Tag Archives: Informatics

Recommended: Data Sharing Network (SHRINE)

I’m ginvg a talk about i2b2 (among other things) and when browsing through their website, I cam across an interesting project, SHRINE. This is an acronym for Shared health Research Informatics NEtwork., and represents a way of allowing users to review information across multiple i2b2 sites. It requires the individual institutions who have i2b2 systems to cooperate with one another, which is not always easy. But this has tremendous potential. Continue reading

Recommended: To combat physician burnout and improve care, fix the electronic health record

This article is a nice counterbalance to all the glowing reports about how moving to the electronic health record is going to revolutionize health care. This effort certainly has value, but it comes at a cost. The article talks about the improvements needed to the crude 1990s interface and how to avoid overburdening the medical record with extraneous data. Continue reading

PMean: Starting a heron-i2b2-analytics repository

I am working on a CTSA grant to develop repeatable downstream pipelines that directly access i2b2 and CDM. In order to promote this work and encourage others to participate, I was given a repository site on github, kumc-bmi/heron-i2b2-analytics. Right now, it is just a shell, but here’s what I want to do with it, short term and long term. Continue reading

PMean: Next stop, BMC Medical Informatics and Decision Making

I’m working part-time on a research grant and I want to publish some of the work I’ve done on this grant. The title of the paper tentatively is “Validating elastic net generated electronic health record breast cancer phenotypes against hospital tumor registries: a case control study.” My co-authors are Dan Connolly and Russ Waitman. I want to summarize the history of the effort so far and why I am considering the BMC Medical Informatics and Decision Making as the next place to submit the article. Continue reading

Recommended: PheKB. A knowledge base for discovering phenotypes from electronic health records

Some of the work I am doing right now could be characterized as discovering phenotypes from electronic health records. So when one of my co-workers mentioned this database, I thought “Oh boy! Oh boy! Oh boy!” This is a list of validated algorithms for various systems, and typically refers to a peer-reviewed publication. So once I get my stuff published, I’m heading here next. Continue reading

Recommended: The Importance of Reproducible Research in High-Throughput Biology

I have not viewed this video yet, but have attended a similar talk and read a similar research paper by Keith Baggerly. His general message is that large biological and genetic experiments are sometimes designed so poorly as to invalidate the results. You can often discover these design flaws through a careful examination of the data sets themselves and their metadata. This process of uncovering design flaws is sometimes called “Forensic Statistics.” Continue reading