Python wrapper around MetaMap. This will take a list of sentences and extract concepts using MetaMap then return them in the form of a list of Concept objects.
Note: This code does not work with Windows because of my use of NamedTemporaryFile in SubprocessBackend.py.
How to Install
First, install MetaMap by using the following instructions: https://metamap.nlm.nih.gov/Installation.shtml
Next, pymetamap can be installed using the following command:
>>> python setup.py install
To start you must create a MetaMap instance from the pymetamap package.
>>> from pymetamap import MetaMap >>> mm = MetaMap.get_instance('/opt/public_mm/bin/metamap12')
You must supply the metamap binary to
get_instance() in order to
extract concepts. Depending on where you installed MetaMap and depending on the version you are using, you will need to change the
/opt/public_mm/bin/metamap12 to the correct location.
For example, if you installed the 2016 version of MetaMap, then the binary will be called
Note: Metamap binary path should be absolute.
To extract concepts from a sentence use the
method. This method takes a list of sentences as input and will return
a list of Concept objects.
>>> sents = ['Heart Attack', 'John had a huge heart attack'] >>> concepts,error = mm.extract_concepts(sents,[1,2]) >>> for concept in concepts: ... print concept Concept(index='1', mm='MM', score='14.64', preferred_name='Myocardial Infarction', cui='C0027051', semtypes='[dsyn]', trigger='["Heart attack"-tx-1-"Heart Attack"]', location='TX', pos_info='1:12', tree_codes='C14.280.647.500;C14.907.585.500') Concept(index='2', mm='MM', score='13.22', preferred_name='Myocardial Infarction', cui='C0027051', semtypes='[dsyn]', trigger='["Heart attack"-tx-1-"heart attack"]', location='TX', pos_info='17:12', tree_codes='C14.280.647.500;C14.907.585.500')
This example shows two separate concepts extracted via MetaMap from two different sentences (sentence 1 and sentence 2).
Licensed under Apache 2.0.
Written by Anthony Rios
Special thanks to joaopalotti and others for their contributions.