Related Experiment Video
Updated: Jan 23, 2026
09:27
Using Eye Movements Recorded in the Visual World Paradigm to Explore the Online Processing of Spoken Language
Published on: October 13, 2018
10.7K
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0
Adrien Rougny1,2, Vasundra Touré3, Stuart Moodie4
1Biotechnology Research Institute for Drug Discovery, AIST, Tokyo135-0064, Japan.
Journal of Integrative Bioinformatics
|June 15, 2019
Summary
The Systems Biology Graphical Notation (SBGN) standardizes biological pathway visualization. This update refines the Process Description language (PD) with new glyphs and clarifications for better knowledge exchange.
Area of Science:
- Systems Biology
- Bioinformatics
- Computational Biology
Background:
- Standardized visualization of biological pathways is crucial for knowledge exchange.
- The Systems Biology Graphical Notation (SBGN) provides a common language for representing biological networks.
- SBGN includes Entity Relationship, Activity Flow, and Process Description (PD) languages.
Purpose of the Study:
- To detail Level 1 Version 2.0 of the SBGN Process Description (PD) specification.
- To introduce improvements for enhanced precision and clarity in biological knowledge representation.
- To support efficient and accurate exchange of biological information across diverse communities.
Main Methods:
- The study details the SBGN Process Description (PD) language specification.
- It focuses on graphical notation for mechanistic and temporal dependencies in biological systems.
- Improvements include new glyphs and clarifications to existing elements.
Main Results:
- The updated PD specification (Level 1 Version 2.0) incorporates new glyphs: equivalence operator, subunit, and annotation.
- Modifications were made to the usage of submaps for better structural representation.
- Clarifications were provided for glyphs such as multimer, empty set, and state variable.
Conclusions:
- The enhanced SBGN PD specification improves the precision and expressiveness of biological pathway visualization.
- These updates facilitate more accurate and efficient communication of complex biological information.
- The standardized notation supports broader accessibility and integration of systems biology data.
Related Concept Videos
01:28Scalar Notation
1.1K
Scalar notation is a useful method for simplifying calculations involving vectors. When vectors are added or subtracted, their components can be added or subtracted separately using scalar notation. For instance, force, a vector quantity, can be broken down into its x and y components, called rectangular components, and then the magnitude and direction of these components can be determined using trigonometric functions.
Consider a man pulling a rope from a hook in the northeast direction. The...
Consider a man pulling a rope from a hook in the northeast direction. The...
1.1K
01:19Cyclic Processes And Isolated Systems
3.4K
A thermodynamic system with zero heat exchange and work is an isolated system. For these systems, the internal energy remains constant.
In the case of a non-isolated system, the change in the internal energy is zero only if the process is cyclic. A thermodynamic process is considered cyclic if the system undergoes a series of changes and returns to its initial state.
Consider a cyclic process that returns to its initial state, undergoing a four-step process. The heat transfer along each...
In the case of a non-isolated system, the change in the internal energy is zero only if the process is cyclic. A thermodynamic process is considered cyclic if the system undergoes a series of changes and returns to its initial state.
Consider a cyclic process that returns to its initial state, undergoing a four-step process. The heat transfer along each...
3.4K
01:09¹H NMR: Pople Notation
2.6K
The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
A proton...
A proton...
2.6K
01:28Cartesian Vector Notation
1.5K
Cartesian vector notation is a valuable tool in mechanical engineering for representing vectors in three-dimensional space, performing vector operations such as determining the gradient, divergence, and curl, and expressing physical quantities such as the displacement, velocity, acceleration, and force. By using Cartesian vector notation, engineers can more easily analyze and solve problems in various areas of mechanical engineering, including dynamics, kinematics, and fluid mechanics. This...
1.5K
01:16Language
898
Language is a unique communication system that uses words and systematic rules to organize and transmit information. Unlike other forms of communication, which may involve postures, movements, odors, or vocalizations, language relies on symbols and grammar. This makes human communication distinct from that of other species, who also communicate but do not use language in the same way humans do.
Corballis and Suddendorf (2007) and Tomasello and Rakoczy (2003) highlight the role of language in...
Corballis and Suddendorf (2007) and Tomasello and Rakoczy (2003) highlight the role of language in...
898
01:09Levels of Organization
139.2K
Biological organization is the classification of biological structures, ranging from atoms at the bottom of the hierarchy to the Earth's biosphere. Each level of the hierarchy represents an increase in complexity that builds upon the previous level.
Molecules Are Composed of Atoms, and Biomolecules Are Assembled from Molecules:
The most basic levels include atoms, molecules, and biomolecules. Atoms, the smallest unit of ordinary matter, are composed of a nucleus and electrons. Molecules...
Molecules Are Composed of Atoms, and Biomolecules Are Assembled from Molecules:
The most basic levels include atoms, molecules, and biomolecules. Atoms, the smallest unit of ordinary matter, are composed of a nucleus and electrons. Molecules...
139.2K