The ACT Network is currently using ACT Ontology 2.0.1, which rolled out through all active and staging ACT sites to better meet the needs of clinical investigators and CTSA hubs. In June 2020, the ACT COVID Ontology V3 was also released, which contains the new COVID-19 ontology.
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Current Ontology Version

The ACT Network is currently using ACT Ontology 2.0.1, which rolled out through all active and staging ACT sites in 2019. This new version provides a substantial increase in the available data elements, including CPT, HCPCS, ICD10 procedures, a full set of LOINC codes and additional medications.

A summary overview of the changes made can be found here.

Currently the ACT Network is upgrading to ACT COVID Ontology V3, which includes the new COVID-19 ontology. This is additive to the current production ontology. All information related to this ontology can be found below.

COVID Ontology Information

Technical Requirements for ACT COVID Oncology V3

The technical requirements for participating in the ACT Network’s COVID-19 are as follows:

SQLServer flavored DDl and insert statements as provided by Barbara Benoit can be found here. ETL instructions will be posted on GitHub shortly.

Please refer to this JIRA Ticket to replace SHRINE’s existing tomcat/webapps/shrine-api/shrine-webclient/index.html. This change add a link to a web page tracking status of cCOVID-19 data available to help researchers interpret the numbers they are seeing.

ACT COVID Ontology V3 Documentation

A folder containing all the ACT COVID-19 Network documentation can be found here. If you do not have editing access to this folder and would like to request it, please email Elaina Sendro at esendro@chartis.com to be given proper permissions.

ACT COVID Ontology V3 Instructions

In order to install this new ontology, please following the following steps:

  • Install the ACT COVID ontology v3 in production (you may also do this in stage, but production is the priority)
  • Refresh your data to pull in data for new terms
  • Start planning for more frequent data refreshes (a web meeting will be scheduled to share tips and recommendations among ACT sites and address questions)
  • Update your status by adding information on this Google sheet

Please document any issues in the ACT Network JIRA Project.

Release Notes

NEW Ontologies

  • CPT Procedures - UMLS 2018AA (Remember only sites that have valid CPT licenses are permitted to use CPT ontology)
  • HCPCS Procedures - UMLS 2018AA
  • ICD10 PCS Procedures - UMLS 2018AA
  • ICD10 CM Diagnosis - UMLS 2018AA
  • Labs LOINC Provisional - Full LOINC tree - UMLS 2018AA LOINC V2.63
  • Medications by Ingredient - Hybrid UMLS 2018AA RxNorm? files and RxNav?

Updated Ontologies

  • ICD9 Diagnosis - UMLS 2018AA modified format. Ordered by code.
  • ICD9 Procedures - UMLS 2018AA modified format. Ordered by code.
  • Medication by VA Class - RxNav? NDFRT and RxNorm? APIs updated to September 2018
  • Demographics - Added Adult >= 18 and Child < 18 terms

Unchanged

  • ICD10/ICD9 Integrated - Curated UMLS 2015AB
  • Visit Details
  • Lab - Curated Approx. 300 Labs

Other Updated Files

  • Schemes
  • Table Access
  • SHRINE Adapter Mapping

Breakdown (coming soon)

Ontology Scripts

ACT Ontology Modifier Removal: The Oracle script to remove modifiers can be found here.

Ontology Installation

All of the ontology installation files can be found in this repository. The ontology archive and its associated files can be accessed here.

Installation instructions for the current ontology can be found here.

COVID-19 Ontology

Links to the COVID-19 ontology and other information related to the ACT Network’s COVID-19 project can be found here.

Current Ontology Documentation

Data Harmonization

Outputs and work products from the Data Harmonization Workgroup can be found here.

Ontology Archive

Archived ontology documentation can be found in this repository.

Ontology Demo Server

ACT ontology on i2b2 Web Client

Username: demo

Password: demouser

Ontology Training Material

i2b2 Transmart Training Program - Ontology For Beginners - Mike Mendis

Contact Information

For additional information, please contact Michele Morris at mim18@pitt.edu.