{"id":"https://openalex.org/W4308951967","doi":"https://doi.org/10.1371/journal.pcbi.1010635","title":"SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more","display_name":"SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more","publication_year":2022,"publication_date":"2022-11-14","ids":{"openalex":"https://openalex.org/W4308951967","doi":"https://doi.org/10.1371/journal.pcbi.1010635","pmid":"https://pubmed.ncbi.nlm.nih.gov/36374853"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010635","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010635","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010635&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010635&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062979397","display_name":"Hasan Balc\u0131","orcid":"https://orcid.org/0000-0001-8319-7758"},"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":"Hasan Balci","raw_affiliation_strings":["i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0001-8319-7758","affiliations":[{"raw_affiliation_string":"i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","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":true,"raw_author_name":"Ugur Dogrusoz","raw_affiliation_strings":["i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-7153-0784","affiliations":[{"raw_affiliation_string":"i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089319314","display_name":"Yusuf Ziya Ozgul","orcid":null},"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":"Yusuf Ziya Ozgul","raw_affiliation_strings":["i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016456334","display_name":"Perman Atayev","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Perman Atayev","raw_affiliation_strings":["Odoo S.A., Chauss\u00e9e de Namur, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Odoo S.A., Chauss\u00e9e de Namur, Belgium","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5006798669"],"corresponding_institution_ids":["https://openalex.org/I168864056"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0868,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.44116067,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"18","issue":"11","first_page":"e1010635","last_page":"e1010635"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976999759674072,"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":0.9976999759674072,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9952999949455261,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9916999936103821,"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/sbml","display_name":"SBML","score":0.9317827224731445},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.642113447189331},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.5926048755645752},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4600391983985901},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3024073839187622},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.18330347537994385},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.11692360043525696}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9317827224731445},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.642113447189331},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.5926048755645752},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4600391983985901},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3024073839187622},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.18330347537994385},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.11692360043525696}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1010635","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010635","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010635&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:36374853","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36374853","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1010635","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010635","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:be172a54801f43deaab6a79fbe23168d","is_oa":true,"landing_page_url":"https://doaj.org/article/be172a54801f43deaab6a79fbe23168d","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":"PLoS Computational Biology, Vol 18, Iss 11, p e1010635 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9704760","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9704760","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/111991","is_oa":true,"landing_page_url":"http://hdl.handle.net/11693/111991","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010635","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010635","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010635&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8429629245","display_name":null,"funder_award_id":"118E131","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4308951967.pdf","grobid_xml":"https://content.openalex.org/works/W4308951967.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1484040084","https://openalex.org/W1969709265","https://openalex.org/W1971937094","https://openalex.org/W1973661008","https://openalex.org/W1998971866","https://openalex.org/W2025183726","https://openalex.org/W2028133290","https://openalex.org/W2066081314","https://openalex.org/W2079589956","https://openalex.org/W2081211779","https://openalex.org/W2093521183","https://openalex.org/W2117364474","https://openalex.org/W2150908245","https://openalex.org/W2163993275","https://openalex.org/W2169528473","https://openalex.org/W2179127114","https://openalex.org/W2767914218","https://openalex.org/W2981350712","https://openalex.org/W2988361147","https://openalex.org/W3019461979","https://openalex.org/W3036988853","https://openalex.org/W3090217015","https://openalex.org/W3178793612"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W291250033","https://openalex.org/W2008385118","https://openalex.org/W2035757446","https://openalex.org/W880955280","https://openalex.org/W2106647072","https://openalex.org/W4246858109","https://openalex.org/W54172855","https://openalex.org/W2170209930","https://openalex.org/W2046782623"],"abstract_inverted_index":{"Visualization":[0],"is":[1,13,17,68,97,295,315],"a":[2,46,101,144,227,241,249,312],"key":[3],"recurring":[4],"requirement":[5],"for":[6,51,103,111,155,289,318],"effective":[7,52],"analysis":[8,53],"of":[9,33,43,54,60,75,90,108,121,158,169,180,184,226,229,244,246,252,275],"relational":[10],"data.":[11,56,77],"Biology":[12,150,207,216],"no":[14],"exception.":[15],"It":[16],"imperative":[18],"to":[19,200,248,269,283],"annotate":[20],"and":[21,116,152,176,194,212,224,266,272,278,286,298,303],"render":[22],"biological":[23,62,91,109,159],"models":[24,277],"in":[25,45,70,93,161,172],"standard,":[26],"widely":[27],"accepted":[28],"formats.":[29],"Finding":[30],"graph-theoretical":[31,231],"properties":[32,232],"pathways":[34,92,110],"as":[35,37,100,165,167,192,203,233,235,262,279],"well":[36,166,234],"identifying":[38],"certain":[39],"paths":[40,118],"or":[41,105,119],"subgraphs":[42,120],"interest":[44,247],"pathway":[47,55,63,251,276],"are":[48,81,126,188,198],"also":[49],"essential":[50],"Given":[57],"the":[58,72,185,307],"size":[59],"available":[61,83,99,300,316],"data":[64,160],"nowadays,":[65],"automatic":[66,112,135,156],"layout":[67,136,157,265,285],"crucial":[69],"understanding":[71],"graphical":[73,88],"representations":[74],"such":[76,191,202],"Even":[78],"though":[79],"there":[80,96,125],"many":[82,127],"software":[84,292],"tools":[85,128],"that":[86,256],"support":[87],"display":[89],"various":[94,162],"formats,":[95],"none":[98],"service":[102,146,268,282],"on-demand":[104],"batch":[106],"processing":[107],"layout,":[113],"customized":[114,170,271],"rendering":[115,131,267,287],"mining":[117],"interest.":[122,253],"In":[123,219,310],"addition,":[124,220,311],"with":[129],"fine":[130],"capabilities":[132,288],"lacking":[133],"decent":[134],"support.":[137],"To":[138],"fill":[139],"this":[140],"void,":[141],"we":[142],"developed":[143],"web":[145],"named":[147],"SyBLaRS":[148,221,257,294],"(Systems":[149],"Layout":[151],"Rendering":[153],"Service)":[154],"standard":[163],"formats":[164,179],"construction":[168],"images":[171],"both":[173,261],"raster":[174],"image":[175],"scalable":[177],"vector":[178],"these":[181],"maps.":[182],"Some":[183],"supported":[186],"standards":[187],"more":[189],"generic":[190],"GraphML":[193],"JSON,":[195],"whereas":[196],"others":[197],"specialized":[199],"biology":[201,291],"SBGNML":[204],"(The":[205,214],"Systems":[206,215],"Graphical":[208],"Notation":[209],"Markup":[210,217],"Language)":[211],"SBML":[213],"Language).":[218],"supports":[222],"calculation":[223],"highlighting":[225],"number":[228],"well-known":[230],"some":[236],"novel":[237],"graph":[238],"algorithms":[239],"turning":[240],"specified":[242],"set":[243],"objects":[245],"minimal":[250],"We":[254],"demonstrate":[255],"can":[258],"be":[259],"used":[260],"an":[263,280],"offline":[264],"construct":[270],"annotated":[273],"pictures":[274],"online":[281],"provide":[284],"systems":[290],"tools.":[293],"open":[296],"source":[297],"publicly":[299],"on":[301],"GitHub":[302],"freely":[304],"distributed":[305],"under":[306],"MIT":[308],"license.":[309],"sample":[313],"deployment":[314],"here":[317],"public":[319],"consumption.":[320]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
