synonymizer

The main objective of this tool is to apply custom rules for entity recognition to supplement the ontology dictionary generated from kgx for ontoRunNER.

Setups

python setup.py install

Steps

• Get termlist files for ontologies:

  • The source here is ontology_nodes.tsv file derived from kgx as shown here
  • From ontoRunNER use prepare-termlist to get ontology_termlist.tsv

• Have a rules.yaml and schema.yaml files prepared that resemble synonym_rules.yaml and schema.yaml in this project.

Python

from synonymizer import synonymize
synonymize.run(
    rule_file = [path to rules.yaml],
    schema_file = [path to schema.yaml],
    data_folder = [location of the folder that cotains the termlist.tsv files]
    )

CLI

python -m synonymizer.cli run 
       -r [path to rules.yaml] 
       -s [path to schema.yaml] 
       -d [location of the folder that cotains the termlist.tsv files]

or

python -m synonymizer.cli run 
       --rule [path to rules.yaml] 
       --schema [path to schema.yaml] 
       --data [location of the folder that cotains the termlist.tsv files]