Everything about BioPAX
Biological Pathway Language
BioPAX is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery. Wikipedia →
🧠Start here: a 6-step reading path
- Read the overview: BioPAXA 5-minute orientation
- Skim a recent paper: Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using semantic web technologiesInfluential work since 2022
- Read the landmark paper: The BioPAX community standard for pathway data sharingCited 596 times
- Go sideways: NCI-Nature Pathway Interaction DatabaseA closely related topic
- Go sideways: GenMAPPA closely related topic
đź“– Definitions
No dictionary entry for this exact phrase.
🗂️ The subject at a glance
🏆 Landmark papers (most cited)
The BioPAX community standard for pathway data sharing
Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX
ChiBE: interactive visualization and manipulation of BioPAX pathway models
rBiopaxParser—an R package to parse, modify and visualize BioPAX data
BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways
Pattern search in BioPAX models
Integrating BioPAX pathway knowledge with SBML models
Qualitative translation of relations from BioPAX to SBML qual
🆕 Influential since 2022
đź“š Books worth reading
Open Library didn't respond; try again in a moment.
đź”— Related topics
- NCI-Nature Pathway Interaction Database The Pathway Interaction Database (PID) is a free biomedical database of human cellular signaling pathways. The database contains information about the…
- GenMAPP GenMAPP (Gene Map Annotator and Pathway Profiler) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in…
- Biological pathway In cell biology, a biological pathway is a series of molecular interactions among molecules within a cell that leads to a specific product or a change…
- ConsensusPathDB The ConsensusPathDB is a molecular functional interaction database, integrating information on protein interactions, genetic interactions signaling, metabolism…
- Systems Biology Ontology The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational…
- NetPath NetPath is a manually curated resource of human signal transduction pathways. It is a joint effort between Pandey Lab at the Johns Hopkins University and…
- Cytoscape Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles…
- Biochemical cascade A biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions that occur within a biological cell when…