{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T19:59:03Z","timestamp":1790193543563,"version":"4.1.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2018,9,26]],"date-time":"2018-09-26T00:00:00Z","timestamp":1537920000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 LM011969"],"award-info":[{"award-number":["R01 LM011969"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P41 GM109824"],"award-info":[{"award-number":["P41 GM109824"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>As the number and complexity of biosimulation models grows, so do demands for tools that can help users understand models and compose more comprehensive and accurate systems from existing models. SemGen is a tool for semantics-based annotation and composition of biosimulation models designed to address this demand. A key SemGen capability is to decompose and then integrate models across existing model exchange formats including SBML and CellML. To support this capability, we use semantic annotations to explicitly capture the underlying biological and physical meanings of the entities and processes that are modeled. SemGen leverages annotations to expose a model\u2019s biological and computational architecture and to help automate model composition.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SemGen is freely available at https:\/\/github.com\/SemBioProcess\/SemGen.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty829","type":"journal-article","created":{"date-parts":[[2018,9,25]],"date-time":"2018-09-25T11:11:10Z","timestamp":1537873870000},"page":"1600-1602","source":"Crossref","is-referenced-by-count":23,"title":["SemGen: a tool for semantics-based annotation and composition of biosimulation models"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2390-6572","authenticated-orcid":false,"given":"Maxwell L","family":"Neal","sequence":"first","affiliation":[{"name":"Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher T","family":"Thompson","sequence":"additional","affiliation":[{"name":"Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8063-6081","authenticated-orcid":false,"given":"Karam G","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan C","family":"James","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel L","family":"Cook","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1353-5907","authenticated-orcid":false,"given":"Brian E","family":"Carlson","sequence":"additional","affiliation":[{"name":"Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8254-4957","authenticated-orcid":false,"given":"John H","family":"Gennari","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,26]]},"reference":[{"key":"2023012806485092100_bty829-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"2023012806485092100_bty829-B2","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1186\/s12859-014-0369-z","article-title":"COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project","volume":"15","author":"Bergmann","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023012806485092100_bty829-B3","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D3 data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans. Vis. Comput. Graph"},{"key":"2023012806485092100_bty829-B4","doi-asserted-by":"crossref","first-page":"e28708","DOI":"10.1371\/journal.pone.0028708","article-title":"Physical properties of biological entities: an introduction to the Ontology of Physics for Biology","volume":"6","author":"Cook","year":"2011","journal-title":"PLoS One"},{"key":"2023012806485092100_bty829-B5","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/2041-1480-4-S1-S2","article-title":"Representing physiological processes and their participants with PhysioMaps","volume":"4","author":"Cook","year":"2013","journal-title":"J. Biomed. Semantics"},{"key":"2023012806485092100_bty829-B6","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1177\/0037549703040939","article-title":"An overview of CellML 1.1, a biological model description language","volume":"79","author":"Cuellar","year":"2003","journal-title":"Simulation"},{"key":"2023012806485092100_bty829-B7","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.jbi.2010.06.007","article-title":"Multiple ontologies in action: composite annotations for biosimulation models","volume":"44","author":"Gennari","year":"2011","journal-title":"J. Biomed. Inform"},{"key":"2023012806485092100_bty829-B8","doi-asserted-by":"crossref","first-page":"D1248","DOI":"10.1093\/nar\/gkx1023","article-title":"BioModels: expanding horizons to include more modelling approaches and formats","volume":"46","author":"Glont","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012806485092100_bty829-B9","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012806485092100_bty829-B10","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.jtbi.2008.03.004","article-title":"A mathematical model of Ca2+ dynamics in rat mesenteric smooth muscle cell: agonist and NO stimulation","volume":"253","author":"Kapela","year":"2008","journal-title":"J. Theor. Biol"},{"key":"2023012806485092100_bty829-B11","doi-asserted-by":"crossref","first-page":"e1003849","DOI":"10.1371\/journal.pcbi.1003849","article-title":"A reappraisal of how to build modular, reusable models of biological systems","volume":"10","author":"Neal","year":"2014","journal-title":"PLoS Comput. Biol"},{"key":"2023012806485092100_bty829-B12","author":"Neal"},{"key":"2023012806485092100_bty829-B13","article-title":"Qualitative causal analyses of biosimulation models","volume":"1747","author":"Neal","year":"2016","journal-title":"CEUR Workshop Proc"},{"key":"2023012806485092100_bty829-B14","doi-asserted-by":"crossref","first-page":"e0145621","DOI":"10.1371\/journal.pone.0145621","article-title":"Semantics-based composition of integrated cardiomyocyte models motivated by real-world use cases","volume":"10","author":"Neal","year":"2015","journal-title":"PLoS One"},{"key":"2023012806485092100_bty829-B15","doi-asserted-by":"crossref","first-page":"2398","DOI":"10.1073\/pnas.032281999","article-title":"A dynamic model of the type-2 inositol trisphosphate receptor","volume":"99","author":"Sneyd","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012806485092100_bty829-B16","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information","volume":"43","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012806485092100_bty829-B17","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1093\/bioinformatics\/btq723","article-title":"The physiome model repository 2","volume":"27","author":"Yu","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/9\/1600\/48940943\/bioinformatics_35_9_1600.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/9\/1600\/48940943\/bioinformatics_35_9_1600.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T08:23:13Z","timestamp":1674894193000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/9\/1600\/5107020"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,9,26]]},"references-count":17,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2019,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty829","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,5,1]]},"published":{"date-parts":[[2018,9,26]]}}}