Biology subjects

Misirli, G.

Publications and source records attributed to Misirli, G..

4 recordsLinked to original sources

bioRxiv2023

libSBOLj3: A graph-based library for design and data exchange in synthetic biology

The Synthetic Biology Open Language version 3 data standard provides a graph-based approach to exchange information about biological designs. The new data model has major updates and offers several features for software tools. Here, we present libSBOLj3 to facilitate data exchange and provide interoperability between computer-aided design and automation tools using this standard. The library adopts a graph-based approach. Tool developers can extend these graphs with application-specific information and use detailed validation reports to identify errors and interoperability issues and apply best practice rules. The libSBOLj3 library is implemented in Java and can be downloaded or used as a Maven dependency. The open-source project, examples and documentation about accessing and using the library are available via GitHub at https://github.com/SynBioDex/libSBOLj3.

synthetic biology↗

bioRxiv2020

SBOL Visual 2 Ontology

Standardising 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 O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

synthetic biology↗

bioRxiv2018

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

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 cant 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.

synthetic biology↗

bioRxiv2018

Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL)

Synthetic biology aims to improve the development of biological systems and in-crease their reproducibility through the use of engineering principles, such as stan-dardisation and modularisation. It is important that these systems can be represented and shared in a standard way to ensure they are easily understood, reproduced, and utilised by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterisation. Thus far, this standard has been used to represent designs in homogeneous systems, where the same design is implemented in every cell. In recent years there has been increasing interest in multicellular systems, where biological designs are split across multiple cells to optimise the system behaviour and function. Here we show how the SBOL standard can be used to represent such multicellular systems, and hence how researchers can better share designs with the community.

synthetic biology↗