The KG-Hub Universalizer provides functions for knowledge graph cleanup and identifier normalization.
Install with pip:
pip install universalizer
OR
Install with Poetry.
git clone https://github.com/Knowledge-Graph-Hub/universalizer.git
cd universalizer
poetry install
With KGX format node and edge files in the same directory:
universalizer run path/to/directory
Or, if they're in a single tar.gz file:
universalizer run -c graph.tar.gz
SSSOM-format maps are supported. Use a single map file:
univeralizer run -m poro-mp-exact-1.0.sssom.tsv path/to/directory
or a whole directory of them:
univeralizer run -m path/to/mapfiles path/to/directory
To map node categories as well as identifiers, use the -u flag:
univeralizer run -m path/to/mapfiles path/to/directory -u
For SSSOM maps from subject_id to object_id, subject node IDs will be remapped to object IDs.
If the object_category value is specified the node's category ID will be remapped as well.
Note that this will complete node normalization and ID remapping.
Maps should use the normalized form (e.g., specify "FBbt:00005201", not "FBBT:00005201", even if the latter form is in the input graph.)