{"id":"https://openalex.org/W2461732257","doi":"https://doi.org/10.12688/f1000research.9090.1","title":"AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations","display_name":"AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations","publication_year":2016,"publication_date":"2016-07-15","ids":{"openalex":"https://openalex.org/W2461732257","doi":"https://doi.org/10.12688/f1000research.9090.1","mag":"2461732257","pmid":"https://pubmed.ncbi.nlm.nih.gov/27830058"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.9090.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.9090.1","pdf_url":"https://f1000research.com/articles/5-1717/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000research.com/articles/5-1717/v1/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036643995","display_name":"Mike Kucera","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Mike Kucera","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Canada","The Donnelly Centre, University of Toronto, Toronto"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060081041","display_name":"Ruth Isserlin","orcid":"https://orcid.org/0000-0002-6805-2080"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ruth Isserlin","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Canada","The Donnelly Centre, University of Toronto, Toronto"],"raw_orcid":"https://orcid.org/0000-0002-6805-2080","affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080373211","display_name":"Arkady Arkhangorodsky","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Arkady Arkhangorodsky","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Canada","The Donnelly Centre, University of Toronto, Toronto"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010789029","display_name":"Gary D. Bader","orcid":"https://orcid.org/0000-0003-0185-8861"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Gary D. Bader","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Canada","The Donnelly Centre, University of Toronto, Toronto"],"raw_orcid":"https://orcid.org/0000-0003-0185-8861","affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5036643995"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":6.8914,"has_fulltext":true,"cited_by_count":409,"citation_normalized_percentile":{"value":0.97431547,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"5","issue":null,"first_page":"1717","last_page":"1717"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.9315999746322632,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9017999768257141,"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":0.7645249366760254},{"id":"https://openalex.org/keywords/personalization","display_name":"Personalization","score":0.6593077182769775},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5741257071495056},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5124407410621643},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36685553193092346},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33414924144744873},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.25290751457214355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1586257815361023}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7645249366760254},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.6593077182769775},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5741257071495056},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5124407410621643},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36685553193092346},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33414924144744873},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.25290751457214355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1586257815361023},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.12688/f1000research.9090.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.9090.1","pdf_url":"https://f1000research.com/articles/5-1717/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},{"id":"pmid:27830058","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27830058","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":"F1000Research","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5082607","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5082607","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"F1000Res","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c884a1f1a7af476a8c8aed08f93296a8","is_oa":true,"landing_page_url":"https://doaj.org/article/c884a1f1a7af476a8c8aed08f93296a8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"F1000Research, Vol 5 (2016)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.9090.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.9090.1","pdf_url":"https://f1000research.com/articles/5-1717/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth"}],"awards":[{"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/G2410752989","display_name":"Administrative Supplement for Equipment in Support of NRNB Aims","funder_award_id":"3p41gm103504-14s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2760231196","display_name":"Cytoscape: A Modeling Platform for Biomolecular Networks","funder_award_id":"4r01gm070743-13","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G286119748","display_name":null,"funder_award_id":"R01 HG009979","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3316149902","display_name":null,"funder_award_id":"P41-GM103504","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3825576971","display_name":null,"funder_award_id":"U41 HG006623","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/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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2461732257.pdf","grobid_xml":"https://content.openalex.org/works/W2461732257.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1649645444","https://openalex.org/W1889220376","https://openalex.org/W1908296277","https://openalex.org/W2070040136","https://openalex.org/W2097948046","https://openalex.org/W2103017472","https://openalex.org/W2136850043","https://openalex.org/W2138487969","https://openalex.org/W2143892509","https://openalex.org/W2163187547","https://openalex.org/W3209604033"],"related_works":["https://openalex.org/W2109940557","https://openalex.org/W2466832359","https://openalex.org/W3172493050","https://openalex.org/W1582019636","https://openalex.org/W1499005795","https://openalex.org/W2593798266","https://openalex.org/W2070126461","https://openalex.org/W4385420271","https://openalex.org/W4312192618","https://openalex.org/W2071659704"],"abstract_inverted_index":{"Networks":[0],"often":[1],"contain":[2],"regions":[3],"of":[4,23,80,162],"tightly":[5],"connected":[6],"nodes,":[7],"or":[8,170],"clusters,":[9],"that":[10,76,120],"highlight":[11],"their":[12],"shared":[13],"relationships.":[14],"An":[15],"effective":[16],"way":[17],"to":[18,27,45,95,105,124,159],"create":[19],"a":[20,24,38,47,62,67,72,100,147],"visual":[21],"summary":[22],"network":[25,48,148],"is":[26,71,157],"identify":[28],"clusters":[29,82,98,132],"and":[30,37,51,83,92,102,112],"annotate":[31,46,97],"them":[32],"with":[33,49,107],"an":[34],"enclosing":[35],"shape":[36],"summarizing":[39],"label.":[40],"Cytoscape":[41,73,141],"provides":[42,103],"the":[43,78,90,122,126,140],"ability":[44],"shapes":[50],"labels,":[52],"however":[53],"these":[54],"annotations":[55,128],"must":[56],"be":[57,66,134],"created":[58],"manually":[59],"one":[60],"at":[61],"time,":[63],"which":[64,144],"can":[65],"laborious":[68],"process.":[69],"AutoAnnotate":[70,156],"3":[74],"App":[75],"automates":[77],"process":[79],"identifying":[81,111],"visually":[84],"annotating":[85],"them.":[86],"It":[87],"greatly":[88],"reduces":[89],"time":[91],"effort":[93],"required":[94],"fully":[96],"in":[99],"network,":[101,163],"freedom":[104],"experiment":[106],"different":[108],"strategies":[109],"for":[110],"labelling":[113],"clusters.":[114],"Many":[115],"customization":[116],"options":[117],"are":[118],"available":[119],"enable":[121],"user":[123],"refine":[125],"generated":[127],"as":[129],"required.":[130],"Annotated":[131],"may":[133],"collapsed":[135],"into":[136],"single":[137],"nodes":[138],"using":[139],"groups":[142],"feature,":[143],"helps":[145],"simplify":[146],"by":[149],"making":[150],"its":[151],"overall":[152],"structure":[153],"more":[154],"visible.":[155],"applicable":[158],"any":[160],"type":[161],"including":[164],"enrichment":[165],"maps,":[166],"protein-protein":[167],"interactions,":[168],"pathways,":[169],"social":[171],"networks.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":31},{"year":2025,"cited_by_count":41},{"year":2024,"cited_by_count":70},{"year":2023,"cited_by_count":48},{"year":2022,"cited_by_count":69},{"year":2021,"cited_by_count":66},{"year":2020,"cited_by_count":42},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-10-10T00:00:00"}
