Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics ...of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general. Availability and implementation: The annotation ontology for rule-based models can be found at purl.org/rbm/rbmo. The krdf tool and associated executable examples are available at purl.org/rbm/rbmo/krdf.
Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about ...the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language. Here, we describe SBOL Visual version 2, which expands previous diagram standards to include new functional interactions, categories of molecular species, support for families of glyph variants, and the ability to indicate modular structure and mappings between elements of a system. SBOL Visual 2 also clarifies a number of requirements and best practices, significantly expands the collection of glyphs available to describe genetic features, and can be readily applied using a wide variety of software tools, both general and bespoke.
Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this ...standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.
While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several academic and commercial genetic design automation (GDA) software tools, it only covers a limited ...number of the requirements for a standardized exchange format for synthetic biology. In particular, SBOL Version 1.1 is capable of representing DNA components and their hierarchical composition via sequence annotations. This proposal revises SBOL Version 1.1, enabling the representation of a wider range of components with and without sequences, including RNA components, protein components, small molecules, and molecular complexes. It also introduces modules to instantiate groups of components on the basis of their shared function and assert molecular interactions between components. By increasing the range of structural and functional descriptions in SBOL and allowing for their composition, the proposed improvements enable SBOL to represent and facilitate the exchange of a broader class of genetic designs.
Synthetic 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 2.0 of SBOL, introducing a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard also includes rules and best practices on how to use this data model and populate it with relevant design details. The publication of this specification is intended to make these capabilities more widely accessible to potential developers and users in the synthetic biology community and beyond.
Synthetic biology open language visual (SBOL visual) version 2.2 Baig, Hasan; Fontanarrosa, Pedro; Kulkarni, Vishwesh ...
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics,
06/2020, Letnik:
17, Številka:
2
Journal Article
Recenzirano
Odprti dostop
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 2.2 of SBOL Visual, which builds on the prior SBOL Visual 2.1 in several ways. First, the grounding of molecular species glyphs is changed from BioPAX to SBO, aligning with the use of SBO terms for interaction glyphs. Second, new glyphs are added for proteins, introns, and polypeptide regions (e. g., protein domains), the prior recommended macromolecule glyph is deprecated in favor of its alternative, and small polygons are introduced as alternative glyphs for simple chemicals.
Synthetic biology open language visual (SBOL Visual) version 2.3 Baig, Hasan; Fontanarossa, Pedro; Kulkarni, Vishwesh ...
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics,
06/2021, Letnik:
18, Številka:
3
Journal Article
Recenzirano
Odprti dostop
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 “interactions with interactions,” 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 “unspecified interaction” glyph is added for visualizing interactions whose nature is unknown, the “insulator” glyph is deprecated in favor of a new “inert DNA spacer” glyph, and the polypeptide region glyph is recommended for showing 2A sequences.
Laboratory-scale column tests were conducted to investigate the retardation of volatile organic compound (VOC) movement through a soil-bentonite (SB) slurry cutoff wall material amended with ground ...tires, which was found to sorb a significant amount of VOCs. The hydraulic conductivity of the SB slurry cutoff wall backfill material was not affected by the addition of ground tires. The hydraulic conductivity of the ground-tire-amended SB backfill specimen increased 1.1 to 1.2 times after the spiking with VOCs; however, that of the conventional SB backfill specimen increased 1.7 to 1.8 times. The effective porosity of the backfill specimens tested was in the range of 70 to 100%. The partition coefficient of trichloroethylene (TCE) increased from 0.96 to 13.41 L/kg when 15% by weight of ground tires was added. As a result, the time for TCE to break through to 10% of the influent concentration became approximately 10 times longer by the addition of 15% ground tires by weight. Ground tire addition to the SB slurry cutoff wall appears to provide a significant amount of VOC retardation capacity without deteriorating the performance of the slurry cutoff wall.
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