Have you ever described a problem you're trying to solve to someone, only to find that there is an actual tool, device, or trick/technique to solve your exact problem? Even better, has that person then just given you the tool, device, or trick/technique to you free of charge? That's what this page is. We'll be posting files, databases, and other types of knowledge here in the hope that we'll save someone (hopefully more than one person) a lot of time and effort. Check back periodically or follow us on LinkedIn to be notified of the latest posting.
CQL for Clinical Trials Matching
Our recent blog 'A Novel CDS Strategy for Molecularly-Guided Clinical Trials Matching' describes the use of CQL for molecularly-guided clinical trials matching, and presents a detailed scenario, which can be downloaded here. The downloaded zip file should be expanded, with retention of folder structure.
If you are interested in manually exploring the files, take a look at 'input/cql/TrialX.cql', which contains the main CQL logic; and the 'input/tests/TrialX/' folder, which contains mock patient data. If you are interested in executing the CQL, you can load this project into Atom, after you've installed Atom's 'language-cql' package.
CPIC PGx Value Sets
Here at Elimu, where we've been developing PGx Clinical Decision Support, we put together a set of value sets that we thought might be of interest to other groups implementing PGx. The spreadsheet has three tabs, each representing a value set - tab 'Ingredients' lists the RxNorm ingredient codes for all CPIC Level A drugs; tab 'Ingredient-Gene Interactions' shows which interactions exist for each ingredient; and tab 'Expanded Ingredient Codes' shows, for each ingredient, all of the RxNorm codes you'd expect to find in an EHR. Hope you find this helpful!
VCF to FHIR Translator
As more and more consumers participate in gene sequencing ordered by their physicians or through Direct-to-Consumer testing centers, that data will be stored in a Variant Call Format (VCF) within large Genomics Archiving and Communication Systems (GACS). Making that data available in FHIR format, which is gaining adoption across EHRs, will help make a person's full genomic data accessible for precision health care. This download contains the VCF to FHIR Translator, sample VCF files, and a number of other helpful resources. Let us know if you need help or have any comments/feedback. Also, be sure to check out our blog on this topic.
LOINC Lab Categorizations
This file contains the top 2000 LOINC codes which we enhanced with associated lab categories for each code. In all there are 15 lab categories including Chemistry, Microbiology, Hematology, Blood Bank, and Gene Mutation. This file can be used to enhance EHR Order Entry and Results viewing, utilization reporting, or anything else applicable. We’d love to hear how you end up using it. For additional thoughts on its uses, check out our accompanying blog.
This file contains CVX to RxNorm mappings. It's useful if you want to run reports or analytics on immunizations within your institution, but all of your immunizations are in various formats (CVX, NDC, RxNorm). This file will help you normalize your CVX codes to RxNorm. Should you need to normalize from CVX to NDC, that can be found here.