Developed as part of semantic data research with UW BIME.
BioModels-DAG is a DAG engine for visualizing SBML BioModels (mathematical models for biological systems). It generates NetworkX DAGs that can be exported and visualized as semantic data networks.
Example network (visualized with Cytoscape):
Network showing parent-child relationships between derived BioModels
(BioModels that name another model as its predecessor).
PubMed models are displayed in red, EBI models in green.
The engine:
- Extracts SBML data from SBML BioModels
- Parses data with user-implemented parsers/classifiers to retrieve semantic data as ordered triples (similar to RDF)
- Processes and loads ordered triples into a NetworkX DAG
- Exports DAG (most graph data formats e.g. JSON, YAML, GraphML, etc. are supported). Compatible with most network visualization tools.
The following flowchart illustrates this process:
Completed example networks are available here.