orchid-initiative / synthetic-database-project

MIT License
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As a database user, I want to see diagnosis and procedure codes in ICD-10 format (not SNOMED) so I can interpret the data as I would with real CA hospital data. #29

Open rileeki opened 1 year ago

rileeki commented 1 year ago

Acceptance Criteria I should be able to take this data and put it into whatever and that understands the whatever.

Background Information

rileeki commented 1 year ago

I applied for and received a UMLS license to access a SNOMED to ICD-10 crosswalk. Here's the info I received:

Dear Riley Kwong,

Thank you for your interest in licensing terminology data from the U.S. National Library of Medicine (NLM). Your UMLS license request has been approved. Your UTS account gives you access to the following resources:

Unified Medical Language System (UMLS) The UMLS integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records.

Value Set Authority Center (VSAC) The VSAC is a repository and authoring tool for public value sets created by external programs. Value sets are lists of codes and corresponding terms, from NLM-hosted standard clinical vocabularies (such as SNOMED CT, RxNorm, LOINC and others), that define clinical concepts to support effective and interoperable health information exchange.

RxNorm RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, Gold Standard Drug Database, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.

SNOMED CT U.S. Edition of SNOMED CT is one of a suite of designated standards for use in U.S. Federal Government systems for the electronic exchange of clinical health information and is also a required standard in interoperability specifications of the U.S. Healthcare Information Technology Standards Panel. The clinical terminology is owned and maintained by SNOMED International, a not-for-profit association.

NIH Common Data Elements (CDE) Repository The NIH Common Data Elements (CDE) Repository has been designed to provide access to structured human and machine-readable definitions of data elements that have been recommended or required by NIH Institutes and Centers and other organizations for use in research and for other purposes. Your UTS license allows you to:

  • Create, edit, and comment on CDEs and forms
  • Save CDEs and forms to boards
  • Obtain additional privileges in an administrator role

Questions? Write to the NLM Help Desk.

rileeki commented 1 year ago

I need to review the terms of the license agreement again before downloading and using the SNOMED to ICD-10 crosswalk. It's on the to-do list!

rileeki commented 1 year ago

@TravisHaussler I haven't looked through the license terms enough yet to have a plan for long-term use. We definitely shouldn't check the dataset in as part of our public repository. I know they have an API, so that might be the way to go, but I'm curious what you think. API details: https://documentation.uts.nlm.nih.gov/rest/home.html

(I'll share my API key via Slack)