universalizer 0.0.11

Provides functions for knowledge graph cleanup and identifier normalization.

universalizer

The KG-Hub Universalizer provides functions for knowledge graph cleanup and identifier normalization.

Installation

Install with pip:

pip install universalizer

OR

Install with Poetry.

git clone https://github.com/Knowledge-Graph-Hub/universalizer.git
cd universalizer
poetry install

Usage

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

ID and category mapping

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.)