cannin/sbgn2sif

Converting SBGN-encoded pathways to the SIF file format

Convert SBGNML to SIF

• SBGNML:
  • https://sbgn.github.io
  • http://co.mbine.org/specifications/sbgnml.version-0.3.release-1
• SIF: Check "Output" section

Installation

• Pipenv: https://github.com/pypa/pipenv

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

• Original work: Copyright 2019 Arnaud Poret
• Modified work: Copyright 2020 Augustin Luna

License

• SPDX-License-Identifier: Apache-2.0