SMOREs is a python application designed to assist institutions with mappings local medications to standardized ontologies. Any local information around a medication can be loaded in and SMOREs will attempt to link the provided information to desired ontologies. These links are achieved through the use of available public API's provided by the National Library of Medicine and the Food and Drug Administration.
These instructions will get you a copy of SMOREs up and running on your local machine.
Python Versions Supported
Python 3.6 or above
Python Libraries Required
PyYAML
tqdm
requests
requests-cache
python-dateutil
pandas
numpy
For ease of access, NC TraCS provides a standalone package for SMOREs that includes all dependencides, including a built in python virtual environment. The package can be found at the NC TraCS Institute ShareHub (Registration Required):
https://tracs.unc.edu/index.php/tracs-resources/sharehub/category/2-informatics
All Python library dependencies must be installed. There are a couple of options on how to ensure that all required dependencies.
A pipfile is included in the install directory of SMOREs to allow for quick setup of a virtual environment with all necessary dependencies. This does require that pipenv is installed.
Instructions on installing pipenv are available at: pipenv.org
Once installed running the following command within the install directory will perform the necessary steps.
pipenv install
pipenv run smores
A compiled list of all package requirements is also available to be installed via pip using the requirements.txt file within the install directory
cd to [smores directory]
pip install -r requirements.txt
Each required package list in the Python Libraries Required section can be installed manually via pip. SMOREs will need to be executed via a python interpreter that has all of the modules available.
pip install PyYAML
etc..
After downloading the source code, installation of all required dependencies and necessary API access can be validated by executing the provided verification program.
cd to [smores directory]
python tests\verifyInstall.py
For more information on available commands, processes and functionality please visit the SMOREs Wiki for up to date descriptions of functionality within the application.
Please contact the development team about making contributions to the source. More detail on contributing to the source will be provided in the future.
We use SemVer for versioning. For the versions available, see the tags on this repository.
- Robert Bradford - Lead - NC Translation and Clinical Sciences Institute
See also the list of contributors who participated in this project.
If your group uses SMOREs in support of a research project, please include the appropriate citation to help acknowledge SMOREs and it's development.
SMOREs is a tool to support institutions by improving semantic relationships to standardized medication ontologies via supported APIs provided by the National Library of Medicine (NLM - RxNav, UMLS) and the US Food and Drug Administration (FDA - openFDA). Standardized ontologies allow a harmonized approach to searching for medications for research, operational, and quality improvement purposes within healthcare. SMOREs was developed at University of North Carolina is supported by the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, through Grant Award Number UL1TR002489.
SMOREs is a tool to support institutions by improving semantic relationships to standardized medication ontologies via supported APIs provided by the National Library of Medicine (NLM - RxNav, UMLS) and the US Food and Drug Administration (FDA - openFDA). SMOREs was developed at University of North Carolina is supported by the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, through Grant Award Number UL1TR002489.
This project is licensed under the MIT License - see the LICENSE.md file for details
This product uses publicly available data from the U.S. National Library of Medicine (NLM), National Institutes of Health, Department of Health and Human Services; NLM is not responsible for the product and does not endorse or recommend this or any other product.
Data provided by the U.S. Food and Drug Administration (https://open.fda.gov/terms/)
This product uses publicly available data from the U.S. National Library of Medicine (NLM), National Institutes of Health, Department of Health and Human Services; NLM is not responsible for the product and does not endorse or recommend this or any other product.
- Hat tip to anyone whose code was used
- Inspiration
- etc