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OpenSource Resources

Hephestus: Health data warehousing tool for public health and clinical research

Originally published by Bell Eapen at nuchange.ca on November 3, 2018. If you have some feedback, reach out to the author on TwitterLinkedIn or Github.

Health data warehousing is becoming an important requirement for deriving knowledge from the vast amount of health data that healthcare organizations collect. A data warehouse is vital for collaborative and predictive analytics. The first step in designing a data warehouse is to decide on a suitable data model. This is followed by the extract-transform-load (ETL) process that converts source data to the new data model amenable for analytics.

The OHDSI – OMOP Common Data Model is one such data model that allows for the systematic analysis of disparate observational databases and EMRs. The data from diverse systems needs to be extracted, transformed and loaded on to a CDM database. Once a database has been converted to the OMOP CDM, evidence can be generated using standardized analytics tools that are already available.

Each data source requires customized ETL tools for this conversion from the source data to CDM. The OHDSI ecosystem has made some tools available for helping the ETL process such as the White Rabbit and the Rabbit In a Hat. However, health data warehousing process is still challenging because of the variability of source databases in terms of structure and implementations.

Hephestus is an open-source python tool for this ETL process organized into modules to allow code reuse between various ETL tools for open-source EMR systems and data sources. Hephestus uses SqlAlchemy for database connection and automapping tables to classes and bonobo for managing ETL. The ultimate aim is to develop a tool that can translate the report from the OHDSI tools into an ETL script with minimal intervention. This is a good python starter project for eHealth geeks.

Anyone anywhere in the world can build their own environment that can store patient-level observational health data, convert their data to OHDSI’s open community data standards (including the OMOP Common Data Model), run open-source analytics using the OHDSI toolkit, and collaborate in OHDSI research studies that advance our shared mission toward reliable evidence generation. Join the journey! here

Disclaimer: Hephestus is just my experiment and is not a part of the official OHDSI toolset.

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Research Resources

McMaster’s start-up incubator to receive $1.2 million from FedDev Ontario

This article was first published on Daily News. Read the original article.

The Government of Canada, through FedDev Ontario, is providing McMaster with $1.2 million to expand The Forge, a collaborative makerspace where entrepreneurs can access advanced equipment to design and build innovative new products.

 

Forge

The Honourable Filomena Tassi, Minister of Seniors and Member of Parliament for Hamilton West-Ancaster-Dundas, made the announcement today on behalf of the Honourable Navdeep Bains, Minister of Innovation, Science and Economic Development and minister responsible for FedDev Ontario.

“FedDev Ontario’s funding is providing invaluable support to the innovation community in Hamilton,” said Tassi. “The government of Canada is proud to support McMaster — one of Canada’s premier research-intensive universities — to expand The Forge’s makerspace and allow more companies to develop and bring new products to market.”

The funding will allow The Forge to expand its makerspace as it moves into a 10,000 square-foot facility shared with partner Innovation Factory. It will also purchase additional 3D printers and other fabricating equipment, and increase support to entrepreneurs through mentoring. As a result, the number of companies supported will almost double from 24 to up to 40 annually, with up to 75 new jobs created as a result.

“This strategic investment from the Government of Canada will strengthen the entrepreneurial capacity of our region by providing McMaster’s students and the wider Hamilton community access to the centralized expertise and infrastructure so essential for creating start-ups and business growth opportunities,” said Karen Mossman, Acting Vice-President of Research at McMaster and chair of the McMaster Innovation Park board of directors.

More than 105 tech companies have graduated from The Forge since its founding in 2014, with more than 300 employees hired and $20 million of private and public investment raised.

The Forge’s expansion further enhances McMaster’s entrepreneurial ecosystem and reputation as a leader in developing innovative manufacturing assets, in particular within the McMaster Innovation Park, which is also home to the McMaster Automotive Research Centre (MARC) and the Centre for Biomedical Engineering and Advanced Manufacturing (BEAM).

This article was first published on Daily News. Read the original article.

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Resources

Oscar eForm Generator

OSCAR Eform Generator
OSCAR Eform Generator

Electronic capture of patient data is vital in any health information system. It ‘s hard to bundle every form that a clinician will ever need along with an EMR. The EMRs adopt various strategies to solve this problem, but a general standard is lacking.

Eforms is OSCAR’s solution to this problem. The OSCAR eForms are arguably one of the most useful features of OSCAR and is being used in many settings beyond which it was initially designed for. Community eForms can be downloaded from the OSCAR Canada Users Society.

EForm is not an elegant solution and creating complex eforms require programming expertise. Reporting of data collected through eForms is difficult because of the way in which the data is abstracted as key-value pairs in the database.

Oscar provides basic eForm generator functionality built-in using a form image in the background with controls transposed on top. However, it is not user-friendly and lacks the ability to save and continue the work later.

Oscar EForm Generator

I have created an online OSCAR eForm generator that solves most of the above-mentioned problems. Here is an advanced OSCAR eform generator with drag and drop controls. You can save the form as a text file and continue editing later after loading the content. It also supports radio-buttons by internally mapping to OSCAR supported code. You can pull OSCAR demographic fields and define complex show/hide rules. You can cut and paste the generated code into the OSCAR eform editor. The form is generated in your browser using javascript and it is not sent or saved on our server.

Watch the video below to see how it is done. This is still being tested and is not ready for production. Contact us for more details. Please report bugs, function requests, and feed backs.

The application is available here: http://nuchange.ca/oscar-eform-generator .