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Download Hi-Res ImageDownload to MS-PowerPointCite This:ACS Synth. Biol. 2021, 10, 9, 2276-2285
    Research Article

    Synthetic Biology Knowledge System
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    • Jeanet Mante
      Jeanet Mante
      University of Colorado Boulder, Boulder, Colorado 80309, United States
      More by Jeanet Mante
      Orcidhttps://orcid.org/0000-0002-1450-5638
    • Yikai Hao
      Yikai Hao
      University of California San Diego, La Jolla, California 92093, United States
      More by Yikai Hao
    • Jacob Jett
      Jacob Jett
      University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
      More by Jacob Jett
    • Udayan Joshi
      Udayan Joshi
      University of California San Diego, La Jolla, California 92093, United States
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    • Kevin Keating
      Kevin Keating
      Worcester Polytechnic Institute, Worcester, Massachusettes 01609, United States
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    • Xiang Lu
      Xiang Lu
      University of California San Diego, La Jolla, California 92093, United States
      More by Xiang Lu
    • Gaurav Nakum
      Gaurav Nakum
      University of California San Diego, La Jolla, California 92093, United States
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    • Nicholas E. Rodriguez
      Nicholas E. Rodriguez
      Virginia Commonwealth University, Richmond, Virginia 23284, United States
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    • Jiawei Tang
      Jiawei Tang
      University of California San Diego, La Jolla, California 92093, United States
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    • Logan Terry
      Logan Terry
      University of Utah, Salt Lake City, Utah 84112, United States
      More by Logan Terry
      Orcidhttps://orcid.org/0000-0002-1380-5874
    • Xuanyu Wu
      Xuanyu Wu
      University of California San Diego, La Jolla, California 92093, United States
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    • Eric Yu
      Eric Yu
      University of Utah, Salt Lake City, Utah 84112, United States
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    • J. Stephen Downie
      J. Stephen Downie
      University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
      More by J. Stephen Downie
    • Bridget T. McInnes
      Bridget T. McInnes
      Virginia Commonwealth University, Richmond, Virginia 23284, United States
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    • Mai H. Nguyen
      Mai H. Nguyen
      University of California San Diego, La Jolla, California 92093, United States
      More by Mai H. Nguyen
    • Brandon Sepulvado
      Brandon Sepulvado
      NORC at the University of Chicago Bethesda, Chicago, Illinois 60637, United States
      More by Brandon Sepulvado
      Orcidhttps://orcid.org/0000-0002-1989-2972
    • Eric M. Young
      Eric M. Young
      Worcester Polytechnic Institute, Worcester, Massachusettes 01609, United States
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      Orcidhttps://orcid.org/0000-0001-5276-2873
    • Chris J. Myers*
      Chris J. Myers
      University of Colorado Boulder, Boulder, Colorado 80309, United States
      *E-mail: [email protected]
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      Orcidhttps://orcid.org/0000-0002-8762-8444
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    ACS Synthetic Biology

    Cite this: ACS Synth. Biol. 2021, 10, 9, 2276–2285
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    https://doi.org/10.1021/acssynbio.1c00188
    Published August 13, 2021
    Copyright © 2021 American Chemical Society
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    Abstract

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    The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub repository that includes text and data information that has been mined from papers published in ACS Synthetic Biology. This paper describes the SBKS curation framework that is being developed to construct the knowledge stored in this repository. The text mining pipeline performs automatic annotation of the articles using natural language processing techniques to identify salient content such as key terms, relationships between terms, and main topics. The data mining pipeline performs automatic annotation of the sequences extracted from the supplemental documents with the genetic parts used in them. Together these two pipelines link genetic parts to papers describing the context in which they are used. Ultimately, SBKS will reduce the time necessary for synthetic biologists to find the information necessary to complete their designs.

    Copyright © 2021 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acssynbio.1c00188.

    • URLs to access sequence libraries (TXT)

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    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

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    This article is cited by 10 publications.

    1. Jeanet Mante, Zach Sents, Duncan Britt, William Mo, Chunxiao Liao, Ryan Greer, Chris J. Myers. SeqImprove: Machine-Learning-Assisted Curation of Genetic Circuit Sequence Information. ACS Synthetic Biology 2024, 13 (9) , 3051-3055. https://doi.org/10.1021/acssynbio.4c00392
    2. Bingyin Peng, Sarah J. Weintraub, Zeyu Lu, Samuel Evans, Qianyi Shen, Liam McDonnell, Manuel Plan, Thomas Collier, Li Chen Cheah, Lei Ji, Christopher B. Howard, Will Anderson, Matt Trau, Geoff Dumsday, Erin L. Bredeweg, Eric M. Young, Robert Speight, Claudia E. Vickers. Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered Saccharomyces cerevisiae. ACS Synthetic Biology 2024, 13 (1) , 141-156. https://doi.org/10.1021/acssynbio.3c00363
    3. Matthew Crowther, Anil Wipat, Ángel Goñi-Moreno. A Network Approach to Genetic Circuit Designs. ACS Synthetic Biology 2022, 11 (9) , 3058-3066. https://doi.org/10.1021/acssynbio.2c00255
    4. Bridget T. McInnes, J. Stephen Downie, Yikai Hao, Jacob Jett, Kevin Keating, Gaurav Nakum, Sudhanshu Ranjan, Nicholas E. Rodriguez, Jiawei Tang, Du Xiang, Eric M. Young, Mai H. Nguyen. Discovering Content through Text Mining for a Synthetic Biology Knowledge System. ACS Synthetic Biology 2022, 11 (6) , 2043-2054. https://doi.org/10.1021/acssynbio.1c00611
    5. Bryan A. Bartley. Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing. ACS Synthetic Biology 2022, 11 (3) , 1373-1376. https://doi.org/10.1021/acssynbio.1c00450
    6. Tianze Wang, Bowen R. Qin, Sihong Li, Zimo Wang, Xuejian Li, Yuanxu Jiang, Chenrui Qin, Qi Ouyang, Chunbo Lou, Long Qian. Discovery of diverse and high-quality mRNA capping enzymes through a language model–enabled platform. Science Advances 2025, 11 (15) https://doi.org/10.1126/sciadv.adt0402
    7. Matthieu Bultelle, Alexis Casas, Richard Kitney. Engineering biology and automation–Replicability as a design principle. Engineering Biology 2024, 8 (4) , 53-68. https://doi.org/10.1049/enb2.12035
    8. So-Hee Son, Jin Kang, YuJin Shin, ChaeYoung Lee, Bong Hyun Sung, Ju Young Lee, Wonsik Lee. Sustainable production of natural products using synthetic biology: Ginsenosides. Journal of Ginseng Research 2024, 48 (2) , 140-148. https://doi.org/10.1016/j.jgr.2023.12.006
    9. Jeanet Mante, Chris J. Myers. Advancing reuse of genetic parts: progress and remaining challenges. Nature Communications 2023, 14 (1) https://doi.org/10.1038/s41467-023-38791-0
    10. Lukas Buecherl, Chris J Myers. Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology. Current Opinion in Microbiology 2022, 68 , 102155. https://doi.org/10.1016/j.mib.2022.102155
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    ACS Synthetic Biology

    Cite this: ACS Synth. Biol. 2021, 10, 9, 2276–2285
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acssynbio.1c00188
    Published August 13, 2021
    Copyright © 2021 American Chemical Society
    Request reuse permissions

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