Our Tips, Codes, Tools:
To make the OMOP ecosystem more compatible with the use of source concepts, we had to develop some hacks, codes, and tools. Some we learned from the community, and others we developed ourselves. Most of these can be helpful to others, and while some may already exist, we couldn’t find them, which is one of the motivations for starting this conversation.
- As part of FinOMOP, we created several custom vocabularies following the Concept & ConceptRelationships methodology. This allows us to use source concepts in ATLAS and other tools. See Skuharuskaya et al.
- In fact, there are so many custom vocabularies that we created an R tool (FinOMOP/ROMOPMappingTools) and a repository (FinOMOP/FinOMOP_OMOP_vocabulary) to manage them. Unfortunately, the repository we use in FinOMOP to maintain our vocabularies is currently private, but we will open it soon. For now, there is a demo version available: FinOMOP/FinOMOP_OMOP_vocabulary_test.
- We extended the Concept & ConceptRelationships methodology to include descendants in the Ancestor tables, making it much easier to create source concept sets in ATLAS.
- We added person counts (PC) and descendant person counts (DPC) for source codes to Achilles. This allows us to view these values in ATLAS we follower this.
- We created some R functions to get source concepts as covariates in the FeatureExtraction package. This makes the Hades packages compatible with source concepts. See FINNGEN/HadesExtras.
- We built a Shiny app to take cohorts from ATLAS (or other sources, such as text files) and run Hades or custom analyses with just a few clicks. See FINNGEN/CohortOperations2 and our showcase at OHDSIGlobal2024.