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}
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.
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.