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

Genomics02:02

Genomics

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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Synthetic Biology02:55

Synthetic Biology

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...

You might also read

Related Articles

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

Sort by
Same author

FAIRification on Trial? A Provenance and Reproducible Metadata Build Pipeline for Clinical Research.

Studies in health technology and informatics·2026
Same author

An Interactive Brain Atlas of Knowledge.

bioRxiv : the preprint server for biology·2025
Same author

Three-layered semantic framework for public health intelligence.

Journal of biomedical semantics·2025
Same author

Knowledge graph-driven curation of heme-TLR4 interactions in inflammatory pathways.

Journal of inorganic biochemistry·2025
Same author

KGG: a fully automated workflow for creating disease-specific knowledge graphs.

Bioinformatics (Oxford, England)·2025
Same author

Evaluating language model embeddings for Parkinson's disease cohort harmonization using a novel manually curated variable mapping schema.

Scientific reports·2025
Same journal

Targeting the GLP-1 receptor pathways for dual management of obesity and depression.

Drug discovery today·2026
Same journal

Chemical intervention strategies targeting MYC for cancer therapy.

Drug discovery today·2026
Same journal

How many protein pairs can we chemically target?

Drug discovery today·2026
Same journal

From trial-and-error to inverse design: how AI is redefining drug delivery systems.

Drug discovery today·2026
Same journal

Critical evaluation of the key mediators causing life-threatening symptoms during human anaphylaxis.

Drug discovery today·2026
Same journal

A20 as a novel immunoregulatory target for neuroinflammation.

Drug discovery today·2026
See all related articles

Related Experiment Video

Updated: May 7, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Text mining for systems biology.

Juliane Fluck1, Martin Hofmann-Apitius2

  • 1Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany.

Drug Discovery Today
|September 28, 2013
PubMed
Summary
This summary is machine-generated.

Text mining, including named entity recognition and relationship extraction, is crucial for advancing systems biology. Improved text mining technologies and benchmarking challenges are key to integrating biomedical data for modeling.

More Related Videos

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

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data
07:11

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data

Published on: November 10, 2023

Related Experiment Videos

Last Updated: May 7, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

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

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data
07:11

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data

Published on: November 10, 2023

Area of Science:

  • Biomedical Informatics
  • Systems Biology
  • Computational Biology

Background:

  • Scientific communication in biomedicine predominantly relies on text.
  • Text mining technologies have advanced for extracting information from unstructured biomedical text.
  • These extracted data are valuable for systems biology modeling.

Purpose of the Study:

  • To review the importance of text mining approaches for systems biology.
  • To highlight the role of benchmarking challenges in advancing text mining.
  • To discuss the future impact of text mining on systems biology.

Main Methods:

  • Review of current text mining technologies, focusing on named entity recognition and relationship extraction.
  • Analysis of the impact of scientific benchmarking challenges on text mining progress.
  • Discussion on the role of ontologies and training corpora in systems biology.

Main Results:

  • Named entity recognition and relationship extraction are fundamental for systems biology.
  • Benchmarking challenges accurately reflect and drive progress in text mining.
  • Interdisciplinary development is crucial for future advancements.

Conclusions:

  • Text mining technologies are increasingly vital for systems biology.
  • Continued development of ontologies and training data will enhance text mining's impact.
  • The integration of text mining will significantly benefit biomedical research and modeling.