{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T14:16:46Z","timestamp":1760710606284,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,6,16]],"date-time":"2021-06-16T00:00:00Z","timestamp":1623801600000},"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":["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":[[2021,12,11]]},"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 better understand models and make those models more findable, shareable and reproducible. Consistent model annotation is a step toward these goals. Both models and tools are written in a variety of different languages; thus, the community has recognized the need for standard, language-independent methods for annotation. Based on the Computational Modeling in Biology Network community consensus, we introduce an open-source, cross-platform software library for semantic annotation of models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>libOmexMeta is freely available at https:\/\/github.com\/sys-bio\/libOmexMeta under the Apache License 2.0. A live demonstration is at github.com\/sys-bio\/pyomexmeta-binder-notebook.<\/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\/btab445","type":"journal-article","created":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T19:12:33Z","timestamp":1623697953000},"page":"4898-4900","source":"Crossref","is-referenced-by-count":8,"title":["libOmexMeta: enabling semantic annotation of models to support FAIR principles"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3659-6817","authenticated-orcid":false,"given":"Ciaran","family":"Welsh","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of Washington , 98195 Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David P","family":"Nickerson","sequence":"additional","affiliation":[{"name":"Auckland Bioengineering Institute, University of Auckland , 1142 Auckland, New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anand","family":"Rampadarath","sequence":"additional","affiliation":[{"name":"Auckland Bioengineering Institute, University of Auckland , 1142 Auckland, New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maxwell L","family":"Neal","sequence":"additional","affiliation":[{"name":"Center for Global Infectious Disease Research, Seattle Children\u2019s Research Institute , 98101 Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Herbert M","family":"Sauro","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of Washington , 98195 Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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 , 98019 Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,6,16]]},"reference":[{"key":"2023051607130333400_btab445-B1","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 modelingproject","volume":"15","author":"Bergmann","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023051607130333400_btab445-B2","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.biosystems.2018.07.006","article-title":"Tellurium: an extensible python-based modeling environment for systems and synthetic biology","volume":"171","author":"Choi","year":"2018","journal-title":"BioSystems"},{"key":"2023051607130333400_btab445-B3","doi-asserted-by":"crossref","first-page":"26","DOI":"10.3389\/fphys.2015.00026","article-title":"OpenCOR: a modular and interoperable approach to computational biology","volume":"6","author":"Garny","year":"2015","journal-title":"Front. 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