{"doi":"10.1093/bioinformatics/btg015","title":"The systems biology markup language (SBML): a medium for\nrepresentation and exchange of biochemical network models","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.</jats:p>\n               <jats:p>Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.</jats:p>\n               <jats:p>Availability: The specification of SBML Level 1 is freely available from http://www.sbml.org/</jats:p>\n               <jats:p>Contact: sysbio-team@caltech.edu</jats:p>\n               <jats:p>* To whom correspondence should be addressed.</jats:p>","journal":"Bioinformatics","year":2003,"id":590907,"datarank":21.570726849164235,"base_score":8.057694194815587,"endowment":8.057694194815587,"self_citation_contribution":1.2086541292223383,"citation_network_contribution":20.362072719941896,"self_endowment_contribution":1.2086541292223383,"citer_contribution":20.362072719941896,"corpus_percentile":null,"corpus_rank":null,"citation_count":3157,"citer_count":200,"citers_with_citation_signal":200,"citers_with_endowment":200,"datacite_reuse_total":16,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1511798,"name":"A. Finney","orcid":null,"position":1,"is_corresponding":false},{"id":1511799,"name":"H. M. Sauro","orcid":null,"position":2,"is_corresponding":false},{"id":1511800,"name":"H. Bolouri","orcid":null,"position":3,"is_corresponding":false},{"id":1511801,"name":"J. C. Doyle","orcid":null,"position":4,"is_corresponding":false},{"id":1511802,"name":"H. Kitano","orcid":null,"position":5,"is_corresponding":false},{"id":1511803,"name":"A. P. Arkin","orcid":null,"position":6,"is_corresponding":false},{"id":1511804,"name":"B. J. Bornstein","orcid":null,"position":7,"is_corresponding":false},{"id":1511805,"name":"D. Bray","orcid":null,"position":8,"is_corresponding":false},{"id":1511806,"name":"A. Cornish-Bowden","orcid":null,"position":9,"is_corresponding":false},{"id":1511807,"name":"A. A. Cuellar","orcid":null,"position":10,"is_corresponding":false},{"id":1511808,"name":"S. Dronov","orcid":null,"position":11,"is_corresponding":false},{"id":1511809,"name":"E. D. Gilles","orcid":null,"position":12,"is_corresponding":false},{"id":1511810,"name":"M. Ginkel","orcid":null,"position":13,"is_corresponding":false},{"id":1511811,"name":"V. Gor","orcid":null,"position":14,"is_corresponding":false},{"id":1511812,"name":"I. I. Goryanin","orcid":null,"position":15,"is_corresponding":false},{"id":1511813,"name":"W. J. Hedley","orcid":null,"position":16,"is_corresponding":false},{"id":1511814,"name":"T. C. Hodgman","orcid":null,"position":17,"is_corresponding":false},{"id":1511815,"name":"J.-H. Hofmeyr","orcid":null,"position":18,"is_corresponding":false},{"id":1511816,"name":"P. J. Hunter","orcid":null,"position":19,"is_corresponding":false},{"id":1511817,"name":"N. S. Juty","orcid":null,"position":20,"is_corresponding":false},{"id":1511818,"name":"J. L. Kasberger","orcid":null,"position":21,"is_corresponding":false},{"id":1511819,"name":"A. Kremling","orcid":null,"position":22,"is_corresponding":false},{"id":1511820,"name":"U. Kummer","orcid":null,"position":23,"is_corresponding":false},{"id":1511821,"name":"N. Le Novère","orcid":null,"position":24,"is_corresponding":false},{"id":1511822,"name":"L. M. Loew","orcid":null,"position":25,"is_corresponding":false},{"id":1511823,"name":"D. Lucio","orcid":null,"position":26,"is_corresponding":false},{"id":1511824,"name":"P. Mendes","orcid":null,"position":27,"is_corresponding":false},{"id":1511825,"name":"E. Minch","orcid":null,"position":28,"is_corresponding":false},{"id":1511826,"name":"E. D. Mjolsness","orcid":null,"position":29,"is_corresponding":false},{"id":1511827,"name":"Y. Nakayama","orcid":null,"position":30,"is_corresponding":false},{"id":394178,"name":"M. R. Nelson","orcid":null,"position":31,"is_corresponding":false},{"id":1511828,"name":"P. F. Nielsen","orcid":null,"position":32,"is_corresponding":false},{"id":1511829,"name":"T. Sakurada","orcid":null,"position":33,"is_corresponding":false},{"id":1511830,"name":"J. C. Schaff","orcid":null,"position":34,"is_corresponding":false},{"id":1511831,"name":"B. E. Shapiro","orcid":null,"position":35,"is_corresponding":false},{"id":1511832,"name":"T. S. Shimizu","orcid":null,"position":36,"is_corresponding":false},{"id":1511833,"name":"H. D. Spence","orcid":null,"position":37,"is_corresponding":false},{"id":54048,"name":"J. Stelling","orcid":null,"position":38,"is_corresponding":false},{"id":25192,"name":"K. Takahashi","orcid":null,"position":39,"is_corresponding":false},{"id":1511834,"name":"M. Tomita","orcid":null,"position":40,"is_corresponding":false},{"id":1511835,"name":"J. Wagner","orcid":null,"position":41,"is_corresponding":false},{"id":625727,"name":"J. Wang","orcid":"0000-0002-8202-6874","position":42,"is_corresponding":false},{"id":1511797,"name":"M. Hucka","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The systems biology markup language (SBML): a medium for\nrepresentation and exchange of biochemical network models","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.</jats:p>\n               <jats:p>Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.</jats:p>\n               <jats:p>Availability: The specification of SBML Level 1 is freely available from http://www.sbml.org/</jats:p>\n               <jats:p>Contact: sysbio-team@caltech.edu</jats:p>\n               <jats:p>* To whom correspondence should be addressed.</jats:p>","is_dataset_classified":null,"base_score":8.057694194815587,"endowment":8.057694194815587,"datacite_reuse_total":16,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"12611808","pmcid":null,"openalex_id":"https://openalex.org/W2150908245","authors":[],"funders":[],"total_grants":0,"fwci":39.0176,"citation_percentile":0.9993764,"influential_citations":0,"citation_trend":[{"year":2012,"count":176},{"year":2013,"count":235},{"year":2014,"count":173},{"year":2015,"count":181},{"year":2016,"count":170},{"year":2017,"count":156},{"year":2018,"count":137},{"year":2019,"count":128},{"year":2020,"count":124},{"year":2021,"count":111},{"year":2022,"count":97},{"year":2023,"count":83},{"year":2024,"count":72},{"year":2025,"count":49},{"year":2026,"count":20}],"oa_status":"green","license":null,"oa_locations":[{"url":"https://doi.org/10.25504/fairsharing.9qv71f","host_type":"repository"},{"url":"https://doi.org/10.25504/fairsharing.9qv71f","host_type":"repository"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/19/4/524/48903880/bioinformatics_19_4_524.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/bioinformatics/btg015","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/12611808","host_type":"repository"},{"url":"https://authors.library.caltech.edu/27322/","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.217.2676","host_type":""},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.562.1085","host_type":""},{"url":"http://edoc.mpg.de/13815","host_type":"repository"},{"url":"https://research.manchester.ac.uk/en/publications/fa81607f-21ba-47a0-89c0-a0cb89ea89f7","host_type":"repository"},{"url":"https://www.research.manchester.ac.uk/portal/en/publications/the-systems-biology-markup-language-sbml-a-medium-for-representation-and-exchange-of-biochemical-network-models(fa81607f-21ba-47a0-89c0-a0cb89ea89f7).html","host_type":"repository"},{"url":"http://hdl.handle.net/11858/00-001M-0000-0013-9F6B-D","host_type":"repository"},{"url":"http://hdl.handle.net/2299/11943","host_type":"repository"}],"fields_of_study":["Gene Regulatory Network Analysis","Microbial Metabolic Engineering and Bioproduction","Bioinformatics and Genomic Networks","Database Management Systems","Databases, Factual","Documentation","Gene Expression Regulation","Hypermedia","Information Storage and Retrieval","Metabolism","Models, Biological","Models, Chemical","Programming Languages","Software","Software Design","Terminology as Topic","Vocabulary, Controlled"],"mesh_terms":["Database Management Systems","Documentation","Gene Expression Regulation","Metabolism","Models, Biological","Models, Chemical","Terminology as Topic","Programming Languages","Software","Software Design","Databases, Factual","Information Storage and Retrieval","Vocabulary, Controlled","Hypermedia"],"keywords":["SBML","Markup language","Systems biology","Computer science","XML","Programming language","Computational biology","Theoretical computer science","Biology","World Wide Web"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.16726894.v1","title":"Additional file 1 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726894","title":"Additional file 1 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726897.v1","title":"Additional file 2 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726897","title":"Additional file 2 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726900.v1","title":"Additional file 3 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726900","title":"Additional file 3 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726903.v1","title":"Additional file 4 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726903","title":"Additional file 4 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726906.v1","title":"Additional file 5 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726906","title":"Additional file 5 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726909.v1","title":"Additional file 6 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16726909","title":"Additional file 6 of Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.20086051.v1","title":"Additional file 1 of Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.20086051","title":"Additional file 1 of Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.4230/lipics.dna.31.4","title":"Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems","publisher":"Schloss Dagstuhl – Leibniz-Zentrum für Informatik","resource_type":"ConferencePaper"},{"doi":"10.25504/fairsharing.9qv71f","title":"FAIRsharing record for: Systems Biology Markup Language","publisher":"FAIRsharing","resource_type":"Dataset"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-25T13:05:01.121856Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}