{"id":"https://openalex.org/W2565927981","doi":"https://doi.org/10.2390/biecoll-jib-2016-290","title":"SBML Level 3 package: Groups, Version 1 Release 1","display_name":"SBML Level 3 package: Groups, Version 1 Release 1","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2565927981","doi":"https://doi.org/10.2390/biecoll-jib-2016-290","mag":"2565927981","pmid":"https://pubmed.ncbi.nlm.nih.gov/28187406"},"language":"en","primary_location":{"id":"pmid:28187406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28187406","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},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://authors.library.caltech.edu/72979/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016716446","display_name":"Michael Hucka","orcid":"https://orcid.org/0000-0001-9105-5960"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hucka, Michael","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Smith, Lucian P.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016716446"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2202,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.81225398,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"13","issue":"3","first_page":"290","last_page":"290"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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":0.9995999932289124,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9983000159263611,"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":0.9934999942779541,"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":0.9903224110603333},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7888121604919434},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6576509475708008},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.4437447190284729},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.43242499232292175},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3965078294277191},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.2845655381679535},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13308191299438477},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.07129079103469849}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9903224110603333},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7888121604919434},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6576509475708008},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.4437447190284729},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.43242499232292175},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3965078294277191},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.2845655381679535},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13308191299438477},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.07129079103469849}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"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}],"locations_count":6,"locations":[{"id":"pmid:28187406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28187406","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:authors.library.caltech.edu:72979","is_oa":true,"landing_page_url":"https://authors.library.caltech.edu/72979/","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:5427","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2017/5427/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=290","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:4305016","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC5451322","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5451322","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5451322","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Integr Bioinform","raw_type":"Text"},{"id":"doi:10.2390/biecoll-jib-2016-290","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2016-290","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:authors.library.caltech.edu:72979","is_oa":true,"landing_page_url":"https://authors.library.caltech.edu/72979/","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":1,"referenced_works":["https://openalex.org/W2187198735"],"related_works":["https://openalex.org/W1992807924","https://openalex.org/W1541440913","https://openalex.org/W2381351160","https://openalex.org/W2914587905","https://openalex.org/W2062427795","https://openalex.org/W1554993229","https://openalex.org/W1533329019","https://openalex.org/W2354642172","https://openalex.org/W1555090906","https://openalex.org/W2360553097"],"abstract_inverted_index":{"Biological":[0],"models":[1],"often":[2],"contain":[3],"components":[4,83],"that":[5,12,107,140],"have":[6],"relationships":[7],"with":[8,21],"each":[9,131],"other,":[10],"or":[11,24],"modelers":[13,112],"want":[14],"to":[15,19,54,76,78,84,104,123,137],"treat":[16],"as":[17],"belonging":[18],"groups":[20,88,127],"common":[22],"characteristics":[23],"shared":[25],"metadata.":[26],"The":[27,64,116],"SBML":[28,52,65,69,77,117],"Level":[29,70],"3":[30,71],"Version":[31],"1":[32],"Core":[33,57],"specification":[34,58],"does":[35,47],"not":[36,90],"provide":[37,48,101],"an":[38],"explicit":[39],"mechanism":[40,50],"for":[41,51,68,111],"expressing":[42],"such":[43],"relationships,":[44],"but":[45,98],"it":[46,146],"a":[49,96,102,121],"packages":[53],"extend":[55],"the":[56,73,92],"and":[59,113,128,144],"add":[60,105],"additional":[61],"syntactical":[62],"constructs.":[63],"Groups":[66,118],"package":[67,119],"adds":[72],"necessary":[74],"features":[75],"allow":[79],"grouping":[80],"of":[81,95,126,132],"model":[82],"be":[85,109,135],"expressed.":[86],"Such":[87],"do":[89,100],"affect":[91],"mathematical":[93],"interpretation":[94],"model,":[97],"they":[99],"way":[103],"information":[106],"can":[108],"useful":[110],"software":[114],"tools.":[115],"enables":[120],"modeler":[122],"include":[124],"definitions":[125],"nested":[129],"groups,":[130],"which":[133],"may":[134],"annotated":[136],"convey":[138],"why":[139],"group":[141],"was":[142],"created,":[143],"what":[145],"represents.":[147]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
