ArticleBriefings in bioinformatics2021
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- momapy: a Python library to work with molecular maps.Bioinformatics (Oxford, England) · 2026Article
- FAIR assessment of Disease Maps fosters open science and scientific crowdsourcing in systems biomedicine.Scientific data · 2025Article
- Developing libraries of semantically-augmented graphics as visual standards for biomedical information systems.Journal of biomedical informatics · 2025Article
- BioKC: a collaborative platform for curation and annotation of molecular interactions.Database : the journal of biological databases and curation · 2024Article
- StonPy: a tool to parse and query collections of SBGN maps in a graph database.Bioinformatics (Oxford, England) · 2023Article
- A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Frontiers in bioinformatics · 2023Article
- Design considerations for representing systems biology information with the Systems Biology Graphical Notation.Journal of integrative bioinformatics · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.