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Related Concept Videos

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,...
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.
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The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...
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Cell Diagrams and IUPAC Conventions

Electrochemical cell notation is a standardized symbolic representation that communicates the structure and reaction pathway of galvanic and electrolytic cells. This notation plays a critical role in describing redox reactions and electrochemical cell configurations without the need for detailed diagrams.In electrochemical cell notation, a single vertical line “|” denotes a phase boundary, such as between a solid electrode and an aqueous solution. A double vertical line “||” represents a salt...
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Mitogen-activated protein kinase, or MAPK pathway, activates three sequential kinases to regulate cellular responses such as proliferation, differentiation, survival, and apoptosis. The canonical MAPK pathway starts with a mitogen or growth factor binding to an RTK. The activated RTKs stimulate Ras, which recruits Raf or MAP3 Kinase (MAPKKK), the first kinase of the MAPK signaling cascade. Raf further phosphorylates and activates MEK or MAP2 Kinases (MAPKK), which in turn phosphorylates MAP...

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Related Experiment Video

Updated: May 24, 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

Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation.

Astrid Junker1, Hendrik Rohn, Tobias Czauderna

  • 1Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Gatersleben, Germany. junkera@ipk-gatersleben.de

Nature Protocols
|March 3, 2012
PubMed
Summary
This summary is machine-generated.

This protocol introduces the Systems Biology Graphical Notation (SBGN) standard for visualizing biological networks. It details using SBGN-ED for map creation, data enrichment, and web export, aiding scientific communication.

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Area of Science:

  • Systems biology
  • Bioinformatics
  • Computational biology

Background:

  • The Systems Biology Graphical Notation (SBGN) is an emerging standard for representing biological processes and networks.
  • Standardized representation is crucial for consistent data interpretation and sharing in systems biology.

Purpose of the Study:

  • To provide a protocol for constructing and enriching Systems Biology Graphical Notation maps.
  • To demonstrate the utility of the SBGN-ED tool for manual and automatic map creation.
  • To facilitate the integration of multi-omics data into biological network visualizations.

Main Methods:

  • Manual drawing and automatic translation of biological networks using the SBGN-ED tool.
  • Enrichment of SBGN maps with various omics data types.
  • Exporting SBGN maps to public websites with interactive features.

Main Results:

  • SBGN-ED enables the creation of SBGN maps from gene regulation and metabolism examples.
  • Integration of omics data enriches network context for experimental data interpretation.
  • Export functionality allows for effective communication of results via clickable web images.
  • SBGN-ED is the only tool currently integrating SBGN representation, data mapping, and website export.

Conclusions:

  • The protocol offers a comprehensive workflow for building and utilizing SBGN maps.
  • SBGN-ED streamlines the process of visualizing and communicating complex biological networks.
  • This approach enhances the interpretation of experimental data and facilitates scientific collaboration.