scholarly journals Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3

2015 ◽  
Vol 12 (2) ◽  
pp. 213-280 ◽  
Author(s):  
Stuart Moodie ◽  
Nicolas Le Novère ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Alice Villéger
Keyword(s):  
Systems Biology ◽  
Biological Knowledge ◽  
Biological Interactions ◽  
Description Language ◽  
Regulatory Pathways ◽  
Graphical Notation ◽  
Biochemical Systems ◽  
Community Effort ◽  
Entity Relationship ◽  
Biological Entities

Summary The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

scholarly journals Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

2019 ◽  
Vol 16 (2) ◽  
Author(s):  
Adrien Rougny ◽  
Vasundra Touré ◽  
Stuart Moodie ◽  
Irina Balaur ◽  
Tobias Czauderna ◽  
...  
Keyword(s):  
Systems Biology ◽  
Biological Knowledge ◽  
Biological Interactions ◽  
Regulatory Pathways ◽  
Graphical Notation ◽  
Biochemical Systems ◽  
Community Effort ◽  
Version 2.0 ◽  
Level 1 ◽  
Entity Relationship

AbstractThe Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).

scholarly journals Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

2015 ◽  
Vol 12 (2) ◽  
pp. 281-339 ◽  
Author(s):  
Anatoly Sorokin ◽  
Nicolas Le Novère ◽  
Augustin Luna ◽  
Tobias Czauderna ◽  
Emek Demir ◽  
...  
Keyword(s):  
Systems Biology ◽  
Biological Knowledge ◽  
Graphical Notation ◽  
Levels Of Detail ◽  
Temporal Aspects ◽  
Biochemical Systems ◽  
Community Effort ◽  
Entity Relationship ◽  
Biological Entities ◽  
Biological Literature

Summary The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

scholarly journals Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

2015 ◽  
Vol 12 (2) ◽  
pp. 340-381 ◽  
Author(s):  
Huaiyu Mi ◽  
Falk Schreiber ◽  
Stuart Moodie ◽  
Tobias Czauderna ◽  
Emek Demir ◽  
...  
Keyword(s):  
Systems Biology ◽  
Biological Activities ◽  
Negative Influence ◽  
Positive Influence ◽  
Binding Activity ◽  
Biological Knowledge ◽  
Protein Kinase Activity ◽  
Graphical Notation ◽  
Biochemical Systems ◽  
Entity Relationship

Summary The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

sbgntikz—a TikZ library to draw SBGN maps

2019 ◽  
Vol 35 (21) ◽  
pp. 4499-4500 ◽  
Author(s):  
Adrien Rougny
Keyword(s):  
Systems Biology ◽  
Operating Systems ◽  
Biological Activities ◽  
The Other ◽  
Supplementary Information ◽  
Markup Language ◽  
Graphical Notation ◽  
Supplementary Material ◽  
Entity Relationship ◽  
Biological Entities

Abstract Summary The systems biology graphical notation (SBGN) has emerged as the main standard to represent biological maps graphically. It comprises three complementary languages: Process Description, for detailed biomolecular processes; Activity Flow, for influences of biological activities and Entity Relationship, for independent relations shared among biological entities. On the other hand, TikZ is one of the most commonly used package to ‘program’ graphics within TEX/LATEX. Here, we present sbgntikz, a TikZ library that allows drawing and customizing SBGN maps directly into TEX/LATEX documents, using the TikZ language. sbgntikz supports all glyphs of the three SBGN languages, and offers options that facilitate the drawing of complex glyph assembly within TikZ. Furthermore, sbgntikz is provided together with a converter that allows transforming any SBGN map stored under the SBGN Markup Language into a TikZ picture, or rendering it directly into a PDF file. Availability and implementation sbgntikz, the SBGN-ML to sbgntikz converter, as well as a complete documentation can be freely downloaded from https://github.com/Adrienrougny/sbgntikz/. The library and the converter are compatible with all recent operating systems, including Windows, MacOS, and all common Linux distributions. Supplementary information Supplementary material is available at Bioinformatics online.

scholarly journals Systems Biology Graphical Notation: Process Description language Level 1

2010 ◽  
Author(s):  
Stuart Moodie ◽  
Nicolas Le Novere ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Falk Schreiber
Keyword(s):  
Systems Biology ◽  
Description Language ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1

scholarly journals Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)

2011 ◽  
Author(s):  
Nicolas Le Novere ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Stuart Moodie ◽  
Alice Villeger
Keyword(s):  
Systems Biology ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1 ◽  
Entity Relationship

scholarly journals Systems Biology Graphical Notation: Process Description language Level 1

2011 ◽  
Author(s):  
Stuart Moodie ◽  
Nicolas Le Novere ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Alice Villeger
Keyword(s):  
Systems Biology ◽  
Description Language ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1

scholarly journals Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

2020 ◽  
Author(s):  
Ryan A Miller ◽  
Martina Kutmon ◽  
Anwesha Bohler ◽  
Andra Waagmeester ◽  
Chris T Evelo ◽  
...  
Keyword(s):  
Domain Knowledge ◽  
Biological Knowledge ◽  
Biological Interactions ◽  
Connectivity Information ◽  
Sufficient Degree ◽  
Description Framework ◽  
Biological Entities ◽  
Machine Readable ◽  
Pathway Diagrams ◽  
Full Network

AbstractBackgroundTo grasp the complexity of biological processes, the biological knowledge is often translated into schematic diagrams of biological pathways, such as signalling and metabolic pathways. These pathway diagrams describe relevant connections between biological entities and incorporate domain knowledge in a visual format that is easier for humans to interpret. It has already been established that these diagrams can be represented in machine readable formats, as done in KEGG, Reactome, and WikiPathways. However, while humans are good at interpreting the message of the creator of such a diagram, algorithms struggle when the diversity in drawing approaches increases. WikiPathways supports multiple drawing styles, and therefore needs to harmonize this to offer semantically enriched access via the Resource Description Framework format. Particularly challenging in the normalization of diagrams are the interactions between the biological entities, so that we can glean information about the connectivity of the entities represented. These interactions include information about the type of interaction (metabolic conversion, inhibition, etc.), the direction, and the participants. Availability of the interactions in a semantic and harmonized format enables searching the full network of biological interactions and integration with the linked data cloud.ResultsWe here study how the graphically modelled biological knowledge in diagrams can be semantified and harmonized efficiently, and exemplify how the resulting data can be used to programmatically answer biological questions. We find that we can translate graphically modelled biological knowledge to a sufficient degree into a semantic model of biological knowledge and discuss some of the current limitations. Furthermore, we show how this interaction knowledge base can be used to answer specific biological questions.ConclusionThis paper demonstrates that most of the graphical biological knowledge from WikiPathways is modelled in the semantic layer of WikiPathways with the semantic information intact and connectivity information preserved. The usability of the WikiPathways pathway and connectivity information has shown to be useful and has been integrated into other platforms. Being able to evaluate how biological elements affect each other is useful and allows, for example, the identification of up or downstream targets that will have a similar effect when modified.

scholarly journals Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)

2011 ◽  
Author(s):  
Nicolas Le Novere ◽  
Nicolas Le Novere ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Stuart Moodie ◽  
...  
Keyword(s):  
Systems Biology ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1 ◽  
Entity Relationship

Systems Biology Graphical Notation: Process Description language Level 1

2009 ◽  
Author(s):  
Stuart Moodie ◽  
Stuart Moodie ◽  
Nicolas Le Novere ◽  
Anatoly Sorokin ◽  
Huaiyu Mi ◽  
...  
Keyword(s):  
Systems Biology ◽  
Description Language ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1
Sign in / Sign up

Export Citation Format

Share Document