from EHRKit import EHRKit
if __name__ == '__main__':
print("Welcome to LILY-EHRKit. Here's a complete run-through of all EHRKit text processing functions.")
# initialize EHRKit object
kit = EHRKit()
print("========== Start of SciSpacy Functions ==========")
print('\n\n')
print('Abbreviations')
record = "Spinal and bulbar muscular atrophy (SBMA) is an " \
"inherited motor neuron disease caused by the expansion" \
"of a polyglutamine tract within the androgen receptor (AR)." \
"SBMA can be caused by this easily."
kit.update_and_delete_main_record(record)
print(kit.get_abbreviations())
print('\n\n')
print('Hyponyms')
record = "Keystone plant species such as fig trees are good for the soil."
kit.update_and_delete_main_record(record)
print(kit.get_hyponyms())
print('\n\n')
print('Linked entities')
record = "Spinal and bulbar muscular atrophy (SBMA) is an " \
"inherited motor neuron disease caused by the expansion" \
"of a polyglutamine tract within the androgen receptor (AR)." \
"SBMA can be caused by this easily."
kit.update_and_delete_main_record(record)
print(kit.get_linked_entities())
print('\n\n')
print('Named entities')
record = """
Myeloid derived suppressor cells (MDSC) are immature
myeloid cells with immunosuppressive activity.
They accumulate in tumor-bearing mice and humans
with different types of cancer, including hepatocellular
carcinoma (HCC).
"""
kit.update_and_delete_main_record(record)
print(kit.get_named_entities())
print("========== End of SciSpacy Functions ==========")
print('\n\n')
# translation
print("========== Start of Translation ==========")
# reference: https://qbi.uq.edu.au/brain/brain-anatomy/what-neuron
record = "Neurons (also called neurones or nerve cells) are the fundamental units of the brain and nervous system, " \
"the cells responsible for receiving sensory input from the external world, for sending motor commands to " \
"our muscles, and for transforming and relaying the electrical signals at every step in between. More than " \
"that, their interactions define who we are as people. Having said that, our roughly 100 billion neurons do" \
" interact closely with other cell types, broadly classified as glia (these may actually outnumber neurons, " \
"although it’s not really known)."
kit.update_and_delete_main_record(record)
print(kit.get_translation('French'))
print("========== End of Translation ==========")
# segmentation
print("========== Start of Sentencizer ==========")
record = "Neurons (also called neurones or nerve cells) are the fundamental units of the brain and nervous system, " \
"the cells responsible for receiving sensory input from the external world, for sending motor commands to " \
"our muscles, and for transforming and relaying the electrical signals at every step in between. More than " \
"that, their interactions define who we are as people. Having said that, our roughly 100 billion neurons do" \
" interact closely with other cell types, broadly classified as glia (these may actually outnumber neurons, " \
"although it’s not really known)."
kit.update_and_delete_main_record(record)
print('Using stanza')
print(kit.get_sentences('stanza'))
print('Using PyRush')
print(kit.get_sentences('pyrush'))
print('Using SciSpacy')
print(kit.get_sentences('scispacy'))
print("========== End of Sentencizer ==========")
# clustering
print("========== Start of Clustering ==========")
record = "Neurons (also called neurones or nerve cells) are the fundamental units of the brain and nervous system, " \
"the cells responsible for receiving sensory input from the external world, for sending motor commands to " \
"our muscles, and for transforming and relaying the electrical signals at every step in between. More than " \
"that, their interactions define who we are as people. Having said that, our roughly 100 billion neurons do" \
" interact closely with other cell types, broadly classified as glia (these may actually outnumber neurons, " \
"although it’s not really known)."
# reference: https://www.investopedia.com/terms/n/neuralnetwork.asp
cand1 = "A neural network is a series of algorithms that endeavors to recognize underlying relationships in a set of " \
"data through a process that mimics the way the human brain operates. In this sense, neural networks refer to " \
"systems of neurons, either organic or artificial in nature."
# reference: https://medlineplus.gov/druginfo/meds/a682878.html
cand2 = "Prescription aspirin is used to relieve the symptoms of rheumatoid arthritis (arthritis caused by swelling " \
"of the lining of the joints), osteoarthritis (arthritis caused by breakdown of the lining of the joints), " \
"systemic lupus erythematosus (condition in which the immune system attacks the joints and organs and causes " \
"pain and swelling) and certain other rheumatologic conditions (conditions in which the immune system " \
"attacks parts of the body)."
# reference: https://www.medicalnewstoday.com/articles/161255
cand3 = "People can buy aspirin over the counter without a prescription. Everyday uses include relieving headache, " \
"reducing swelling, and reducing a fever. Taken daily, aspirin can lower the risk of cardiovascular events, " \
"such as a heart attack or stroke, in people with a high risk. Doctors may administer aspirin immediately" \
" after a heart attack to prevent further clots and heart tissue death."
kit.update_and_delete_main_record(record)
kit.replace_supporting_records([cand1, cand2, cand3])
print(kit.get_clusters())
print("========== End of Clustering ==========")
# similar documents
print("========== Start of Similar Documents ==========")
record = "Neurons (also called neurones or nerve cells) are the fundamental units of the brain and nervous system, " \
"the cells responsible for receiving sensory input from the external world, for sending motor commands to " \
"our muscles, and for transforming and relaying the electrical signals at every step in between. More than " \
"that, their interactions define who we are as people. Having said that, our roughly 100 billion neurons do" \
" interact closely with other cell types, broadly classified as glia (these may actually outnumber neurons, " \
"although it’s not really known)."
# reference: https://www.investopedia.com/terms/n/neuralnetwork.asp
cand1 = "A neural network is a series of algorithms that endeavors to recognize underlying relationships in a set of " \
"data through a process that mimics the way the human brain operates. In this sense, neural networks refer to " \
"systems of neurons, either organic or artificial in nature."
# reference: https://medlineplus.gov/druginfo/meds/a682878.html
cand2 = "Prescription aspirin is used to relieve the symptoms of rheumatoid arthritis (arthritis caused by swelling " \
"of the lining of the joints), osteoarthritis (arthritis caused by breakdown of the lining of the joints), " \
"systemic lupus erythematosus (condition in which the immune system attacks the joints and organs and causes " \
"pain and swelling) and certain other rheumatologic conditions (conditions in which the immune system " \
"attacks parts of the body)."
# reference: https://www.medicalnewstoday.com/articles/161255
cand3 = "People can buy aspirin over the counter without a prescription. Everyday uses include relieving headache, " \
"reducing swelling, and reducing a fever. Taken daily, aspirin can lower the risk of cardiovascular events, " \
"such as a heart attack or stroke, in people with a high risk. Doctors may administer aspirin immediately" \
" after a heart attack to prevent further clots and heart tissue death."
kit.update_and_delete_main_record(record)
kit.replace_supporting_records([cand1, cand2, cand3])
print(kit.get_similar_documents(3))
print("========== End of Similar Documents ==========")
""" UNDER CONSTRUCTION """
""" stanza functions """
# print dependencies
record = "A neural network is a series of algorithms that endeavors to recognize underlying relationships in a set of " \
"data through a process that mimics the way the human brain operates. In this sense, neural networks refer to " \
"systems of neurons, either organic or artificial in nature."
kit.update_and_delete_main_record(record)
kit.get_dependency()
