Installation

Create a virtual environment

python -m venv nodeNormalization-env

Activate the virtual environment

source nodeNormalization-env/bin/activate

Install requirements

pip install -r requirements.txt

Generating equivalence data

The equivalence data can be generated by running Babel. An example of the contents of a compendia file is shown below:

{"id": {"identifier": "PUBCHEM:50986940"}, "equivalent_identifiers": [{"identifier": "PUBCHEM:50986940"}, {"identifier": "INCHIKEY:CYMOSKLLKPIPCD-UHFFFAOYSA-N"}], "type": ["chemical_substance", "named_thing", "biological_entity", "molecular_entity"]}
{"id": {"identifier": "CHEMBL.COMPOUND:CHEMBL1546789", "label": "CHEMBL1546789"}, "equivalent_identifiers": [{"identifier": "CHEMBL.COMPOUND:CHEMBL1546789", "label": "CHEMBL1546789"}, {"identifier": "PUBCHEM:4879549"}, {"identifier": "INCHIKEY:FUIYIXDZTPMQEH-UHFFFAOYSA-N"}], "type": ["chemical_substance", "named_thing", "biological_entity", "molecular_entity"]}