{"id":"https://openalex.org/W2098769288","doi":"https://doi.org/10.1093/bioinformatics/btp642","title":"Annotation and merging of SBML models with semanticSBML","display_name":"Annotation and merging of SBML models with semanticSBML","publication_year":2009,"publication_date":"2009-11-17","ids":{"openalex":"https://openalex.org/W2098769288","doi":"https://doi.org/10.1093/bioinformatics/btp642","mag":"2098769288","pmid":"https://pubmed.ncbi.nlm.nih.gov/19933161"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp642","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp642","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/3/421/48860330/bioinformatics_26_3_421.pdf","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,"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/3/421/48860330/bioinformatics_26_3_421.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111505379","display_name":"Falko Krause","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Falko Krause","raw_affiliation_strings":["Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030718435","display_name":"Jannis Uhlendorf","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jannis Uhlendorf","raw_affiliation_strings":["Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070204223","display_name":"Timo Lubitz","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Timo Lubitz","raw_affiliation_strings":["Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079222008","display_name":"Marvin Schulz","orcid":"https://orcid.org/0009-0009-7565-9460"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marvin Schulz","raw_affiliation_strings":["Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003799374","display_name":"Edda Klipp","orcid":"https://orcid.org/0000-0002-0567-7075"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Edda Klipp","raw_affiliation_strings":["Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046914403","display_name":"Wolfram Liebermeister","orcid":"https://orcid.org/0000-0002-2568-2381"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Wolfram Liebermeister","raw_affiliation_strings":["Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046914403"],"corresponding_institution_ids":["https://openalex.org/I39343248"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.1083,"has_fulltext":false,"cited_by_count":102,"citation_normalized_percentile":{"value":0.94672889,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"26","issue":"3","first_page":"421","last_page":"422"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9997000098228455,"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":0.9976999759674072,"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":0.9125610589981079},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8243383765220642},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.8083466291427612},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7883822917938232},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6053341031074524},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5874529480934143},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5383639335632324},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4594886898994446},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4037548899650574},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.36972612142562866},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3449679911136627},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.2260264754295349},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12937703728675842}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9125610589981079},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8243383765220642},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.8083466291427612},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7883822917938232},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6053341031074524},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5874529480934143},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5383639335632324},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4594886898994446},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4037548899650574},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.36972612142562866},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3449679911136627},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.2260264754295349},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12937703728675842}],"mesh":[{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp642","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp642","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/3/421/48860330/bioinformatics_26_3_421.pdf","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,"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:19933161","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19933161","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp642","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp642","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/3/421/48860330/bioinformatics_26_3_421.pdf","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,"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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2098769288.pdf"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2001758733","https://openalex.org/W2020561965","https://openalex.org/W2107062718","https://openalex.org/W2135290856","https://openalex.org/W2150908245","https://openalex.org/W2155049977","https://openalex.org/W2160751597","https://openalex.org/W2289848377","https://openalex.org/W6696749078"],"related_works":["https://openalex.org/W4317567302","https://openalex.org/W2405441773","https://openalex.org/W4308825558","https://openalex.org/W4384816957","https://openalex.org/W2972393600","https://openalex.org/W4225301751","https://openalex.org/W2098769288","https://openalex.org/W4287673820","https://openalex.org/W3083022888","https://openalex.org/W2951522607"],"abstract_inverted_index":{"SUMMARY:":[0],"Systems":[1,15],"Biology":[2],"Markup":[3],"Language":[4],"(SBML)":[5],"is":[6,45,63,108],"the":[7,52,56,96,111,131,135,153,189],"leading":[8],"exchange":[9],"format":[10],"for":[11,47,162],"mathematical":[12],"models":[13,38],"in":[14,78,94,100,138,148],"Biology.":[16],"Semantic":[17],"annotations":[18,74,98,113],"link":[19],"model":[20,48],"elements":[21],"with":[22,175],"external":[23],"knowledge":[24],"via":[25],"unique":[26],"database":[27,89],"identifiers":[28],"and":[29,36,71,75,88,99,114,120,150,169],"ontology":[30],"terms,":[31],"enabling":[32],"software":[33,146],"to":[34,69,133],"check":[35,70],"process":[37,137],"by":[39],"their":[40],"biochemical":[41,86],"meaning.":[42],"Such":[43],"information":[44],"essential":[46],"merging,":[49],"one":[50],"of":[51,58,85,173],"key":[53],"steps":[54],"towards":[55],"construction":[57],"large":[59,83],"kinetic":[60],"models.":[61,80,103],"SemanticSBML":[62,141],"a":[64,82,144,159,166],"tool":[65],"that":[66],"helps":[67],"users":[68],"edit":[72],"MIRIAM":[73,112],"SBO":[76],"terms":[77],"SBML":[79],"Using":[81],"collection":[84],"names":[87],"identifiers,":[90],"it":[91],"supports":[92],"modellers":[93],"finding":[95],"right":[97],"merging":[101,136],"existing":[102],"Initially,":[104],"an":[105,170],"element":[106,116],"matching":[107],"derived":[109],"from":[110],"conflicting":[115],"attributes":[117],"are":[118,178,201],"categorized":[119],"highlighted.":[121],"Conflicts":[122],"can":[123,185],"then":[124],"be":[125,186],"resolved":[126],"automatically":[127],"or":[128],"manually,":[129],"allowing":[130],"user":[132],"control":[134],"detail.":[139],"AVAILABILITY:":[140],"comes":[142],"as":[143],"free":[145],"written":[147],"Python":[149],"released":[151],"under":[152],"GPL":[154],"3.":[155],"A":[156,182],"Debian":[157],"package,":[158],"source":[160],"package":[161],"other":[163],"Linux":[164,190],"distributions,":[165],"Windows":[167],"installer":[168],"online":[171],"version":[172,184],"semanticSBML":[174],"limited":[176],"functionality":[177],"available":[179,194,202],"at":[180,195,203],"http://www.semanticsbml.org.":[181],"preinstalled":[183],"found":[187],"on":[188],"live":[191],"DVD":[192],"SB.OS,":[193],"http://www.sbos.eu.":[196],"SUPPLEMENTARY":[197],"INFORMATION:":[198],"Supplementary":[199],"data":[200],"Bioinformatics":[204],"online.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":16},{"year":2012,"cited_by_count":8}],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2016-06-24T00:00:00"}
