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Python library for calling TERMite and TExpress and processing results

Project description

Project Description

Python library for making calls to SciBite's NER engine, TERMite, as well as the TExpress module for defining more complex semantic patterns. The library also enables post-processing of the JSON returned from such requests.

Install

$ pip3 install termite_toolkit

Example call to TERMite

from termite_toolkit import termite
from pprint import pprint


# specify termite API endpoint
termite_home = "http://localhost:9090/termite"

# specify entities to annotate
entities = "DRUG"

# initialise a request builder
t = termite.TermiteRequestBuilder()
# individually add items to your TERMite request
t.set_url(termite_home)
t.set_fuzzy(True)
t.set_text("citrate macrophage colony sildenafil stimulating factor influenza hedgehog")
t.set_entities(entities)
t.set_subsume(True)
t.set_input_format("txt")
t.set_output_format("doc.jsonx")
t.set_reject_ambiguous(False)
t.set_options({'fragmentSize': 20})

# execute the request
termite_response = t.execute(display_request=True)

pprint(termite_response)

Example call to TExpress

from pprint import pprint
from termite_toolkit import texpress

# specify termite API endpoint
termite_home = "http://localhost:9090/termite"
# specify the pattern you wish to search for- this can created in the TERMite UI
pattern = ":(INDICATION):{0,5}:(GENE)"

t = texpress.TexpressRequestBuilder()

# individually add items to your TERMite request
t.set_url(termite_home)
t.set_text("breast cancer brca1")
t.set_subsume(True)
t.set_input_format("txt")
t.set_output_format("json")
t.set_allow_ambiguous(False)
t.set_pattern(pattern)

# execute the request
texpress_response = t.execute(display_request=True)
pprint(texpress_response)

License

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Project details


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