metagraph

A utility for deriving a metagraph from node and edge tsv files.

The Biomedical Data Translator project, funded by NCATS, generates, uses and shares knowledge graphs (KG). One standard exchange format involves two tsv files, one describing graph nodes and the other the edges. This utility studies the two tsv files representing a KG, identifies node types and which predicates connect these node types (paying attention to Biolink entities), and produces a metagraph representing this structure. The metagraph is saved in graphml format, which can be opened in utilities like yEd for visualization.

Installing

To install this software, simply clone this repository:
git clone https://github.com/multiomicsKP/metagraph

Usage

1. Create the graphml file:
   perl bin/metagraph.pl path/to/nodes_file.tsv path/to/edges_file.tsv > path/to/metagraph_file.graphml

2. Open the resulting graphml file in yEd.

3. In yEd, select menu Tools, command Fit Node to Label, unselect 'Ignore Width' and 'Ignore Height' if they're selected, and click OK.

4. Perform a layout. For example, select menu Layout, command Circular, and press OK.