{"id":"https://openalex.org/W4292089355","doi":"https://doi.org/10.1093/bioinformatics/btac540","title":"Comparing Petri net-based models of biological systems using Holmes","display_name":"Comparing Petri net-based models of biological systems using Holmes","publication_year":2022,"publication_date":"2022-08-17","ids":{"openalex":"https://openalex.org/W4292089355","doi":"https://doi.org/10.1093/bioinformatics/btac540","pmid":"https://pubmed.ncbi.nlm.nih.gov/35976128"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac540","doi":"https://doi.org/10.1093/bioinformatics/btac540","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac540","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","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/A5067065872","display_name":"Bart\u0142omiej Szawulak","orcid":"https://orcid.org/0000-0002-7584-7383","observed_orcids":["https://orcid.org/0000-0002-7584-7383"]},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Bart\u0142omiej Szawulak","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology , Poznan 60-965, Poland"],"raw_orcid":"https://orcid.org/0000-0002-7584-7383","affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology , Poznan 60-965, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081839975","display_name":"Marcin Radom","orcid":"https://orcid.org/0000-0002-4174-7069","observed_orcids":["https://orcid.org/0000-0002-4174-7069"]},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Marcin Radom","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan 61-704, Poland","Institute of Computing Science, Poznan University of Technology , Poznan 60-965, Poland"],"raw_orcid":"https://orcid.org/0000-0002-4174-7069","affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan 61-704, Poland","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology , Poznan 60-965, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054092040","display_name":"Piotr Formanowicz","orcid":"https://orcid.org/0000-0003-2719-3677","observed_orcids":["https://orcid.org/0000-0003-2719-3677"]},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Piotr Formanowicz","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology , Poznan 60-965, Poland"],"raw_orcid":"https://orcid.org/0000-0003-2719-3677","affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology , Poznan 60-965, Poland","institution_ids":["https://openalex.org/I46597724"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067065872"],"corresponding_institution_ids":["https://openalex.org/I46597724"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1471,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.32355501,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":95},"biblio":{"volume":"38","issue":"19","first_page":"4652","last_page":"4653"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5185999870300293,"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":0.5185999870300293,"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/T11125","display_name":"Petri Nets in System Modeling","score":0.42289999127388,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.025699999183416367,"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/petri-nets","display_name":"Petri nets","score":0.9929999709129333},{"id":"https://openalex.org/keywords/model-comparison","display_name":"model comparison","score":0.8289999961853027},{"id":"https://openalex.org/keywords/mathematical-biology","display_name":"mathematical biology","score":0.7580000162124634},{"id":"https://openalex.org/keywords/t-invariants","display_name":"T-invariants","score":0.8790000081062317},{"id":"https://openalex.org/keywords/decomposition","display_name":"decomposition","score":0.6650000214576721},{"id":"https://openalex.org/keywords/graphlets","display_name":"graphlets","score":0.9959999918937683}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.8205732703208923},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6764030456542969},{"id":"https://openalex.org/C14166107","wikidata":"https://www.wikidata.org/wiki/Q253829","display_name":"Net (polyhedron)","level":2,"score":0.5622356534004211},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4781557023525238},{"id":"https://openalex.org/C197551870","wikidata":"https://www.wikidata.org/wiki/Q7617809","display_name":"Stochastic Petri net","level":3,"score":0.46446484327316284},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1732730269432068},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac540","doi":"https://doi.org/10.1093/bioinformatics/btac540","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac540","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35976128","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35976128","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,"listed_in":[],"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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322481","display_name":"Politechnika Pozna\u0144ska","ror":"https://ror.org/00p7p3302"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1813686880","https://openalex.org/W1980796249","https://openalex.org/W2012459404","https://openalex.org/W2104812688","https://openalex.org/W2148762636","https://openalex.org/W2743050849"],"related_works":["https://openalex.org/W4407363558","https://openalex.org/W2743050849","https://openalex.org/W2110012716","https://openalex.org/W4310937523","https://openalex.org/W7208048661","https://openalex.org/W2011835017","https://openalex.org/W2809538995","https://openalex.org/W7099265934","https://openalex.org/W6920929737","https://openalex.org/W1993980414"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,69],"first":[2],"and":[3,40,108,127],"necessary":[4],"step":[5],"in":[6,59,105,110],"systems":[7,62],"approach":[8],"to":[9,23],"study":[10],"biological":[11,61],"phenomena":[12],"is":[13,22,84],"building":[14],"a":[15,25,80,85,98],"formal":[16,48],"model.":[17],"One":[18],"of":[19,87],"the":[20,42,120],"possibilities":[21],"construct":[24],"model":[26],"based":[27,122],"on":[28,37,41,123],"Petri":[29,73],"nets.":[30],"They":[31],"have":[32],"an":[33],"intuitive":[34],"graphical":[35],"representation":[36],"one":[38],"hand,":[39],"other,":[43],"can":[44,63],"be":[45,64],"analyzed":[46],"using":[47],"mathematical":[49],"methods.":[50],"Finding":[51],"homologies":[52],"or":[53],"conserved":[54],"processes":[55],"playing":[56],"important":[57],"roles":[58],"various":[60],"done":[65],"by":[66],"comparing":[67],"models.":[68],"ones":[70,121],"expressed":[71],"as":[72],"nets":[74],"are":[75,140],"especially":[76],"well-suited":[77],"for":[78,90],"such":[79],"comparison,":[81],"but":[82],"there":[83],"lack":[86],"software":[88],"tools":[89],"this":[91,96,111],"task.":[92],"RESULTS:":[93],"To":[94],"resolve":[95],"problem,":[97],"new":[99],"analytical":[100],"tool":[101],"has":[102],"been":[103],"implemented":[104],"Holmes":[106],"application":[107],"described":[109],"article.":[112],"It":[113],"offers":[114],"four":[115],"different":[116],"comparison":[117],"methods,":[118],"i.e.":[119],"t-invariants,":[124],"decomposition,":[125],"graphlets":[126],"branching":[128],"vertices.":[129],"AVAILABILITY":[130],"AND":[131],"IMPLEMENTATION:":[132],"Available":[133],"at":[134,142],"http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html.":[135],"SUPPLEMENTARY":[136],"INFORMATION:":[137],"Supplementary":[138],"data":[139],"available":[141],"Bioinformatics":[143],"online.":[144]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2022-08-17T00:00:00"}