TY - JOUR
T1 - Synthetic biology open language (SBOL) version 3.0.0
AU - Baig, Hasan
AU - Fontanarrosa, Pedro
AU - Kulkarni, Vishwesh
AU - McLaughlin, James Alastair
AU - Vaidyanathan, Prashant
AU - Bartley, Bryan
AU - Beal, Jacob
AU - Crowther, Matthew
AU - Gorochowski, Thomas E
AU - Grünberg, Raik
AU - Misirli, Goksel
AU - Scott-Brown, James
AU - Oberortner, Ernst
AU - Wipat, Anil
AU - Myers, Chris J.
PY - 2020/6/25
Y1 - 2020/6/25
N2 - 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 syn- thetic 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.
AB - 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 syn- thetic 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.
KW - bioengineering
KW - biological design
KW - data standards
KW - synthetic biology
U2 - 10.1515/jib-2020-0017
DO - 10.1515/jib-2020-0017
M3 - Article (Academic Journal)
C2 - 32589605
SN - 1613-4516
VL - 2020
JO - Journal of Integrative Bioinformatics
JF - Journal of Integrative Bioinformatics
M1 - 20200017
ER -