{"id":"https://openalex.org/W2093521183","doi":"https://doi.org/10.1093/nar/gkq352","title":"VISIBIOweb: visualization and layout services for BioPAX pathway models","display_name":"VISIBIOweb: visualization and layout services for BioPAX pathway models","publication_year":2010,"publication_date":"2010-05-11","ids":{"openalex":"https://openalex.org/W2093521183","doi":"https://doi.org/10.1093/nar/gkq352","mag":"2093521183","pmid":"https://pubmed.ncbi.nlm.nih.gov/20460470"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq352","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq352","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W150/3849260/gkq352.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W150/3849260/gkq352.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062804198","display_name":"A. Dilek","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"A. Dilek","raw_affiliation_strings":["Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara 06800, Turkey"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara 06800, Turkey","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080092881","display_name":"Mehmet E. Belviranl\u0131","orcid":"https://orcid.org/0000-0001-9434-9833"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"M. E. Belviranli","raw_affiliation_strings":["Center for Bioinformatics and 2Computer Engineering Department, Bilkent University, Ankara 06800, Turkey"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and 2Computer Engineering Department, Bilkent University, Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006798669","display_name":"U\u011fur Do\u011frus\u00f6z","orcid":"https://orcid.org/0000-0002-7153-0784"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"U. Dogrusoz","raw_affiliation_strings":["Center for Bioinformatics and 2Computer Engineering Department, Bilkent University, Ankara 06800, Turkey"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and 2Computer Engineering Department, Bilkent University, Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5062804198"],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.6759,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.694709,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"38","issue":"Web Server","first_page":"W150","last_page":"W154"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.998199999332428,"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/visualization","display_name":"Visualization","score":0.7304930686950684},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6851785182952881},{"id":"https://openalex.org/keywords/zoom","display_name":"Zoom","score":0.6182779669761658},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.46907681226730347},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4511401951313019},{"id":"https://openalex.org/keywords/hypertext","display_name":"Hypertext","score":0.4447326958179474},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4245694875717163},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.41255903244018555},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34381103515625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.329278826713562},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.23884254693984985}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7304930686950684},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6851785182952881},{"id":"https://openalex.org/C124913957","wikidata":"https://www.wikidata.org/wiki/Q1232548","display_name":"Zoom","level":3,"score":0.6182779669761658},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.46907681226730347},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4511401951313019},{"id":"https://openalex.org/C162215914","wikidata":"https://www.wikidata.org/wiki/Q93241","display_name":"Hypertext","level":2,"score":0.4447326958179474},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4245694875717163},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.41255903244018555},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34381103515625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.329278826713562},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.23884254693984985},{"id":"https://openalex.org/C15336307","wikidata":"https://www.wikidata.org/wiki/Q1766051","display_name":"Lens (geology)","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkq352","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq352","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W150/3849260/gkq352.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20460470","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20460470","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W150","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W150","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:2896092","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkq352","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/22323","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/22323","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq352","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq352","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W150/3849260/gkq352.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2093521183.pdf","grobid_xml":"https://content.openalex.org/works/W2093521183.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1877439477","https://openalex.org/W1999895438","https://openalex.org/W2038264484","https://openalex.org/W2069157810","https://openalex.org/W2091789479","https://openalex.org/W2096766502","https://openalex.org/W2099007946","https://openalex.org/W2107062718","https://openalex.org/W2116864243","https://openalex.org/W2123060905","https://openalex.org/W2128601422","https://openalex.org/W2140947746","https://openalex.org/W2143969914","https://openalex.org/W2150908245","https://openalex.org/W2155967165","https://openalex.org/W2160540739","https://openalex.org/W4230392683"],"related_works":["https://openalex.org/W1536970214","https://openalex.org/W1565135491","https://openalex.org/W2788595494","https://openalex.org/W1815780662","https://openalex.org/W2897383060","https://openalex.org/W2264492131","https://openalex.org/W3048792174","https://openalex.org/W1791756088","https://openalex.org/W2244676099","https://openalex.org/W2337877695"],"abstract_inverted_index":{"With":[0,54],"recent":[1],"advancements":[2],"in":[3,51,105],"techniques":[4],"for":[5,48],"cellular":[6,11,30],"data":[7],"acquisition,":[8],"information":[9],"on":[10],"processes":[12,31],"has":[13],"been":[14],"increasing":[15],"at":[16],"a":[17,39],"dramatic":[18],"rate.":[19],"Visualization":[20],"is":[21,34,38,134,143,148],"critical":[22],"to":[23,138],"analyzing":[24],"and":[25,45,75,93,136,141],"interpreting":[26],"complex":[27],"information;":[28],"representing":[29],"or":[32],"pathways":[33],"no":[35,144],"exception.":[36],"VISIBIOweb":[37,117],"free,":[40],"open-source,":[41],"web-based":[42],"pathway":[43,49,62,96],"visualization":[44],"layout":[46,114],"service":[47],"models":[50,63],"BioPAX":[52],"format.":[53],"VISIBIOweb,":[55],"one":[56],"can":[57,76],"obtain":[58],"well-laid-out":[59],"views":[60,79,87],"of":[61,68,116],"using":[64,91,126],"the":[65,69,106],"standard":[66],"notation":[67],"Systems":[70],"Biology":[71],"Graphical":[72],"Notation":[73],"(SBGN),":[74],"embed":[77],"such":[78],"within":[80],"one's":[81],"web":[82,132],"pages":[83],"as":[84],"desired.":[85],"Pathway":[86],"may":[88,108,118],"be":[89,109,120],"navigated":[90],"zoom":[92],"scroll":[94],"tools;":[95],"object":[97],"properties,":[98],"including":[99],"any":[100],"external":[101],"database":[102],"references":[103],"available":[104,149],"data,":[107],"inspected":[110],"interactively.":[111],"The":[112,131],"automatic":[113],"component":[115],"also":[119],"accessed":[121],"programmatically":[122],"from":[123],"other":[124],"tools":[125],"Hypertext":[127],"Transfer":[128],"Protocol":[129],"(HTTP).":[130],"site":[133],"free":[135],"open":[137],"all":[139],"users":[140],"there":[142],"login":[145],"requirement.":[146],"It":[147],"at:":[150],"http://visibioweb.patika.org.":[151]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
