SBOL Visual 2 Ontology

AbstractStandardising the visual representation of genetic parts and circuits is vital for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts and their relationships. However, the implementation and maintenance of the relationships between biological elements or concepts and their associated glyphs has to now been left up to tool developers. We address this need with the SBOL Visual 2 Ontology, a machine-accessible resource that provides rules for mapping from genetic parts, molecules, and interactions between them, to agreed SBOL Visual glyphs. This resource, together with a web service, can be used as a library to simplify the development of visualization tools, as a stand-alone resource to computationally search for suitable glyphs, and to help facilitate integration with existing biological ontologies and standards in synthetic biology.Graphical TOC Entry

A standard-enabled workflow for synthetic biology

Biochemical Society Transactions ◽

10.1042/bst20160347 ◽

2017 ◽

Vol 45 (3) ◽

pp. 793-803 ◽

Cited By ~ 24

Author(s):

Chris J. Myers ◽

Jacob Beal ◽

Thomas E. Gorochowski ◽

Hiroyuki Kuwahara ◽

Curtis Madsen ◽

...

Keyword(s):

Systems Biology ◽

Synthetic Biology ◽

Markup Language ◽

Design Tools ◽

Data Standards ◽

Data Repositories ◽

Simulation Tools ◽

Systems Biology Markup Language ◽

Visualization Tools ◽

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

paraSBOLv: A Foundation for Standard-Compliant Genetic Design Visualization Tools

Synthetic Biology ◽

10.1093/synbio/ysab022 ◽

2021 ◽

Author(s):

Charlie J Clark ◽

James Scott-Brown ◽

Thomas E Gorochowski

Keyword(s):

Synthetic Biology ◽

Design Process ◽

Physical System ◽

Computational Tools ◽

Design Information ◽

Complex Design ◽

Visualization Tools ◽

Machine Readable ◽

Python Package

Abstract Diagrams constructed from standardized glyphs are central to communicating complex design information in many engineering fields. For example, circuit diagrams are commonplace in electronics and allow for a suitable abstraction of the physical system that helps support the design process. With the development of the Synthetic Biology Open Language Visual (SBOLv), bioengineers are now positioned to better describe and share their biological designs visually. However, development of computational tools to support the creation of these diagrams is currently hampered by an excessive burden in maintenance due to the large and expanding number of glyphs present in the standard. Here, we present a Python package called paraSBOLv that enables access to the full suite of SBOLv glyphs through use of machine-readable parametric glyph definitions. These greatly simplify the rendering process while allowing extensive customization of the resulting diagrams. We demonstrate how adoption of paraSBOLv can accelerate the development of highly specialized biodesign visualization tools or even form the basis for more complex software by removing the burden of maintaining glyph specific rendering code. Looking forward, we suggest that incorporation of machine-readable parametric glyph definitions into the SBOLv standard could further simplify the development of tools to produce standard-compliant diagrams and integration of visual standards across fields.

SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits

10.1101/499970 ◽

2018 ◽

Author(s):

Goksel Misirli ◽

Renee Taylor ◽

Angel Goni-Moreno ◽

James Alastair McLaughlin ◽

Chris Myers ◽

...

Keyword(s):

Synthetic Biology ◽

Semantic Representation ◽

Genetic Circuit ◽

Free Text ◽

Genetic Circuits ◽

Biological Ontologies ◽

Text Document ◽

Ontological Approach ◽

New Perspective ◽

Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent genetic circuit designs, and it is based on capturing data using graphs. The language provides the syntax using a free text document which is accessible to humans only. Here, we provide SBOL-OWL, an ontology for a machine understandable definition of SBOL. This ontology acts as a semantic layer for genetic circuit designs. As a result, computational tools can understand the meaning of design entities in addition to parsing structured SBOL data. SBOL-OWL not only describes how genetic circuits can be constructed computationally, it also facilitates the use of several existing Semantic Web tooling for synthetic biology. Here, we demonstrate some of these features, for example, to validate designs and check for inconsistencies. Through the use of SBOL-OWL, queries are simplified and become more intuitive. Moreover, existing reasoners can be used to infer information about genetic circuit designs that can't be directly retrieved using existing querying mechanisms. This ontological representation of the SBOL standard provides a new perspective to the verification, representation and querying of information about synthetic genetic circuits and is important to incorporate complex design information via the integration of biological ontologies.

An Experiment on the Short-Term Effects of Engagement and Representation in Program Animation

Journal of Educational Computing Research ◽

10.2190/ec.39.4.e ◽

2008 ◽

Vol 39 (4) ◽

pp. 395-430 ◽

Cited By ~ 1

Author(s):

Seppo Nevalainen ◽

Jorma Sajaniemi

Keyword(s):

Computer Programming ◽

Visual Representation ◽

Research Literature ◽

Current Experiment ◽

Short Term ◽

Programming Education ◽

Series Of Experiments ◽

Visualization Tools ◽

Short Term Effects

When visualization tools utilized in computer programming education have been evaluated empirically, the results have remained controversial. To address this problem, we have developed a model of short-term effects of program animation, and used it in a series of experiments. In the current experiment, we varied visual representation of an animation tool and the type of students' engagement. Results of the current experiment analyzed together with the results from the earlier experiments provided support for the hypothesis that what a student does plays a more central role in the usefulness of a visualization than representation used by the tool. Moreover, the levels of engagement as they are generally used in the research literature seem not to be the best possible indicators of the effectiveness of a visualization.

A Validator and Converter for the Synthetic Biology Open Language

ACS Synthetic Biology ◽

10.1021/acssynbio.6b00277 ◽

2017 ◽

Vol 6 (7) ◽

pp. 1161-1168 ◽

Cited By ~ 1

Author(s):

Zach Zundel ◽

Meher Samineni ◽

Zhen Zhang ◽

Chris J. Myers

Keyword(s):

Synthetic Biology ◽

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

Journal of Integrative Bioinformatics ◽

10.1515/jib-2018-0101 ◽

2019 ◽

Vol 16 (2) ◽

Cited By ~ 6

Author(s):

Curtis Madsen ◽

Angel Goni Moreno ◽

Zachary Palchick ◽

Umesh P ◽

Nicholas Roehner ◽

...

Keyword(s):

Nucleic Acid ◽

Synthetic Biology ◽

Molecular Species ◽

Chemical Process ◽

Structure And Function ◽

Genomic Context ◽

Functional Relationships ◽

And Function ◽

Biological Organisms

AbstractPeople 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 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.

Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL)

ACS Synthetic Biology ◽

10.1021/acssynbio.9b00092 ◽

2019 ◽

Vol 8 (7) ◽

pp. 1519-1523

Author(s):

Nicholas Roehner ◽

Bryan Bartley ◽

Jacob Beal ◽

James McLaughlin ◽

Matthew Pocock ◽

...

Keyword(s):

Synthetic Biology ◽

Combinatorial Designs ◽

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Nucleic Acids Research ◽

10.1093/nar/gkz1024 ◽

2019 ◽

Vol 48 (D1) ◽

pp. D1164-D1170 ◽

Cited By ~ 17

Author(s):

Esteban Martínez-García ◽

Angel Goñi-Moreno ◽

Bryan Bartley ◽

James McLaughlin ◽

Lucas Sánchez-Sampedro ◽

...

Keyword(s):

Synthetic Biology ◽

Bacterial Species ◽

Web Based ◽

Genomic Engineering ◽

Bioinformatic Tools ◽

User Friendly ◽

Machine Readable ◽

Genetic Constructs

Abstract The Standard European Vector Architecture 3.0 database (SEVA-DB 3.0, http://seva.cnb.csic.es) is the update of the platform launched in 2013 both as a web-based resource and as a material repository of formatted genetic tools (mostly plasmids) for analysis, construction and deployment of complex bacterial phenotypes. The period between the first version of SEVA-DB and the present time has witnessed several technical, computational and conceptual advances in genetic/genomic engineering of prokaryotes that have enabled upgrading of the utilities of the updated database. Novelties include not only a more user-friendly web interface and many more plasmid vectors, but also new links of the plasmids to advanced bioinformatic tools. These provide an intuitive visualization of the constructs at stake and a range of virtual manipulations of DNA segments that were not possible before. Finally, the list of canonical SEVA plasmids is available in machine-readable SBOL (Synthetic Biology Open Language) format. This ensures interoperability with other platforms and affords simulations of their behaviour under different in vivo conditions. We argue that the SEVA-DB will remain a useful resource for extending Synthetic Biology approaches towards non-standard bacterial species as well as genetically programming new prokaryotic chassis for a suite of fundamental and biotechnological endeavours.

Synthetic Biology Open Language (SBOL) Version 2.1.0

Journal of Integrative Bioinformatics ◽

10.1515/jib-2016-291 ◽

2016 ◽

Vol 13 (3) ◽

Cited By ~ 9

Author(s):

Jacob Beal ◽

Robert Sidney Cox ◽

Raik Grünberg ◽

James McLaughlin ◽

Tramy Nguyen ◽

...

Keyword(s):

Metabolic Engineering ◽

Synthetic Biology ◽

Molecular Biology ◽

Best Practices ◽

Basic Sequence ◽

Special Issue ◽

Biological Design ◽

Version 2.0 ◽

Topology Information ◽

SummarySynthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 of SBOL that builds upon version 2.0 published in last year’s JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.

Synthetic biology open language visual (SBOL visual) version 3.0

Journal of Integrative Bioinformatics ◽

10.1515/jib-2021-0013 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Hasan Baig ◽

Pedro Fontanarossa ◽

James McLaughlin ◽

James Scott-Brown ◽

Prashant Vaidyanathan ◽

...

Keyword(s):

Nucleic Acid ◽

Synthetic Biology ◽

Molecular Species ◽

Data Model ◽

Structure And Function ◽

Sequence Features ◽

Functional Relationships ◽

And Function ◽

Biological Organisms

Abstract People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 3.0 of SBOL Visual, a new major revision of the standard. The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model. A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed, pending future determination on how to represent general SBOL 3 constraints; in the interim, this annotation can still be used as an annotation. Finally, deprecated material has been removed from collection of glyphs: the deprecated “insulator” glyph and “macromolecule” alternative glyphs have been removed, as have the deprecated BioPAX alternatives to SBO terms.