Synthetic Biology Knowledge System

Mante, Jeanet; Hao, Yikai; Jett, Jacob; Joshi, Udayan; Keating, Kevin W; Xiang, Lei; Nakum, Gaurav; Rodriguez, Nicholas E.; Tang, Jiawei; Terry, L. Irene; Wu, Xiaoyu; Yu, E.; Downie, J. Stephen; McInnes, Bridget T.; Nguyen, Manh Duc; Sepulvado, Brandon; Young, Eric M.; Myers, Chris J.

doi:10.1021/acssynbio.1c00188

Cited by 11 publications

(13 citation statements)

References 36 publications

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“…This could happen in a variety of situations that involve massive data set labeling, such as automated genome annotation, 17 automated reconstruction of genome-scale metabolic models, 18 or automated annotation of scientific articles using natural language processing. 19 To avoid this issue, Tyto maintains a local cache following a Least Recently Used (LRU) strategy which maintains an in-memory store of the most frequently queried terms. Dynamic querying can also be fragile if the lookup services or the network connection is unstable.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…For example, it can negatively impact performance, especially when a large volume of requests are made over the network. This could happen in a variety of situations that involve massive data set labeling, such as automated genome annotation, automated reconstruction of genome-scale metabolic models, or automated annotation of scientific articles using natural language processing . To avoid this issue, Tyto maintains a local cache following a Least Recently Used (LRU) strategy which maintains an in-memory store of the most frequently queried terms.…”

Section: Resultsmentioning

confidence: 99%

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Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing

Bartley

2022

ACS Synth. Biol.

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As synthetic biology becomes increasingly automated and data-driven, tools that help researchers implement FAIR (findable-accessible-interoperable-reusable) data management practices are needed. Crucially, in order to support machine processing and reusability of data, it is important that data artifacts are appropriately annotated with metadata drawn from controlled vocabularies. Unfortunately, adopting standardized annotation practices is difficult for many research groups to adopt, given the set of specialized database science skills usually required to interface with ontologies. In response to this need, Take Your Terms from Ontologies (Tyto) is a lightweight Python tool that supports the use of controlled vocabularies in everyday scripting practice. While Tyto has been developed for synthetic biology applications, its utility may extend to users working in other areas of bioinformatics research as well. Tyto is available as a Python package distribution or available as source at https://github.com/SynBioDex/tyto.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing

Bartley

2022

ACS Synth. Biol.

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“…Finally, sequence searching along with SynBioHub is being used as part of the Synthetic Biology Knowledge System (SBKS), 10 which leverages existing data repositories and publications to create a single interface in order to deliver effective and efficient access to collectively available information. More information can be found at https://web.synbioks.org/.…”

Section: ■ Discussionmentioning

confidence: 99%

Sequence-Based Searching for SynBioHub Using VSEARCH

Mante

Myers

2022

ACS Synth. Biol.

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The ability to search for a part by its sequence is crucial for a large repository of parts. Prior to this work, however, this was not possible on SynBioHub. Sequence-based search is now integrated into SynBioHub, allowing users to find a part by a sequence provided in plain text or a supported file format. This sequence-based search feature is accessible to users via SynBioHub's web interface, or programmatically through its API. The core implementation of the tool uses VSEARCH, an open source, global alignment search tool, and it is integrated into SBOLExplorer, an open source distributed search engine used by SynBioHub. We present a new approach to scoring part similarity using SBOLExplorer, which takes into account both the popularity and percentage match of parts.

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“…Designs are often the first step in each iteration of a synthetic biology project, and an implementation can be challenging without a well-conceived design and solid understanding. Furthermore, mathematical and computational tools, automation methods, , knowledge-based systems, , and repositories assist circuit design to minimize the iterations within the design-build-test-learn research cycle. These processes generate a consortium of information beyond DNA sequences, such as modularity, hierarchy, implementation instructions, dynamical predictions, and validation strategies.…”

Section: Introductionmentioning

confidence: 99%

A Network Approach to Genetic Circuit Designs

2022

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As genetic circuits become more sophisticated, the size and complexity of data about their designs increase. The data captured goes beyond genetic sequences alone; information about circuit modularity and functional details improves comprehension, performance analysis, and design automation techniques. However, new data types expose new challenges around the accessibility, visualization, and usability of design data (and metadata). Here, we present a method to transform circuit designs into networks and showcase its potential to enhance the utility of design data. Since networks are dynamic structures, initial graphs can be interactively shaped into subnetworks of relevant information based on requirements such as the hierarchy of biological parts or interactions between entities. A significant advantage of a network approach is the ability to scale abstraction, providing an automatic sliding level of detail that further tailors the visualization to a given situation. Additionally, several visual changes can be applied, such as coloring or clustering nodes based on types (e.g., genes or promoters), resulting in easier comprehension from a user perspective. This approach allows circuit designs to be coupled to other networks, such as metabolic pathways or implementation protocols captured in graph-like formats. We advocate using networks to structure, access, and improve synthetic biology information.

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Synthetic Biology Knowledge System

Cited by 11 publications

References 36 publications

Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing

Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing

Sequence-Based Searching for SynBioHub Using VSEARCH

A Network Approach to Genetic Circuit Designs

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