{"id":"https://openalex.org/W2978318970","doi":"https://doi.org/10.1109/tcbb.2019.2944905","title":"DORMAN: Database of Reconstructed MetAbolic Networks","display_name":"DORMAN: Database of Reconstructed MetAbolic Networks","publication_year":2019,"publication_date":"2019-10-01","ids":{"openalex":"https://openalex.org/W2978318970","doi":"https://doi.org/10.1109/tcbb.2019.2944905","mag":"2978318970","pmid":"https://pubmed.ncbi.nlm.nih.gov/31581093"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2944905","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2944905","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Furkan Ozden","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":"Furkan Ozden","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Metin Can Siper","orcid":"https://orcid.org/0000-0002-7556-093X"},"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":"Metin Can Siper","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-7556-093X","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Necmi Acarsoy","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":"Necmi Acarsoy","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tugrulcan Elmas","orcid":"https://orcid.org/0000-0002-4305-1479"},"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":"Tugrulcan Elmas","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-4305-1479","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Bryan Marty","orcid":null},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bryan Marty","raw_affiliation_strings":["EECS Department, Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EECS Department, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Xinjian Qi","orcid":null},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinjian Qi","raw_affiliation_strings":["EECS Department, Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EECS Department, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":null,"display_name":"A. Ercument Cicek","orcid":"https://orcid.org/0000-0001-8613-6619"},"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":"A. Ercument Cicek","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0001-8613-6619","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0829,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.46742804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"18","issue":"4","first_page":"1474","last_page":"1480"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9894999861717224,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9894999861717224,"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":0.001500000013038516,"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/T12643","display_name":"Sustainability and Ecological Systems Analysis","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/2305","display_name":"Environmental Engineering"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6032000184059143},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.5920000076293945},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.49709999561309814},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.43799999356269836},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.4244999885559082},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.412200003862381},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.39149999618530273}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8025000095367432},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6032000184059143},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.5920000076293945},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.49709999561309814},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.43799999356269836},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.4244999885559082},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.412200003862381},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40860000252723694},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.39149999618530273},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.3853999972343445},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.3813999891281128},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.36419999599456787},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34860000014305115},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3431999981403351},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3359000086784363},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31209999322891235},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2689000070095062},{"id":"https://openalex.org/C3018263672","wikidata":"https://www.wikidata.org/wiki/Q1296251","display_name":"Efficient algorithm","level":2,"score":0.25920000672340393},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.25450000166893005}],"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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2019.2944905","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2944905","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31581093","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31581093","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/76850","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/76850","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":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310281","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666"},{"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":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1952732684","https://openalex.org/W1974325331","https://openalex.org/W1978435670","https://openalex.org/W1993967688","https://openalex.org/W2005786953","https://openalex.org/W2010707723","https://openalex.org/W2026725606","https://openalex.org/W2027109445","https://openalex.org/W2028561804","https://openalex.org/W2042141122","https://openalex.org/W2050153048","https://openalex.org/W2075283200","https://openalex.org/W2079366428","https://openalex.org/W2083011190","https://openalex.org/W2093925352","https://openalex.org/W2100084634","https://openalex.org/W2111796963","https://openalex.org/W2120599990","https://openalex.org/W2134221731","https://openalex.org/W2140947746","https://openalex.org/W2161309440","https://openalex.org/W2165373392","https://openalex.org/W2167539386","https://openalex.org/W2169336096","https://openalex.org/W2202347610","https://openalex.org/W4238101851","https://openalex.org/W4256259619","https://openalex.org/W6683401941","https://openalex.org/W6685327987"],"related_works":[],"abstract_inverted_index":{"Genome-scale":[0],"reconstructed":[1,31,87,109],"metabolic":[2,32,110],"networks":[3,33,111],"have":[4],"provided":[5],"an":[6],"organism":[7],"specific":[8],"understanding":[9],"of":[10,28,45,85,94,130,140],"cellular":[11],"processes":[12],"and":[13,52,58,116,123,148,174,176,195],"their":[14],"relations":[15],"to":[16,23,35,42,75,159],"phenotype.":[17],"As":[18],"they":[19],"are":[20,67,79,132],"deemed":[21],"essential":[22],"study":[24],"metabolism,":[25],"the":[26,43,73,83,86,92,114,125,141,150,163],"number":[27],"organisms":[29],"with":[30,185],"continues":[34],"increase.":[36],"This":[37],"everlasting":[38],"research":[39],"interest":[40],"lead":[41],"development":[44],"online":[46,104,194],"systems/repositories":[47],"that":[48,63,106,137,155,169,181],"store":[49],"existing":[50],"reconstructions":[51],"enable":[53],"new":[54],"model":[55,65,126,178],"generation,":[56],"integration,":[57],"constraint-based":[59],"analyses.":[60],"While":[61],"features":[62,129],"support":[64],"reconstruction":[66],"widely":[68],"available,":[69],"current":[70],"systems":[71],"lack":[72],"means":[74],"help":[76],"users":[77],"who":[78],"interested":[80],"in":[81,113,162],"analyzing":[82,124],"topology":[84],"networks.":[88],"Here,":[89],"we":[90],"present":[91],"Database":[93],"Reconstructed":[95],"Metabolic":[96],"Networks":[97],"-":[98],"DORMAN.":[99],"DORMAN":[100,131,192],"is":[101,193],"a":[102],"centralized":[103],"database":[105],"stores":[107],"SBML-based":[108],"published":[112],"literature,":[115],"provides":[117,156],"web-based":[118],"computational":[119],"tools":[120],"for":[121],"visualizing":[122],"topology.":[127],"Novel":[128],"(i)":[133],"interactive":[134],"visualization":[135],"interface":[136,168],"allows":[138],"rendering":[139],"complete":[142],"network":[143],"as":[144,146],"well":[145],"editing":[147],"exporting":[149],"model,":[151,164],"(ii)":[152],"hierarchical":[153],"navigation":[154],"efficient":[157],"access":[158],"connected":[160],"entities":[161],"(iii)":[165],"built-in":[166],"query":[167],"allow":[170],"posing":[171],"topological":[172],"queries,":[173],"finally,":[175],"(iv)":[177],"comparison":[179],"tool":[180],"enables":[182],"comparing":[183],"models":[184],"different":[186],"nomenclatures,":[187],"using":[188],"approximate":[189],"string":[190],"matching.":[191],"freely":[196],"accessible":[197],"at":[198],"http://ciceklab.cs.bilkent.edu.tr/dorman.":[199]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2019-10-10T00:00:00"}
