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Converting SBGN-encoded pathways to the SIF file format

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Convert SBGNML to SIF

Installation

pipenv install

or

pip3 install -r requirements.txt 

Example with Conversion to SVG and Verbose Output

pipenv run python main.py -s pamp.sbgn -c -v

Output

SIF: Simple Interaction Format: Tabular Format

PARTICIPANT_A INTERACTION_TYPE PARTICIPANT_B ANNOTATION_SOURCE ANNOTATION_INTERACTION ANNOTATION_TARGET SOURCE_CLASS TARGET_CLASS
TP53 stimulation MDM2 HGNC:X PUBMED:Y HGNC:Y macromolecule macromolecule

Graphviz DOT/SVG

An simplified graphical representation showing connections between SBGN glyphs

Intermediate Versus Projected/Simplified Outputs

  • Intermediate output includes: entity pool, logic, and process glyphs.
  • Simplified output removes logic and process
    • Process nodes are removed using bipartite network projection. The graph represented by SBGNML is
      • Decomposed into bipartite and non-bipartite subgraphs
      • Bipartite network projection is used on the bipartite subgraph
      • The non-bipartite and projected subgraphs are integrated
  • Logic nodes and connections are removed (TODO)
  • Interactions between complex members are not represented (TODO)

Contributors

License

  • SPDX-License-Identifier: Apache-2.0

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  • Python 100.0%