SBOL可视化的十年:工程生物学图表标准的日益采用。

IF 3.9 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Lukas Buecherl, Felipe X Buson, Georgie Hau Sørensen, Carolus Vitalis, Erik Kubaczka, Gonzalo Vidal, Bryan Bartley, Yan-Kay Ho, Göksel Mısırlı, Thomas E Gorochowski, Jacob Beal, Chris J Myers, Prashant Vaidyanathan
{"title":"SBOL可视化的十年:工程生物学图表标准的日益采用。","authors":"Lukas Buecherl, Felipe X Buson, Georgie Hau Sørensen, Carolus Vitalis, Erik Kubaczka, Gonzalo Vidal, Bryan Bartley, Yan-Kay Ho, Göksel Mısırlı, Thomas E Gorochowski, Jacob Beal, Chris J Myers, Prashant Vaidyanathan","doi":"10.1021/acssynbio.5c00417","DOIUrl":null,"url":null,"abstract":"<p><p>Standards play a crucial role in ensuring consistency, interoperability, and efficiency of communication across various disciplines. In the field of synthetic biology, the Synthetic Biology Open Language (SBOL) Visual standard was introduced in 2013 to establish a structured framework for visually representing genetic designs. Over the past decade, SBOL Visual has evolved from a simple set of 21 glyphs into a comprehensive diagrammatic language for biological designs. This perspective reflects on the first ten years of SBOL Visual, tracing its evolution from inception to version 3.0. We examine the standard's adoption over time, highlighting its growing use in scientific publications, the development of supporting visualization tools, and ongoing efforts to enhance clarity and accessibility in communicating genetic design information. While trends in adoption show steady increases, achieving full compliance and use of best practices will require additional efforts. Looking ahead, the continued refinement of SBOL Visual and broader community engagement will be essential to ensuring its long-term value as the field of synthetic biology develops.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9000,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A Decade of SBOL Visual: Growing Adoption of a Diagram Standard for Engineering Biology.\",\"authors\":\"Lukas Buecherl, Felipe X Buson, Georgie Hau Sørensen, Carolus Vitalis, Erik Kubaczka, Gonzalo Vidal, Bryan Bartley, Yan-Kay Ho, Göksel Mısırlı, Thomas E Gorochowski, Jacob Beal, Chris J Myers, Prashant Vaidyanathan\",\"doi\":\"10.1021/acssynbio.5c00417\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Standards play a crucial role in ensuring consistency, interoperability, and efficiency of communication across various disciplines. In the field of synthetic biology, the Synthetic Biology Open Language (SBOL) Visual standard was introduced in 2013 to establish a structured framework for visually representing genetic designs. Over the past decade, SBOL Visual has evolved from a simple set of 21 glyphs into a comprehensive diagrammatic language for biological designs. This perspective reflects on the first ten years of SBOL Visual, tracing its evolution from inception to version 3.0. We examine the standard's adoption over time, highlighting its growing use in scientific publications, the development of supporting visualization tools, and ongoing efforts to enhance clarity and accessibility in communicating genetic design information. While trends in adoption show steady increases, achieving full compliance and use of best practices will require additional efforts. Looking ahead, the continued refinement of SBOL Visual and broader community engagement will be essential to ensuring its long-term value as the field of synthetic biology develops.</p>\",\"PeriodicalId\":26,\"journal\":{\"name\":\"ACS Synthetic Biology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2025-09-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACS Synthetic Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1021/acssynbio.5c00417\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Synthetic Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1021/acssynbio.5c00417","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

摘要

标准在确保跨不同学科的一致性、互操作性和通信效率方面起着至关重要的作用。在合成生物学领域,合成生物学开放语言(SBOL)可视化标准于2013年推出,旨在建立可视化表示遗传设计的结构化框架。在过去的十年中,SBOL Visual已经从一组简单的21个符号演变成一种用于生物设计的综合图表语言。这个视角反映了SBOL Visual的前十年,跟踪了它从初始到3.0版本的演变。我们考察了该标准在一段时间内的采用情况,重点介绍了它在科学出版物中越来越多的使用,支持可视化工具的开发,以及为提高遗传设计信息交流的清晰度和可及性所做的持续努力。虽然采用的趋势显示出稳定的增长,但要实现完全遵守和使用最佳实践将需要额外的努力。展望未来,随着合成生物学领域的发展,SBOL可视化的不断完善和更广泛的社区参与对于确保其长期价值至关重要。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A Decade of SBOL Visual: Growing Adoption of a Diagram Standard for Engineering Biology.

Standards play a crucial role in ensuring consistency, interoperability, and efficiency of communication across various disciplines. In the field of synthetic biology, the Synthetic Biology Open Language (SBOL) Visual standard was introduced in 2013 to establish a structured framework for visually representing genetic designs. Over the past decade, SBOL Visual has evolved from a simple set of 21 glyphs into a comprehensive diagrammatic language for biological designs. This perspective reflects on the first ten years of SBOL Visual, tracing its evolution from inception to version 3.0. We examine the standard's adoption over time, highlighting its growing use in scientific publications, the development of supporting visualization tools, and ongoing efforts to enhance clarity and accessibility in communicating genetic design information. While trends in adoption show steady increases, achieving full compliance and use of best practices will require additional efforts. Looking ahead, the continued refinement of SBOL Visual and broader community engagement will be essential to ensuring its long-term value as the field of synthetic biology develops.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
8.00
自引率
10.60%
发文量
380
审稿时长
6-12 weeks
期刊介绍: The journal is particularly interested in studies on the design and synthesis of new genetic circuits and gene products; computational methods in the design of systems; and integrative applied approaches to understanding disease and metabolism. Topics may include, but are not limited to: Design and optimization of genetic systems Genetic circuit design and their principles for their organization into programs Computational methods to aid the design of genetic systems Experimental methods to quantify genetic parts, circuits, and metabolic fluxes Genetic parts libraries: their creation, analysis, and ontological representation Protein engineering including computational design Metabolic engineering and cellular manufacturing, including biomass conversion Natural product access, engineering, and production Creative and innovative applications of cellular programming Medical applications, tissue engineering, and the programming of therapeutic cells Minimal cell design and construction Genomics and genome replacement strategies Viral engineering Automated and robotic assembly platforms for synthetic biology DNA synthesis methodologies Metagenomics and synthetic metagenomic analysis Bioinformatics applied to gene discovery, chemoinformatics, and pathway construction Gene optimization Methods for genome-scale measurements of transcription and metabolomics Systems biology and methods to integrate multiple data sources in vitro and cell-free synthetic biology and molecular programming Nucleic acid engineering.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信