{"id":"https://openalex.org/W2794465419","doi":"https://doi.org/10.1142/s0219720018500075","title":"EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes","display_name":"EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes","publication_year":2018,"publication_date":"2018-03-27","ids":{"openalex":"https://openalex.org/W2794465419","doi":"https://doi.org/10.1142/s0219720018500075","mag":"2794465419","pmid":"https://pubmed.ncbi.nlm.nih.gov/29783871"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720018500075","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720018500075","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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":"https://openalex.org/A5071263485","display_name":"Hasan Fehmi Danaci","orcid":null},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Hasan Fehmi Danaci","raw_affiliation_strings":["Department of Computer Engineering, Middle East Technical University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037440533","display_name":"Reng\u00fcl \u00c7etin-Atalay","orcid":"https://orcid.org/0000-0003-2408-6606"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Rengul Cetin-Atalay","raw_affiliation_strings":["KanSiL, Cancer Systems Biology Laboratory, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KanSiL, Cancer Systems Biology Laboratory, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042515589","display_name":"Volkan Atalay","orcid":"https://orcid.org/0000-0001-7850-0601"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Volkan Atalay","raw_affiliation_strings":["Department of Computer Engineering, Middle East Technical University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0001-7850-0601","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071263485"],"corresponding_institution_ids":["https://openalex.org/I201799495"],"apc_list":null,"apc_paid":null,"fwci":0.1062,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.42331387,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"16","issue":"04","first_page":"1850007","last_page":"1850007"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9890999794006348,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.984000027179718,"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/biological-network","display_name":"Biological network","score":0.697494626045227},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6180861592292786},{"id":"https://openalex.org/keywords/graph-layout","display_name":"Graph Layout","score":0.5990527272224426},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5544996857643127},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5015618801116943},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.4980590343475342},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.47394469380378723},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.43669217824935913},{"id":"https://openalex.org/keywords/directed-graph","display_name":"Directed graph","score":0.43647098541259766},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.42627424001693726},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40673747658729553},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.3958676755428314},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3763056993484497},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.25963807106018066},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.20078149437904358},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18991827964782715},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1711389422416687},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1529322862625122}],"concepts":[{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.697494626045227},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6180861592292786},{"id":"https://openalex.org/C2911174283","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph Layout","level":4,"score":0.5990527272224426},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5544996857643127},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5015618801116943},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4980590343475342},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47394469380378723},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.43669217824935913},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.43647098541259766},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.42627424001693726},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40673747658729553},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.3958676755428314},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3763056993484497},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.25963807106018066},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.20078149437904358},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18991827964782715},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1711389422416687},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1529322862625122},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720018500075","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720018500075","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:29783871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29783871","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:open.metu.edu.tr:11511/42845","is_oa":false,"landing_page_url":"https://hdl.handle.net/11511/42845","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W634834491","https://openalex.org/W1985653533","https://openalex.org/W2075220720","https://openalex.org/W2116864243","https://openalex.org/W2117737004","https://openalex.org/W2121905803","https://openalex.org/W2137439611","https://openalex.org/W2147714160","https://openalex.org/W2159675211","https://openalex.org/W2167482691"],"related_works":["https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W2098027521","https://openalex.org/W2171298469","https://openalex.org/W4214598766","https://openalex.org/W2165891030","https://openalex.org/W4256036414","https://openalex.org/W1561795279","https://openalex.org/W2119031886","https://openalex.org/W2082199132"],"abstract_inverted_index":{"Visualizing":[0],"large-scale":[1],"data":[2],"produced":[3],"by":[4],"the":[5,36,48,58,70,74,79,84,87,90,96,101,118,127],"high":[6],"throughput":[7],"experiments":[8],"as":[9,55,133],"a":[10,22,112,134],"biological":[11,29,71,115],"graph":[12],"leads":[13],"to":[14,126,136],"better":[15],"understanding":[16],"and":[17,73,94,117],"analysis.":[18],"This":[19],"study":[20],"describes":[21],"customized":[23],"force-directed":[24],"layout":[25],"algorithm,":[26],"EClerize,":[27],"for":[28],"graphs":[30],"that":[31,82,99],"represent":[32],"pathways":[33,116],"in":[34,121],"which":[35],"nodes":[37,46,63,88],"are":[38,53,64],"associated":[39],"with":[40,47,124],"Enzyme":[41],"Commission":[42],"(EC)":[43],"attributes.":[44],"The":[45],"same":[49,59,91],"EC":[50,92,106],"class":[51],"numbers":[52],"treated":[54],"members":[56],"of":[57,62,89,114],"cluster.":[60],"Positions":[61],"then":[65],"determined":[66],"based":[67],"on":[68,111],"both":[69],"similarity":[72],"connection":[75],"structure.":[76],"EClerize":[77,108,130],"minimizes":[78],"intra-cluster":[80],"distance,":[81,98],"is":[83,100,109,122,131],"distance":[85,102],"between":[86,103],"cluster":[93],"maximizes":[95],"inter-cluster":[97],"two":[104],"distinct":[105],"clusters.":[107],"tested":[110],"number":[113],"improvement":[119],"brought":[120],"presented":[123],"respect":[125],"original":[128],"algorithm.":[129],"available":[132],"plug-in":[135],"Cytoscape":[137],"(":[138],"http://apps.cytoscape.org/apps/eclerize":[139],").":[140]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
