--- a +++ b/wrapper_functions/demo.py @@ -0,0 +1,179 @@ +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() + + + + + +