":[68,96],"value":[69],"of":[70,79],"attribute":[72],"computed":[74],"as":[76],"function":[78],"other":[80],"attributes":[81],"properties.":[84],"AVAILABILITY":[85],"AND":[86],"IMPLEMENTATION:":[87],"desktop":[91],"Java":[92],"application":[93],"released":[94],"under":[95],"Library":[97],"Gnu":[98],"Public":[99],"License":[100],"(LGPL).":[101],"Binary":[102],"install":[103],"bundles":[104],"source":[106],"code":[107],"are":[111],"available":[112],"download":[114],"from":[115],"http://cytoscape.org.":[116]},"counts_by_year":[{"year":2026,"cited_by_count":90},{"year":2025,"cited_by_count":182},{"year":2024,"cited_by_count":279},{"year":2023,"cited_by_count":306},{"year":2022,"cited_by_count":361},{"year":2021,"cited_by_count":411},{"year":2020,"cited_by_count":410},{"year":2019,"cited_by_count":324},{"year":2018,"cited_by_count":295},{"year":2017,"cited_by_count":335},{"year":2016,"cited_by_count":316},{"year":2015,"cited_by_count":420},{"year":2014,"cited_by_count":453},{"year":2013,"cited_by_count":444},{"year":2012,"cited_by_count":307}],"updated_date":"2026-07-11T18:08:03.149640","created_date":"2025-10-10T00:00:00"}
