appliedinfo / pymetamap

Python wraper for MetaMap

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.

How to Install

>>> 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.

To extract concepts from a sentence use the extract_concepts() method. This method taks 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 seperate concepts extracted via MetaMap from two different sentences (sentence 1 and sentence 2).

More Information

Licensed under Apache 2.0.

Written by Anthony Rios