{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T16:46:12Z","timestamp":1761324372897,"version":"3.41.2"},"reference-count":0,"publisher":"Walter de Gruyter GmbH","issue":"3","license":[{"start":{"date-parts":[[2021,6,8]],"date-time":"2021-06-08T00:00:00Z","timestamp":1623110400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level \u201cinteractions with interactions,\u201d such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new \u201cunspecified interaction\u201d glyph is added for visualizing interactions whose nature is unknown, the \u201cinsulator\u201d glyph is deprecated in favor of a new \u201cinert DNA spacer\u201d glyph, and the polypeptide region glyph is recommended for showing 2A sequences.<\/jats:p>","DOI":"10.1515\/jib-2020-0045","type":"journal-article","created":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T22:12:40Z","timestamp":1623103960000},"source":"Crossref","is-referenced-by-count":8,"title":["Synthetic biology open language visual (SBOL Visual) version 2.3"],"prefix":"10.1515","volume":"18","author":[{"given":"Hasan","family":"Baig","sequence":"first","affiliation":[{"name":"University of Connecticut , Storrs , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0535-2684","authenticated-orcid":false,"given":"Pedro","family":"Fontanarossa","sequence":"additional","affiliation":[{"name":"University of Utah , Salt Lake City , USA"}]},{"given":"Vishwesh","family":"Kulkarni","sequence":"additional","affiliation":[{"name":"University of Warwick , Coventry , USA"}]},{"given":"James","family":"McLaughlin","sequence":"additional","affiliation":[{"name":"Newcastle University , Newcastle upon Tyne , UK"}]},{"given":"Prashant","family":"Vaidyanathan","sequence":"additional","affiliation":[{"name":"Microsoft Research , Cambridge , UK"}]},{"given":"Bryan","family":"Bartley","sequence":"additional","affiliation":[{"name":"Raytheon BBN Technologies , Cambridge , USA"}]},{"given":"Shyam","family":"Bhakta","sequence":"additional","affiliation":[{"name":"Rice University , Houston , USA"}]},{"given":"Swapnil","family":"Bhatia","sequence":"additional","affiliation":[{"name":"Boston University , Boston , USA"}]},{"given":"Mike","family":"Bissell","sequence":"additional","affiliation":[{"name":"Shipyard Toolchains LLC , Emeryville , USA"}]},{"given":"Kevin","family":"Clancy","sequence":"additional","affiliation":[{"name":"Thermo Fisher Scientific , San Diego , USA"}]},{"given":"Robert Sidney","family":"Cox","sequence":"additional","affiliation":[{"name":"Kobe University , Kobe , Japan"}]},{"given":"Angel","family":"Go\u00f1i Moreno","sequence":"additional","affiliation":[{"name":"Newcastle University , Newcastle upon Tyne , UK"}]},{"given":"Thomas","family":"Gorochowski","sequence":"additional","affiliation":[{"name":"University of Bristol , Bristol , UK"}]},{"given":"Raik","family":"Grunberg","sequence":"additional","affiliation":[{"name":"KAUST , Thuwal , Saudi Arabia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5426-2765","authenticated-orcid":false,"given":"Jihwan","family":"Lee","sequence":"additional","affiliation":[{"name":"Rice University , Houston , USA"}]},{"given":"Augustin","family":"Luna","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston , USA"}]},{"given":"Curtis","family":"Madsen","sequence":"additional","affiliation":[{"name":"Boston University , Boston , USA"}]},{"given":"Goksel","family":"Misirli","sequence":"additional","affiliation":[{"name":"Keele University , Keele , UK"}]},{"given":"Tramy","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Raytheon BBN Technologies , Cambridge , USA"}]},{"given":"Nicolas","family":"Le Novere","sequence":"additional","affiliation":[{"name":"Babraham Institute , Cambridge , UK"}]},{"given":"Zachary","family":"Palchick","sequence":"additional","affiliation":[{"name":"Zymergen , Emeryville , USA"}]},{"given":"Matthew","family":"Pocock","sequence":"additional","affiliation":[{"name":"Turing Ate My Hamster, Ltd. , Newcastle , UK"}]},{"given":"Nicholas","family":"Roehner","sequence":"additional","affiliation":[{"name":"Raytheon BBN Technologies , Cambridge , USA"}]},{"given":"Herbert","family":"Sauro","sequence":"additional","affiliation":[{"name":"University of Washington , Seattle , USA"}]},{"given":"James","family":"Scott-Brown","sequence":"additional","affiliation":[{"name":"University of Oxford , Oxford , UK"}]},{"given":"John T.","family":"Sexton","sequence":"additional","affiliation":[{"name":"Rice University , Houston , USA"}]},{"given":"Guy-Bart","family":"Stan","sequence":"additional","affiliation":[{"name":"Imperial College , London , UK"}]},{"given":"Jeffrey J.","family":"Tabor","sequence":"additional","affiliation":[{"name":"Rice University , Houston , USA"}]},{"given":"Logan","family":"Terry","sequence":"additional","affiliation":[{"name":"University of Utah , Salt Lake City , USA"}]},{"given":"Marta","family":"Vazquez Vilar","sequence":"additional","affiliation":[{"name":"Universitat Politecnica de Valencia , Valencia , Spain"}]},{"given":"Christopher A.","family":"Voigt","sequence":"additional","affiliation":[{"name":"MIT , Cambridge , USA"}]},{"given":"Anil","family":"Wipat","sequence":"additional","affiliation":[{"name":"Newcastle University , Newcastle upon Tyne , UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8157-4780","authenticated-orcid":false,"given":"David","family":"Zong","sequence":"additional","affiliation":[{"name":"Rice University , Houston , USA"}]},{"given":"Zach","family":"Zundel","sequence":"additional","affiliation":[{"name":"University of Utah , Salt Lake City , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1663-5102","authenticated-orcid":false,"given":"Jacob","family":"Beal","sequence":"additional","affiliation":[{"name":"Raytheon BBN Technologies , Cambridge , USA"}]},{"given":"Chris","family":"Myers","sequence":"additional","affiliation":[{"name":"University of Colorado Boulder , Boulder , USA"}]}],"member":"374","published-online":{"date-parts":[[2021,6,8]]},"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2020-0045\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2020-0045\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T08:26:14Z","timestamp":1680337574000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2020-0045\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,8]]},"references-count":0,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2021,6,8]]},"published-print":{"date-parts":[[2021,10,29]]}},"alternative-id":["10.1515\/jib-2020-0045"],"URL":"https:\/\/doi.org\/10.1515\/jib-2020-0045","relation":{},"ISSN":["1613-4516"],"issn-type":[{"type":"electronic","value":"1613-4516"}],"subject":[],"published":{"date-parts":[[2021,6,8]]},"article-number":"20200045"}}