{"id":"https://openalex.org/W3041939341","doi":"https://doi.org/10.1515/jib-2020-0015","title":"Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2","display_name":"Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2","publication_year":2020,"publication_date":"2020-06-01","ids":{"openalex":"https://openalex.org/W3041939341","doi":"https://doi.org/10.1515/jib-2020-0015","mag":"3041939341","pmid":"https://pubmed.ncbi.nlm.nih.gov/32628633"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2020-0015","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0015","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0015/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0015/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074158993","display_name":"Fengkai Zhang","orcid":"https://orcid.org/0000-0001-7112-9328"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Fengkai Zhang","raw_affiliation_strings":["NIAID/NIH , Bethesda , USA"],"raw_orcid":"https://orcid.org/0000-0001-7112-9328","affiliations":[{"raw_affiliation_string":"NIAID/NIH , Bethesda , USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucian P. Smith","raw_affiliation_strings":["University of Washington , Seattle , USA"],"raw_orcid":"https://orcid.org/0000-0001-7002-6386","affiliations":[{"raw_affiliation_string":"University of Washington , Seattle , USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107139754","display_name":"Michael L. Blinov","orcid":"https://orcid.org/0000-0002-9363-9705"},"institutions":[{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael L. Blinov","raw_affiliation_strings":["UConn Health , Farmington , USA"],"raw_orcid":"https://orcid.org/0000-0002-9363-9705","affiliations":[{"raw_affiliation_string":"UConn Health , Farmington , USA","institution_ids":["https://openalex.org/I75929689"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020336186","display_name":"James R. Faeder","orcid":"https://orcid.org/0000-0001-8127-609X"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Faeder","raw_affiliation_strings":["University of Pittsburgh , Pittsburgh , USA"],"raw_orcid":"https://orcid.org/0000-0001-8127-609X","affiliations":[{"raw_affiliation_string":"University of Pittsburgh , Pittsburgh , USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016126519","display_name":"William S. Hlavacek","orcid":"https://orcid.org/0000-0003-4383-8711"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William S. Hlavacek","raw_affiliation_strings":["Los Alamos National Laboratory , Los Alamos , USA"],"raw_orcid":"https://orcid.org/0000-0003-4383-8711","affiliations":[{"raw_affiliation_string":"Los Alamos National Laboratory , Los Alamos , USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040464646","display_name":"Jos\u00e9 Juan Tapia","orcid":"https://orcid.org/0000-0002-8392-6022"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose Juan Tapia","raw_affiliation_strings":["University of Pittsburgh , Pittsburgh , USA"],"raw_orcid":"https://orcid.org/0000-0002-8392-6022","affiliations":[{"raw_affiliation_string":"University of Pittsburgh , Pittsburgh , USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049649026","display_name":"Sarah Keating","orcid":"https://orcid.org/0000-0002-3356-3542"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah M. Keating","raw_affiliation_strings":["European Bioinformatics Institute , Cambridge , UK"],"raw_orcid":"https://orcid.org/0000-0002-3356-3542","affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute , Cambridge , UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002460040","display_name":"Nicol\u00e1s Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-9290-7894"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicolas Rodriguez","raw_affiliation_strings":["Babraham Institute , Cambridge , UK"],"raw_orcid":"https://orcid.org/0000-0002-9290-7894","affiliations":[{"raw_affiliation_string":"Babraham Institute , Cambridge , UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065854572","display_name":"Andreas Dr\u00e4ger","orcid":"https://orcid.org/0000-0002-1240-5553"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Dr\u00e4ger","raw_affiliation_strings":["Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens , Institute for Bioinformatics and Medical Informatics (IBMI), University of T\u00fcbingen , T\u00fcbingen , Germany"],"raw_orcid":"https://orcid.org/0000-0002-1240-5553","affiliations":[{"raw_affiliation_string":"Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens , Institute for Bioinformatics and Medical Informatics (IBMI), University of T\u00fcbingen , T\u00fcbingen , Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010400772","display_name":"Leonard A. Harris","orcid":"https://orcid.org/0000-0003-2112-6940"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leonard A. Harris","raw_affiliation_strings":["Vanderbilt University School of Medicine , Nashville , USA"],"raw_orcid":"https://orcid.org/0000-0003-2112-6940","affiliations":[{"raw_affiliation_string":"Vanderbilt University School of Medicine , Nashville , USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090126272","display_name":"Andrew Finney","orcid":null},"institutions":[{"id":"https://openalex.org/I4210115305","display_name":"German Center for Infection Research","ror":"https://ror.org/028s4q594","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210115305","https://openalex.org/I4405256427"]},{"id":"https://openalex.org/I4210142761","display_name":"Osys Technology","ror":"https://ror.org/04zhxxe39","country_code":"GB","type":"other","lineage":["https://openalex.org/I4210142761"]},{"id":"https://openalex.org/I4210157649","display_name":"Ansys (United Kingdom)","ror":"https://ror.org/0579hfc41","country_code":"GB","type":"company","lineage":["https://openalex.org/I21160419","https://openalex.org/I4210157649"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE","GB"],"is_corresponding":false,"raw_author_name":"Andrew Finney","raw_affiliation_strings":["Ansys UK Ltd , Abingdon , UK","Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen , Germany","German Center for Infection Research (DZIF) , partner site T\u00fcbingen , Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ansys UK Ltd , Abingdon , UK","institution_ids":["https://openalex.org/I4210142761","https://openalex.org/I4210157649"]},{"raw_affiliation_string":"Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen , Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"German Center for Infection Research (DZIF) , partner site T\u00fcbingen , Germany","institution_ids":["https://openalex.org/I4210115305"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Bin Hu","orcid":"https://orcid.org/0000-0002-3775-387X"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Hu","raw_affiliation_strings":["Los Alamos National Laboratory , Los Alamos , USA"],"raw_orcid":"https://orcid.org/0000-0002-3775-387X","affiliations":[{"raw_affiliation_string":"Los Alamos National Laboratory , Los Alamos , USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016716446","display_name":"Michael Hucka","orcid":"https://orcid.org/0000-0001-9105-5960"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Hucka","raw_affiliation_strings":["California Institute of Technology , Pasadena , USA"],"raw_orcid":"https://orcid.org/0000-0001-9105-5960","affiliations":[{"raw_affiliation_string":"California Institute of Technology , Pasadena , USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059988994","display_name":"Martin Meier\u2010Schellersheim","orcid":"https://orcid.org/0000-0002-8754-6377"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Martin Meier-Schellersheim","raw_affiliation_strings":["NIAID/NIH , Bethesda , USA"],"raw_orcid":"https://orcid.org/0000-0002-8754-6377","affiliations":[{"raw_affiliation_string":"NIAID/NIH , Bethesda , USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5074158993"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6669,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.67416266,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"17","issue":"2-3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9958999752998352,"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":0.9958999752998352,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9900000095367432,"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":0.9819999933242798,"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":0.9887620210647583},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.9122909903526306},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.785847544670105},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5321663618087769},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.47571995854377747},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.464843213558197},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4316136837005615},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.15338367223739624},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10885128378868103},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.09362521767616272},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07837259769439697},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0677449107170105}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9887620210647583},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.9122909903526306},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.785847544670105},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5321663618087769},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.47571995854377747},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.464843213558197},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4316136837005615},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.15338367223739624},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10885128378868103},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.09362521767616272},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07837259769439697},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0677449107170105},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1515/jib-2020-0015","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0015","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0015/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32628633","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32628633","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 integrative bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7756619","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7756619","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:authors.library.caltech.edu:104357","is_oa":false,"landing_page_url":"https://resolver.caltech.edu/CaltechAUTHORS:20200713-124645293","pdf_url":null,"source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:d421821be04f470bbb1e01bec3b7f69d","is_oa":true,"landing_page_url":"https://doaj.org/article/d421821be04f470bbb1e01bec3b7f69d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 17, Iss 2-3 (2020)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1843172","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1843172","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"doi:10.1515/jib-2020-0015","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2020-0015","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2020-0015/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6399999856948853}],"awards":[{"id":"https://openalex.org/G1911442100","display_name":null,"funder_award_id":"R01 GM070923","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2036822895","display_name":null,"funder_award_id":"EXC 2124","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2512198698","display_name":null,"funder_award_id":"R01 GM070923","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3030034556","display_name":null,"funder_award_id":"P41 GM103313","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G306747657","display_name":null,"funder_award_id":"GM103712","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3771654662","display_name":null,"funder_award_id":"GM070923","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5188192957","display_name":null,"funder_award_id":"P41 GM103712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5207768667","display_name":null,"funder_award_id":"P41 GM103712","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5467440750","display_name":null,"funder_award_id":"P41 GM103313","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5578042355","display_name":null,"funder_award_id":"R01 GM111510","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6380147298","display_name":null,"funder_award_id":"GM103712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8404086034","display_name":null,"funder_award_id":"GM111510","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320311052","display_name":"Deutsches Zentrum f\u00fcr Infektionsforschung","ror":"https://ror.org/028s4q594"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3041939341.pdf","grobid_xml":"https://content.openalex.org/works/W3041939341.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1986649132","https://openalex.org/W2014449669","https://openalex.org/W2040860090","https://openalex.org/W2069941324","https://openalex.org/W2081098704","https://openalex.org/W2121525198","https://openalex.org/W2148819930","https://openalex.org/W2175715045","https://openalex.org/W4230886699","https://openalex.org/W4231917197","https://openalex.org/W6646730330","https://openalex.org/W6660483197","https://openalex.org/W6667917037","https://openalex.org/W6678038633"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2981332207","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W1546010648","https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2043776573"],"abstract_inverted_index":{"Rule-based":[0],"modeling":[1],"is":[2],"an":[3],"approach":[4],"that":[5,125,145],"permits":[6],"constructing":[7],"reaction":[8,120],"networks":[9],"based":[10],"on":[11],"the":[12,28,33,39,75,102,110,114,158,167,180,194,199],"specification":[13,159],"of":[14,38,60,77,163,166,182,196,201],"rules":[15,22,121],"for":[16,151,160],"molecular":[17],"interactions":[18],"and":[19,32,35,86,116,129,140,187,198],"transformations.":[20],"These":[21],"can":[23,49,66,72,126],"encompass":[24],"details":[25],"such":[26,46,137],"as":[27,47,69,138],"interacting":[29],"sub-molecular":[30],"domains":[31],"states":[34],"binding":[36],"status":[37],"involved":[40],"components.":[41],"Conceptually,":[42],"fine-grained":[43],"spatial":[44],"information":[45],"locations":[48],"also":[50,147],"be":[51,67,127],"provided.":[52],"Through":[53],"\"wildcards\"":[54],"representing":[55],"component":[56],"states,":[57,85],"entire":[58],"families":[59],"molecule":[61],"complexes":[62],"sharing":[63],"certain":[64],"properties":[65],"specified":[68],"patterns.":[70],"This":[71,155],"significantly":[73],"simplify":[74],"definition":[76],"models":[78,183],"involving":[79],"species":[80,124],"with":[81,109],"multiple":[82,84,87,132],"components,":[83],"compartments.":[88],"The":[89],"systems":[90],"biology":[91],"markup":[92],"language":[93],"(SBML)":[94],"Level":[95,104,169],"3":[96,105,170],"Multi":[97,171],"Package":[98],"Version":[99,106,164],"1":[100,107,165,186],"extends":[101],"SBML":[103,168],"core":[108],"\"type\"":[111],"concept":[112],"in":[113,131],"Species":[115],"Compartment":[117],"classes.":[118],"Therefore,":[119],"may":[122],"contain":[123],"patterns":[128],"exist":[130],"locations.":[133],"Multiple":[134],"software":[135],"tools":[136],"Simmune":[139],"BioNetGen":[141],"support":[142],"this":[143],"standard":[144],"thus":[146],"becomes":[148],"a":[149],"medium":[150],"exchanging":[152],"rule-based":[153],"models.":[154],"document":[156],"provides":[157],"Release":[161,185,188],"2":[162],"package.":[172],"No":[173],"design":[174],"changes":[175,190],"have":[176],"been":[177],"made":[178],"to":[179,193],"description":[181],"between":[184],"2;":[189],"are":[191],"restricted":[192],"correction":[195],"errata":[197],"addition":[200],"clarifications.":[202]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}