Informatics Nerd

The field of health and biomedical informatics is ever changing, not only just in name (noticing perhaps the recent pre-pending of “health and”), but also by the individuals who are practitioners.  Review of early works in the field show many of the seminal pieces originated from doctors who understood the impact that technology could play in healthcare [1, 2].  As the field expanded and grew, it was perhaps natural that other healthcare providers (i.e. nurses and public health practitioners) realized the special needs that pertained to their unique practice and workflow.  With this realization blossomed a growth of sub-disciplines within HBI, to the point that nursing informatics and public health informatics are vibrant components of the broader HBI community, and large enough to warrant annual meetings. The growth, of course, is not limited to just a few disciplines within the spectrum of providing healthcare, but also to the side of those who are focused on health information tech

This is the first in a series of posts I'll be doing to recount the recent AMIA 2011 Symposium in Washington D.C.  What can I say - WOW!  It was a week ago already that I arrived, and after a few days of having my brain filled I (needless to say) needed a few days to relax and decompress. I began AMIA on Sunday night with a Late Breaking session about the Sorrell v. IMS Health case in Vermont where it was outlawed for pharmacies from selling prescription information to data mining and pharma companies.  While I make it no secret the details of legal proceedings are often over my head (I initially attended to see a fellow OHSU classmate present), this was a great discussion and raised some important considerations about the sharing of data. While many of the details of the discussion revolved around the legalities of how data miners were justifying the acquisition of the data under "Freedom of Speech", I found the discussion around how data could and should be used ver

I'm always amazed by the plethora and quality of software released by the biomedical informatics community.  I personally have benefited from great projects like i2b2 and cTAKES amongst many others, and know of a ton of others that are available for use. While not to question or point out any particular project, there are examples where there is an existing system that does something quite well, and another organization either funds or gets funding to build another similar system.  It's true that in many cases this can bring about a new innovation or new direction in solving a problem, but one also has to question the amount of resource that's being used to reinvent basic components. To make this more concrete, let's come up with a hypothetical example of two open source de-identification systems.  System A is developed and provides an algorithm that performs fairly well, as well as a user interface that allows people to review documents.  System B is also develop

University of Tennessee, Knoxville researchers, led by Dr. Xiaopeng Zhao, have developed a new algorithm to improve ECGs that are conducted remotely over a smartphone.  First, since I find telemedicine fascinating but don't follow the field closely, I wasn't even aware that you could conduct an ECG on a smartphone.  Knowing that, the algorithm described improves the ability to conduct one remotely (and possibly by someone who is not a trained expert) by attempting to analyze the possibility of noise in the signal, and even tries to provide suggestions about electrode placement. This is amazing, fascinating, and my big question is how soon this can be rolled out into care!  Obviously proper evaluation needs to be done, but this has great implications for providing care in remote settings, not only internationally but even domestically.  The implications for medical research may also be addressed if studies could benefit from field conduction of ECGs. From a technical standp

There's an interesting summary on CMIO , about an equally interesting article over at JAMIA regarding design and user acceptance of an EHR over one year.  We should applaud the authors for proving a long-held tenant of developing EHRs - that a well-designed EHR will be well-accepted (and increasingly so) over time.  Part of the explanation for an increased acceptance over time can be attributed to a learning effect, and the fact that the users are getting comfortable using the system.  This holds true especially for well-designed software.  I can only speculate that poorly designed software would also see better (relatively speaking) acceptance as users just get worn down on using poorly designed software.  Definitely another reason to design it right the first time. The tangent from here that my mind takes is that when technology changes and new innovations are made, how do we get users to buy into changing what they've grown to like?  Assuming that the enhanced software/fe

After much slacking and shuffling on my part, I've finally gone ahead and signed up for a GitHub account.  The first project I'll be getting updated is the UIMA.NET support library.  The purpose of this project is to allow .NET developers (like myself) to have an easy-to-use assembly for accessing UIMA documents.  This is being developed specifically around cTAKES NLP engine to begin with, so perhaps the title is slightly misleading, but I'm hoping that it will grow over time. Right now the library offers basic functionality for identifying cTAKES objects within a document and being able to extract those items or merge them with other types of objects.  Ideally there will be more advanced LINQ support, but I see that as being a few months out before I'll probably have time to get to it.

For those who are not familiar with the NHGRI sponsored Electronic Medical Records and Genomics ( eMERGE ) network, the first 4-year phase is drawing to a close.  One of the results from this network, as shown in multiple publications and reports, is the feasibility of using longitudinal data in the EHR for genome-wide association studies (GWAS), and draws out some of the imperfections in those data.  That's probably not unexpected, since we know EHRs have room to improve, and really provides results for EHR developers to learn from history and to plan for the future. As phase 1 draws to its conclusion, phase 2 will soon begin.  One of the goals as per the RFA of eMERGE II is to evaluate how to incorporate genetic test results into the EHR.  While there are invariably many ELSI and organizational issues related to this, it also begs an informatics question: how to best enter and display this type of information in the EHR?  Traditionally (or perhaps just from my simplified view

It's an informatician and programmer's dream contest!  The NLM is sponsoring a competition to develop an application of some sort which utilizes publicly accessible NLM data (either through an API or data set).  More information is at:  http://challenge.gov/NIH/132-nlm-show-off-your-apps-innovative-uses-of-nlm-information Submissions are due August 31, so I know I'm going to need to get busy to come up with some ideas.  If anyone is looking to collaborate on a submission, please feel free to get in touch as well.

While on vacation this week, I was getting caught up on some articles and reports I had found at the The National Academies Press .  I was reading an excellent report from the National Research Council entitled " Computational Technology for Effective Health Care: Immediate Steps and Strategic Directions ".  Even if you are short on time, I would highly recommend reading the Summary alone.  This report identifies some very relevant and addressable issues with HIT, and lays a short-term and long-term vision for how this can be improved by informaticians and system developers (calling specifically to the fields of computer science and biomedical informatics).  While those involved with this report are undoubtedly recognized within the field, they also conducted 8 site visits in order to supplement their existing knowledge. One of the comments that stuck out for me was the need to improve "cognitive support for health care providers and for patients and family caregiver

I'll admit, it's been a bit since I've stopped out at the AMIA website .  I was pleasantly surprised by the overhaul they did of the site!  It's very sleek, well-organized and I like how they tied together the various, related resources at the top.  If you haven't been out there in awhile, stop by and check it out.

So how did the "Informatics Nerd" come to be? I am a computer programmer with almost 10 years experience in the realm of healthcare.  About half of that time was spent developing electronic medical record software, and since then it has been spent working to help clinical and genomics researchers.  While working with biomedical informatics researchers for the past 5 years, and even before then (before I even knew what biomedical informatics was all about) I found myself unable to get enough knowledge about how technology can help those clinicians and researchers working to make the world a better place.  I realized that in addition to being a general computer nerd (as I am very passionate about technology, which you will undoubtedly see focused here as well), I was also essentially a nerd about informatics.  My idea of a fun time is going to an informatics conference, attending every possible session/talk/workgroup that I can, then going back and trying out new things and