Synthetic biology open language (SBOL) version 3.1.0

Abstract

Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applyingengineering principles to the design of biological systems. When designing a synthetic system, synthetic biolo-gists need to exchange information about multiple types of molecules, the intended behavior of the system, andactual experimental measurements. TheSynthetic Biology Open Language(SBOL) has been developed as a stan-dard to support the specification and exchange of biological design information in synthetic biology, followingan open community process involving both bench scientists and scientific modelers and software develop-ers, across academia, industry, and other institutions. This document describes SBOL 3.1.0, which improveson version 3.0.0 by including a number of corrections and clarifications as well as several other updates andenhancements. First, this version includes a complete set of validation rules for checking whether documentsare valid SBOL 3. Second, the best practices section has been moved to an online repository that allows formore rapid and interactive of sharing these conventions. Third, it includes updates based upon six commu-nity approved enhancement proposals. Two enhancement proposals are related to the representation of anobject’s namespace. In particular, theNamespaceclass has been removed and replaced with anamespaceproperty on each class. Another enhancement is the generalization of theCombinatorialDeriviationclass toallow direct use ofFeaturesandMeasures.Next,theParticipationclass now allowInteractionsto bepartic-ipantsto describe higher-order interactions. Another change is the use ofSequence Ontologyterms forFeatureorientation. Finally, this version of SBOL has generalized from using Unique Reference Identifiers (URIs) toInternationalized Resource Identifiers(IRIs) to support international character sets.