EHRKit-WF: we provide many off-shelf methods for processing medical text.

python3 -m venv virtenv/ 
source virtenv/bin/activate

pip install pip==21.3.1
pip install -U spacy
pip install scispacy
pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz
pip install pandas==1.1.5
pip install numpy==1.19.5
pip install transformers==4.12.3
pip install torch==1.10.0
pip install torchvision==0.11.1
pip install sentencepiece==0.1.96
pip install sklearn
pip install PyRuSH
pip install stanza==1.3.0
pip install ipywidgets
pip install ipykernel
pip install summa==1.2.0
pip install negspacy==1.0.2
pip install medspacy==0.2.0.0
wget https://github.com/jianlins/PyRuSH/raw/master/conf/rush_rules.tsv -P conf

from EHRKit import EHRkit

# create kit 
kit = EHRKit()

main_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."

# add main_record
kit.update_and_delete_main_record(main_record)

# call single-document tasks on main_record
kit.get_abbreviations()
>> [('SBMA', 'Spinal and bulbar muscular atrophy'),
 ('SBMA', 'Spinal and bulbar muscular atrophy'),
 ('AR', 'androgen receptor')]

from EHRKit import EHRkit

# create kit 
kit = EHRKit()

''' A document about 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)."

''' A document about neural network. '''
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."

''' A document about aspirin. '''
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)."

''' Another document about aspirin. '''
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."

# add main_record
kit.update_and_delete_main_record(record)

# add supporting_records
kit.replace_supporting_records([cand1, cand2, cand3])

# performs k-means clustering on the 4 documents
kit.get_clusters(k=2)

>>                                     note   cluster
   0  Neurons (also called neurones or ...    0
   1  A neural netwrok is a series of ...     0
   2  Prescription aspirin is used to ...     1
   3  People can buy aspirin over the ...     1