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  • Walter de Gruyter GmbH  (6)
  • Oberortner, Ernst  (6)
  • 1
    Online Resource
    Online Resource
    Synthetic biology open language (SBOL) version 3.0.0
    Walter de Gruyter GmbH ; 2020
    In:  Journal of Integrative Bioinformatics Vol. 17, No. 2-3 ( 2020-08-24)
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 17, No. 2-3 ( 2020-08-24)
    Abstract: Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. 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, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2020-0017
    Language: English
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2020
    detail.hit.zdb_id: 2147212-9
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  • 2
    Online Resource
    Online Resource
    Synthetic Biology Open Language (SBOL) Version 2.1.0
    Walter de Gruyter GmbH ; 2016
    In:  Journal of Integrative Bioinformatics Vol. 13, No. 3 ( 2016-09-1)
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 13, No. 3 ( 2016-09-1)
    Abstract: 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 2.1 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.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2016-291
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2016
    detail.hit.zdb_id: 2147212-9
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  • 3
    Online Resource
    Online Resource
    Synthetic Biology Open Language (SBOL) Version 2.3
    Walter de Gruyter GmbH ; 2019
    In:  Journal of Integrative Bioinformatics Vol. 16, No. 2 ( 2019-06-13)
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 16, No. 2 ( 2019-06-13)
    Abstract: 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 is 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 2.3.0 of SBOL, which builds upon version 2.2.0 published in last year’s JIB Standards in Systems Biology special issue. In particular, SBOL 2.3.0 includes means of succinctly representing sequence modifications, such as insertion, deletion, and replacement, an extension to support organization and attachment of experimental data derived from designs, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, refinement of a number of validation rules, improved figures and examples, and clarification on a number of issues related to the use of external ontology terms.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2019-0025
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2019
    detail.hit.zdb_id: 2147212-9
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  • 4
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    Online Resource
    Synthetic biology open language (SBOL) version 3.1.0
    Walter de Gruyter GmbH ; 2023
    In:  Journal of Integrative Bioinformatics Vol. 20, No. 1 ( 2023-03-31)
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 20, No. 1 ( 2023-03-31)
    Abstract: Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. 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, following an open community process involving both bench scientists and scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.1.0, which improves on version 3.0.0 by including a number of corrections and clarifications as well as several other updates and enhancements. First, this version includes a complete set of validation rules for checking whether documents are valid SBOL 3. Second, the best practices section has been moved to an online repository that allows for more rapid and interactive of sharing these conventions. Third, it includes updates based upon six community approved enhancement proposals. Two enhancement proposals are related to the representation of an object’s namespace. In particular, the Namespace class has been removed and replaced with a namespace property on each class. Another enhancement is the generalization of the CombinatorialDeriviation class to allow direct use of Features and Measures . Next, the Participation class now allow Interactions to be participants to describe higher-order interactions. Another change is the use of Sequence Ontology terms for Feature orientation . Finally, this version of SBOL has generalized from using Unique Reference Identifiers (URIs) to Internationalized Resource Identifiers (IRIs) to support international character sets.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2022-0058
    Language: English
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2023
    detail.hit.zdb_id: 2147212-9
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  • 5
    Online Resource
    Online Resource
    Synthetic Biology Open Language (SBOL) Version 2.0.0
    Walter de Gruyter GmbH ; 2015
    In:  Journal of Integrative Bioinformatics Vol. 12, No. 2 ( 2015-06-1), p. 902-991
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 12, No. 2 ( 2015-06-1), p. 902-991
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2015-272
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2015
    detail.hit.zdb_id: 2147212-9
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  • 6
    Online Resource
    Online Resource
    Synthetic Biology Open Language (SBOL) Version 2.2.0
    Walter de Gruyter GmbH ; 2018
    In:  Journal of Integrative Bioinformatics Vol. 15, No. 1 ( 2018-04-2)
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 15, No. 1 ( 2018-04-2)
    Abstract: 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 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2018-0001
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2018
    detail.hit.zdb_id: 2147212-9
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