Genomics


KOIOS

Github: OHDSI/KOIOS

KOIOS is a tool developed by Odysseus Data Services Inc that allows you to find matching and missing concepts in OMOP Genomic Vocabulary for most types of raw patient-level genomic data. The current tool functionality allows to extract relevant variant information from VCF files, or detect HGVS in any TXT/CSV file. In the next step, KOIOS finds corresponding HGVS references in ClinGen for each variant, and maps the results to OMOP Genomic vocabulary. Extracted HGVS references can be used as either synonyms for the existing OMOP Genomic concepts, or as new entities.

Regimen Derivation


ARTEMIS

Github: OdyOSG/ARTEMIS

ARTEMIS provides an interface for utilizing a modified Temporal Smith-Waterman (TSW) algorithm, derived from 10.1109/DSAA.2015.7344785, to summarize longitudinal EHR data into discrete regimen eras. Primarily intended to be used for cancer patients, ARTEMIS utilizes data derived from the HemOnc oncology reference to form the basic regimen data used in testing.

OncoRegimenFinder

Last update 2021

Github: OHDSI/OncologyWG/OncoRegimenFinder

This package identifies oncology regimens. Firstly, it identifies all patients who have been exposed with an Antineoplastic Agent (ATC code). Then it collapses the antineoplastic agents into regimens when there is a date difference less that @date_lag_input(30days is used as standard).

Development


Delta Vocabulary

Documentation: Delta Vocabulary

Maintaining the change between the official OMOP Vocabulary release and the Oncology Development Vocabulary allows for rapid development of OHDSI Oncology studies that are untethered from the official OMOP Vocabulary release cadence. By preserving only the changed elements, instead of the entire Oncology Development Vocabulary, this method provides a lightweight, GitHub-friendly solution, that is also respectful of (by way of avoiding) the licensed vocabulary terms.

Data Quality and Characterization


Adoption Validation Framework

Documentation: Validation Framework

A semi-automated and extensible framework for generating, visualizing, and sharing database characterization and adherence to the OHDSI Oncology Standard Conventions.