{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:50:04Z","timestamp":1760161804311,"version":"3.41.2"},"reference-count":0,"publisher":"Walter de Gruyter GmbH","issue":"2-3","license":[{"start":{"date-parts":[[2020,6,1]],"date-time":"2020-06-01T00:00:00Z","timestamp":1590969600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"U.S. National Institutes of Health","doi-asserted-by":"crossref","award":["P41-EB023912"],"award-info":[{"award-number":["P41-EB023912"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"German Federal Ministry of Education and Research (BMBF) as part of the e:Bio program SEMS","award":["FKZ 031 6194"],"award-info":[{"award-number":["FKZ 031 6194"]}]},{"name":"Aotearoa Foundation Physiome Fellowship"},{"name":"German Federal Ministry of Education and Research (BMBF) as part of the research network Systems Medicine of the Liver","award":["031L0054"],"award-info":[{"award-number":["031L0054"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. Distributing modeling projects within these archives is a best practice established by COMBINE, and the OMEX metadata specification presented here provides a harmonized, community-driven approach for annotating a variety of standardized model and data representation formats within an archive. The specification primarily includes technical guidelines for encoding archive metadata, so that software tools can more easily utilize and exchange it, thereby spurring broad advancements in model reuse, discovery, and semantic analyses.<\/jats:p>","DOI":"10.1515\/jib-2020-0020","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T12:41:40Z","timestamp":1594384900000},"source":"Crossref","is-referenced-by-count":10,"title":["Open modeling and exchange (OMEX) metadata specification version 1.0"],"prefix":"10.1515","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2390-6572","authenticated-orcid":false,"given":"Maxwell L.","family":"Neal","sequence":"first","affiliation":[{"name":"Seattle Children\u2019s Research Institute , Seattle , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8254-4957","authenticated-orcid":false,"given":"John H.","family":"Gennari","sequence":"additional","affiliation":[{"name":"University of Washington , Seattle , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5886-5563","authenticated-orcid":false,"given":"Dagmar","family":"Waltemath","sequence":"additional","affiliation":[{"name":"University Medicine Greifswald , Greifswald , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4667-9779","authenticated-orcid":false,"given":"David P.","family":"Nickerson","sequence":"additional","affiliation":[{"name":"University of Auckland , Auckland , New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1725-179X","authenticated-orcid":false,"given":"Matthias","family":"K\u00f6nig","sequence":"additional","affiliation":[{"name":"Humboldt University Berlin , Berlin , Germany"}]}],"member":"374","published-online":{"date-parts":[[2020,6,25]]},"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/view\/journals\/jib\/17\/2-3\/article-20200020.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2020-0020\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2020-0020\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T09:46:09Z","timestamp":1680342369000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2020-0020\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,1]]},"references-count":0,"journal-issue":{"issue":"2-3","published-online":{"date-parts":[[2020,6,22]]},"published-print":{"date-parts":[[2020,8,24]]}},"alternative-id":["10.1515\/jib-2020-0020"],"URL":"https:\/\/doi.org\/10.1515\/jib-2020-0020","relation":{},"ISSN":["1613-4516"],"issn-type":[{"type":"electronic","value":"1613-4516"}],"subject":[],"published":{"date-parts":[[2020,6,1]]},"article-number":"20200020"}}