/bmeg_to_cytoscape

renders bmeg schema into cytoscape import files

Primary LanguagePython

bmeg to cytoscape

Generates sif file and associated tables for import into cytoscape.

instructions

$ python3 schema_to_cytoscape.py

The app reads bmeg, so you will need credentials in ~/.bmeg_credentials.json

>>> edge_labels.json
>>> node_labels.json

Note that the graph rendered by https://bmeg.io/meta/schema.json will be used.

  • File->Import->Import Network from file <graph_name>.sif
  • File->Import->Table from file <graph_name>_edges.tsv <graph_name>_nodes.tsv

gotchas

  • There are timeouts in bmeg, so there will be missing count fields in edge_labels.json. You will need to find and edit them manually.

  • We have a large number of publications, edit the node_labels file to adjust.