Columbia’s Natural Language Processing Technology Licensed to NLP International

Congratulations to our friends at Columbia

New York — Columbia University reports that it has licensed MedLEE, a natural language processing technology, to Columbia spin-out, NLP International Corp.

Millions of dictated and typed medical reports require laborious and time-consuming processing by highly trained and expensive experts who manually review and extract the required information. MedLEE reduces the time and expense associated with these processes by automatically extracting and encoding all relevant clinical information. Once coded, the information is easily available and accessible for further clinical processes like billing, reimbursement, quality assurance analytics, data mining, accreditation and others.

“A significant proportion of the [electronic] health care record (EHR) resides in the form of unstructured, natural language text and both the amount of data and the number of records is growing dramatically,” said Bernie Keppler, founder and chief executive of NLP International. “Ready access to this information is critical to save costs and improve the quality and access to health care.”

MedLEE has been successfully tested by large hospital systems and government agencies, including the NewYork-Presbyterian Hospital , the National Cancer Institute and the U.S. Department of Defense. Several pharmaceutical companies and healthcare information system vendors are currently evaluating MedLEE for a variety of applications.

“I am excited that this technology will now be more broadly available to hospitals and other health care organizations, where it can continue to contribute to improving patient care,” said Carol Friedman Ph.D., Professor of Biomedical Informatics at Columbia University , who developed the technology. “MedLEE has been used in the academic community for many years to develop clinical applications that have been shown to improve the quality of health care.”

“MedLEE is considered by many in the field as the gold standard for unstructured medical text processing, but it has not been available as a commercial, enterprise-ready product,” said Donna See, Director of Strategic Initiatives at STV, which brokered the deal. “We are very pleased to be partnering with NLP International to introduce MedLEE to these markets.”

Robert Sideli, M.D., CIO at Columbia University Medical Center , said the already widespread deployment and use of MedLEE throughout the research and healthcare communities prove the system’s future commercial success. “It will contribute substantially to higher efficiency in the electronic medical record industry due to its superior functionality in medical data extraction, coding, analytics and data mining,” Sideli said.

David Lerner, who oversees new ventures for STV, said Columbia has found the right partner in NLP International. “This venture will add to the many successful technology spin-off ventures for which Columbia University is known,” Lerner said.

A build Point

I have reached a point where I was able to hand the code for gmap-polygon to Felicia so she could use it to draw polygons for data that her services were returning. Many thanks to Felicia and Brian. Felicia for her patience for all the "oh crap, that's not doing what I thought, sync and try again" moments. Brian for doing some textedit niftiness to turn the KML files into easier to parse flat-files.

Otherwise, I am going to be off on vacation for the next couple of days, and some of them Felicia will still be coding, so I am glad I got a chance to explain the inner workings of the code and that I spent a lot of time trying to make it as agnostic as possible.

Otherwise, that being said, I really need to step up my Javadoc documentation. I'm committing to spending the last hour of each day documenting all my new stuff (and old stuff I forgot to document) and checking it in. That way, people who AREN'T sitting right next to me will have a much easier time figuring out how to do stuff and why I did the things I did the way I did them.

Cheers, and Happy Holidays.

AMDS White Paper

Wil posted an initial draft of an Aggregate Minimum Data Set white paper over on the wiki. Please read and submit comments on how to improve the document. The purpose of the document is to show how aggregate data can be useful for biosurveillance. This isn't a new concept, but we wanted to put a clarification document of how our AMDS-related activities can benefit biosurveillance.

I'll be offline due to Christmas and New Year's and won't be back online (I hope) until January 5. So Merry Christmas, Happy Hanukkah and Happy New Year.

A plague of ticks (and by ticks, I mean little truncating errors)

So, I am sort of excited because I think that I am ready with Gmap Polygon, but on Friday I noticed that some of the polygons weren't getting drawn well at all, namely because the polygon strings (long lists of coordinates separated by spaces) were way too short and were getting cut off.

So today I spent a lot of time monkeying around with the little SAX engine I was using, and now I am sure my issue is that I need to just not use the sax engine anymore, because while it was a quick class and rather fast, it is really screwing up some of the stuff I am trying to do and some of the cases I am trying to handle and I am no further along figuring out how to make it stop doing that.

So tonight, I am going to read up on JAXB and maybe work a tutorial, and tomorrow, I hope to get this fixed.

Otherwise, there are some other fun questions about what everything will end up looking-like and how crazy some borders are. It seems that zip3s can be inside other zip3s and it also might seem there are more than one area covered by a zip3. I guess that's what happens when you base your centers on mailing routes. Zip3s have a lot of 'outer boundaries', that make me wonder about the best way to store the polygons, we might have to go to a many to one relationship.

I'll keep ya'll posted, and hopefully there will be a cool little demo app soon next year, or even cooler, my mapper on top of Felicia's RODS service.

Cheers!

DRN Test

We ran into some network connectivity problems and configuration issues during the the Geisinger test. We were unable to connect to port 8443 from the NCPHI node. Joel and I worked with Geisinger network support to resolve the issue. Once this was resolved, we began configuring the Simple Transfer Service. Joel was able to download the service, but we ran into some Java exceptions while trying to test the client from the command prompt. Felicia assisted us in resolving the Java exceptions. I sent Joel instructions on setting up the container to run the Transfer service.

We need to schedule another test of the DRN service. I talked to Beth and I left a voice-mail message for Jeff Brown informing him of the testing status.

SaTScan on the Cloud Update

Lately I've been working on the first draft of paper regarding SaTScan on the cloud

and familiarizing myself the the client-side objects of Nimbus that I will  instantiate

to programmaticlly create SaTScan resources on the cloud on-demand. 

So, things are going pretty well.

Happy Holidays!

NHIN Presentation, AMDS

The presentation that would have been presented at the NHIN forum is now on the wiki. Unfortunately, the agenda gods conspired against us. Regardless, it is a good intro to the ideas of the AMDS, and how this is the type of service that enables population health situational awareness.

RODSA-DAI Script for NHIN Demo

In order to support the demonstration of the RODSA-DAI services tomorrow morning at the 5th NHIN Public Forum, John and I wrote a script to explain our PH scenario.

It goes something like this:
Setting:
1. This is all sample data
2. The counts and colors are not statistically meaningful. This is for demonstration purposes only.
Scenario:
Two public health data providers with overlapping catchment areas assist a local epidemiologist with biosurveillance. In this scenario, the systems do not share detailed data electronically due to technical or policy incompatibility.
As a part of his routine work, a county epidemiologist must check to see if there is a cumulative spike in flu activity in the region. He can do this by sending a query for ‘fever’ to a service on each node. This query is based on a draft AMDS that is mapped to each system.
• Step 1 – Launch page (http://ncphi.phgrid.net:8080/rodsadai-web/jsmulticache.jsp). You will see that NCPHI Server is ‘on’. This shows data from the NCPHI research lab node, with the pin points representing counts of cases of fever per ZIP Code. When the user mouses over the pin for ZIP 15227, it is Green, indicating 10 cases.

• Step 2 – Click NCPHI Server ‘off’ and DallasServer ‘on’, and press submit. This map shows data from the other node, again with counts of fever per ZIP code. ZIP 15227 is Yellow, with 14 cases.


• Step 3 – Check both boxes, press submit and you will see the cumulative count. As a result of this query, you will see that ZIP code 15227 is now Red, with 24 cases.

OSU/Emory Meeting

We had some interesting meetings with the Emory and Ohio State grid teams this week. Specifically we were able to sit in on the Emory/OSU collaboration session and to meet with Steve Langella in person and Shannon Hastings over the phone about the activities ongoing and planned for PHGrid.

Steve was especially useful in meeting with Dan, Raja and Joseph about how cagrid's security components work and how they can help with our planning for the AMDS Pilot that is ramping up.

We're going to be updating our architecture diagrams to incorporate Steve's ideas and cagrid's infrastructure components.

Gmap Polygon objectier.

I basically have the test I was running before working. Ironically, there are still about 5 lines of java code in the JSP when there should be more like 2 or 3.

But, this is because I need to go ahead and implement the framework that will provide the polygons rather than coding some into the test JSP. This means the two courses of action are to reformat poicondai to use the new system, or to make a set of forms and controllers that are more generic and allow for the automation of a lot of the map controls.

After some discussions with Brian and Felicia, it appears I will be working on the latter: A set of generic map controls... thus making it easier for anyone else to use the map controls for their own display needs.

I think it will also make it even easier to revamp poicondai and integrate with Felicias RodsHDS.