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README.rst

pymetamap

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

Example Usage

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 metamap16.

We now support MetaMapLite. To use MetaMapLite, rather than MetaMap, create a MetaMapLite instance:

>>> from pymetamap import MetaMapLite
>>> mm = MetaMapLite.get_instance('/opt/public_mm_lite_3.6.2rc3/')

Note: The MetaMap binary path and MetaMapLite home directory should be absolute.

To extract concepts from a sentence with MetaMapLite and MetaMap use the extract_concepts() 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).

More Information

Licensed under Apache 2.0.

Written by Anthony Rios

Special thanks to joaopalotti and others for their contributions.