Python wraper for MetaMap
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kaushikacharya and AnthonyMRios Added options: allow overmatches, concept gaps, term processing reque…
…sted in issue #30 (#33)

* Added option restrict_to_sts, exclude_sts to restrict/exclude semantic types

* Added options: allow overmatches, concept gaps, term processing
Latest commit cdf4a3b Aug 15, 2018

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.

Note: Metamap binary path should be absolute.

To extract concepts from a sentence 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.