data-dictionary-cui-mapping 1.0.5

This package allows you to load in a data dictionary and map cuis to defined fields using either the UMLS API or MetaMap API from NLM.

data-dictionary-cui-mapping

This package allows you to load in a data dictionary and map cuis to defined fields using either the UMLS API or MetaMap API from NLM.

Installation

Use the package manager pip to install data-dictionary-cui-mapping or pip install from the GitHub repo.

pip install data-dictionary-cui-mapping
#pip install git+https://github.com/kevon217/data-dictionary-cui-mapping.git

Usage

# import batch_query_pipeline modules from metamap OR umls package
from data_dictionary_cui_mapping.metamap import batch_query_pipeline as mm_bqp
from data_dictionary_cui_mapping.umls import batch_query_pipeline as umls_bqp

# import helper functions for loading, viewing, composing configurations for pipeline run
from data_dictionary_cui_mapping.utils import helper
from omegaconf import OmegaConf

# import modules to create data dictionary with curated CUIs and check the file for missing mappings
from data_dictionary_cui_mapping.curation import create_dictionary_import_file
from data_dictionary_cui_mapping.curation import check_cuis

# LOAD/EDIT CONFIGURATION FILES
cfg = helper.compose_config.fn(overrides=["custom=de", "apis=config_metamap_api"]) # custom config for MetaMap on data element 'title' column
# cfg = helper.compose_config.fn(overrides=["custom=de", "apis=config_umls_api"]) # custom config for UMLS API on data element 'title' column
# cfg = helper.compose_config.fn(overrides=["custom=pvd", "apis=config_metamap_api"]) # custom config for MetaMap on 'permissible value descriptions' column
# cfg = helper.compose_config.fn(overrides=["custom=pvd", "apis=config_umls_api"]) # custom config for UMLS API on 'permissible value descriptions' column
cfg.apis.user_info.email = '' # enter your email
cfg.apis.user_info.apiKey = '' # enter your api key
print(OmegaConf.to_yaml(cfg))

# STEP-1: RUN BATCH QUERY PIPELINE
df_final_mm = mm_bqp.main(cfg) # run MetaMap batch query pipeline
# df_final_umls = umls_bqp.main(cfg) # run UMLS API batch query pipeline

# MANUAL CURATION STEP IN EXCEL FILE (see curation example in notebooks/examples_files/DE_Step-1_curation_keepCol.xlsx)

# STEP-2: CREATE DATA DICTIONARY IMPORT FILE
cfg = helper.load_config.fn(helper.choose_input_file.fn("Load config file from Step 1"))
create_dictionary_import_file.main(cfg)

# CHECK CURATED CUI MAPPINGS
cfg = helper.load_config.fn(helper.choose_input_file.fn("Load config file from Step 2"))
check_cuis.main(cfg)

Acknowledgements

The MetaMap API code included is from Will J Roger's repository --> https://github.com/lhncbc/skr_web_python_api

Special thanks to Olga Vovk and Henry Ogoe for their guidance, feedback, and testing of this package.

License

MIT