README.txt
MedRec v0.01
This is Dr. Herskovic's medication reconciliation algorithm. It takes two lists
of medications and returns three lists: a reconciled list, the part of list 1
that could not be reconciled, and the part of list 2 that could not be reconciled.
This implementation requires RXNorm, which is part of the UMLS. You can extract
RXNorm from the UMLS to use with this program by using the included
generate_rxnorm_file.py script. You must have an RRF version of the UMLS to use
this script. Invoke it as:
python generate_rxnorm_file.py /path/to/umls/metathesaurus rxnorm.pickle.bz2
It also requires a treatment database in a pickled bz2 file. You may ignore this
file, and treatment intent reconciliation will be skipped. If you want to
provide one, it should be a pickle dictionary of the form
{'CUI_of_drug': set(['CUI_of_condition', 'CUI_of_another_condition', etc.])}
I apologize in advance, but I can not share the dataset we used to create our
own copy of the treatment file, nor the treatment file itself. The algorithm
will still work without it.
After you have your rxnorm pickled file, please try out:
python reconcile.py
to perform a demo reconciliation.
I also included the SMARTApp version of the reconciliation algorithm. You will
need Josh Mandel's smart client modules, available from
https://github.com/chb/smart_client_python and placed in the smart_client
subdirectory (and, of course, all its dependencies). Try:
python reconcile_smart.py 8000
and run it inside the SMART sandbox to play with it.
Our original evaluation of this algorithm was published in the Proceedings of
the AMIA Symposium:
Bozzo Silva PA, Bernstam EV, Markowitz E, Johnson TR, Zhang J, Herskovic JR.
Automated medication reconciliation and complexity of care transitions.
Proc AMIA Ann Symp 2011.