SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks.
Computer Graphics
Gene Expression Regulation
Gene Ontology
Gene Regulatory Networks
Humans
Insulin
/ genetics
Insulin Receptor Substrate Proteins
/ genetics
Mitogen-Activated Protein Kinases
/ genetics
Models, Biological
Molecular Sequence Annotation
Protein Isoforms
/ genetics
Receptors, Somatomedin
/ genetics
Signal Transduction
Software
Somatomedins
/ genetics
Systems Biology
/ methods
Systems Biology Graphical Notation (SBGN)
annotation
molecular network
ontology
template-based construction
visualisation
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
02 09 2021
02 09 2021
Historique:
received:
02
11
2020
revised:
13
01
2021
pubmed:
25
3
2021
medline:
20
11
2021
entrez:
24
3
2021
Statut:
ppublish
Résumé
A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.
Identifiants
pubmed: 33758926
pii: 6184415
doi: 10.1093/bib/bbab049
pmc: PMC8425392
pii:
doi:
Substances chimiques
IRS1 protein, human
0
Insulin
0
Insulin Receptor Substrate Proteins
0
Protein Isoforms
0
Receptors, Somatomedin
0
Somatomedins
0
Mitogen-Activated Protein Kinases
EC 2.7.11.24
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press.
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