Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Synthetic Biology02:55

Synthetic Biology

5.0K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
5.0K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.4K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.4K
Genomics02:02

Genomics

37.6K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
37.6K
RNA-seq03:21

RNA-seq

10.4K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.4K
Sanger Sequencing01:57

Sanger Sequencing

758.4K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
758.4K
From DNA to Protein03:06

From DNA to Protein

19.2K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
19.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Automated Genetic Engineering in the Laboratory.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

In reply to the Letter to Editor regarding "Comment on "Development and validation of a predictive model for profiling antibiotic resistance phenotypes of Acinetobacter baumannii strains via clinical MALDI-TOF mass spectra: A multicenter study".

International journal of antimicrobial agents·2026
Same author

<i>Dendrobium devonum</i> juice modulates aroma formation in coffee cherry husks processing: insights into key pathways and flavour enhancement.

Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment·2026
Same author

Retinal vascular features enhance short-term prediction of delivery in hypertensive disorders of pregnancy.

Journal of hypertension·2026
Same author

Multilayer microcapsules improved the tolerance to adverse conditions of Pseudomonas aeruginosa A14 and biocontrol effect against cabbage Fusarium wilt.

Pest management science·2026
Same author

Lipase-Catalyzed Enantioselective Resolution of Chiral Pesticides and Herbicides: Advances in Biocatalysis and Enzyme Engineering.

Journal of agricultural and food chemistry·2026

Related Experiment Video

Updated: Sep 20, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

1.8K

Discovering Content through Text Mining for a Synthetic Biology Knowledge System.

Bridget T McInnes1, J Stephen Downie2, Yikai Hao3

  • 1Virginia Commonwealth University, Richmond, Virginia 23284, United States.

ACS Synthetic Biology
|June 7, 2022
PubMed
Summary

This study introduces a text processing pipeline for synthetic biology knowledge systems (SBKS). It uses natural language processing to extract crucial experimental data from scientific literature, aiding researchers.

Keywords:
concept groundingnamed entity recognitionnatural language processingrelation extractionsynthetic biology text processing pipelinetopic modeling

More Related Videos

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
11:13

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

11.1K
Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

596

Related Experiment Videos

Last Updated: Sep 20, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

1.8K
Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
11:13

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

11.1K
Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

596

Area of Science:

  • Biotechnology
  • Bioinformatics
  • Computational Biology

Background:

  • Scientific literature contains valuable experimental data on biological designs.
  • Extracting this information is challenging due to unstructured text, ambiguity, and variability.
  • A structured knowledge system is needed to organize and access this data.

Purpose of the Study:

  • To develop a text processing pipeline for the synthetic biology knowledge system (SBKS).
  • To extract and correlate information from scientific literature for synthetic biology researchers.
  • To link published literature to elements within a knowledge system.

Main Methods:

  • Utilized natural language processing (NLP) techniques.
  • Applied named entity recognition (NER) to identify key biological entities.
  • Employed relation extraction, concept grounding, and topic modeling for information correlation.

Main Results:

  • Demonstrated the effectiveness of individual NLP components on synthetic biology literature.
  • Successfully extracted and correlated information from scientific articles.
  • Established a method to link literature to a knowledge system.

Conclusions:

  • The developed SBKS text processing pipeline effectively extracts and correlates information from scientific literature.
  • The pipeline enhances data accessibility for synthetic biology research.
  • Future work will focus on advancing the pipeline's components and capabilities.