ASHEX WEB ID PROGRAM
pschreck.com has moved to solely sustain the WIP (Web ID Program) for identification purposes. This system — along with the broader AID Cloud — was introduced in July 2012 as a new way to access the ASHEX matrix for the identification of glucose non-fermenting species. The WIP runs completely through one’s web browser. This app computes ID probabilities without the need to download programs onto a machine. It will work on any Windows, MAC, or smartphone system with an active internet connection. Click the ‘ASHEX(GNNFB) WIP’ link*** in the sidebar menu to access the ASHEX WIP or click the 'Which WIP? AID Cloud' button for more information about other utilities. If you are working in a small window or on a mobile device, the sidebar menu might be minimized. You can click the button in the upper-right corner of the page to access it in that case.
If you wish to access the ASHEX matrix itself for informational/educational purposes, download instructions are posted below.
***You probably see that there are two ASHEX links in the WIP Sidebar Menu. The ASHEX14X link takes users to the version of the identification matrix in place at the time of my father’s passing. ASHEX17XB was built using a stack of biochemical test results that my dad had waiting for me to enter, and ASHEX23XB was made possible thanks to the clinical microbiology laboratory at Loyola. Huge props to the Loyola Micro Lab, in particular Kathleen McKinley, for her assistance in gathering and explaining various research notes that made the upgrade possible. ASHEX14X will remain, for I understand that some users may not be comfortable using the version of the matrix I am maintaining; thus, I included both because it’s not really a burden on resources.
The ASHEX23XB WIP utilizes the 23X version of the matrix. The master table has been upgraded. It now represents 109 taxa with 1001 clinical isolates. The big difference between the 23XB and 14X WIPs is the development and inclusion of a Wilson Binomial Matrix, which can be toggled on by selecting YES at the bottom of the ASHEX23XB submission form.
The default setting is NO, which tells the program to perform the calculation in exactly the same manner as the previous WIP versions. The reason I included the binomial matrix is so that users can now account for sample sizes in the database while exploring unknown organisms.
The Wilson Binomial Matrix is not better than the standard matrix; it is meant to be used as a supplement.
Essentially, the standard matrix doesn’t differentiate between, say, 0/1 and 0/10. Both are recorded in the same manner in the table. In other words, the standard matrix treats all taxa equally regardless of the number of isolates. The strength here is that one can ID rarely observed organisms by matching the trends of the biolchemical test results. The weakness is that a small sample size might actually be composed of outlier results.
The Wilson Binomial Matrix is formed by taking the average of the 95% Confidence Level band produced by the biochemical test results. As the number of isolates for a particular taxon increases, the size of the CL band decreases. I’ll include the following example as an illustration:
Consider the Catalase test for Achromobacter piechaudii and Achromobacter xylosoxidans. In all of the clinical isolates for both of these organisms the test result was positive. In the standard matrix, both 13/13 (A. piechaudii) and 63/63 (A. xylosoxidans) would have the same value indicaitve of 100%. In the Wilson Binomial Matrix, the 63/63 gets a stronger weight. The 13/13 becomes an 88.6%, whereas the 63/63 becomes a 97.1%.
The takeaway is that if you find a discrepancy between ASHEX WIP, MALDI-TOF, and/or gene sequencing results, setting the Wilson Binomial Check to “YES” could provide valuable insight.
While the video below was developed before the 23XB Version of the WIP (and the current version of the website) went live, the tutorial video below provides a fairly comprehensive overview of the tools that emerged from Adam's Simple Helper Experiment.
DOWNLOAD THE ASHEX IDENTIFICATION MATRIX
The identification matrix is available for download from this page. Since these organisms can be difficult to identify, my father and I are pleased to bring to you this tool that electronically compiles over 30 years of research in this field. The aim of this section of the website is to provide instructions so that users can download and effectively use the ASHEX database.
Current Version: ASHEX23X
Legacy Version: ASHEX14X
COPYRIGHT INFORMATION & OTHER PUBLICATIONS
ASHEX Glucose Non-Fermenting Gram-Negative Bacilli Automatic Identification Tables & Manual
ASHEX Web Identification Program
ASHEX appears to be open source information, are there any protections on this material?
The ASHEX Project is copyrighted under U.S. Law and is located on file at the Library of Congress. All parts of the project, from the tutorial to the matrix are protected.
Who owns the rights to ASHEX?
The Copyright on the ASHEX Database is held by A.P. Schreckenberger.
I run a laboratory and decided to use the ASHEX Matrix; however, I would like to add my own notes, values, or lab reactions… Am I allowed to do this?
I encourage hospitals and doctors to add notes as they see fit. At the end of the day, it is our ability to treat patients that matter. The whole point of this project is to provide an open source, yet this comes with certain risks that must be avoided. Users may not distribute modified versions of this matrix or derivative materials. This webpage is the only webpage authorized to distribute the ASHEX Matrix. If you would like to help our cause and spread the word, feel free to post a link on your own pages (or in emails) to direct people to this page.
In addition, please remember to give credit where credit is due. Adam maintains the site, database, and WIP technology as a free service to all of those in the field.
Please forward any questions to Adam’s email @ [email protected]
In Mid-2004, my father approached me with the idea of creating a new identification table for GNNFBs using the decades of data he had collected. The last major table was tabbed in 1986, and the system in place at the time was relying upon older technologies. The goal was to allow for unknown identification and to facilitate record maintenance.
Coincidentally, we were informed by Brent Barrett, from the Indiana State Dept. of Health, of a probabalistic identification program called PIBWin, made by Dr. Trevor Bryant. Instead of running on older DOS-based systems, PIBWin ran in a Windows environment and was fully capable of using our excel file as a data source. It was a seamless fit, and hence, we pushed forward.
Frankly, I am a firm believer in open source information, and one of the things that bugged me about the tables of yore is that they did not include full research notes. Thus, as I developed the ASHEX matrix, I made it a personal point to preserve all of the information such that individuals could return and look at the raw numbers behind the percentages shown. To do anything else seemed a disservice to not only the end user, but my father as well.
After I went to graduate school to get my Ph.D. in physics, I acquired the coding skills needed to finally move things in a direction I had envisioned long before. I wrote my own identification code that served as a web application, and in doing so ushered in a new era for our little program here. In this spirit, the ASHEX project has carried on for over a decade.