The concept_recommended table must be created in the vocabulary schema referenced in the source_daimon table. Often this is the same schema as the CDM schema but they can be different.
Thanks Chris & Anthony for providing this clarification.
Hi @aostropolets, I was trying to better understand how the phoebe csv was generated. Is the code used available on github somewhere?
I would like to build on top of the phoebe results and if people have an OMOP CDM with the concept_recommended table included alongside their other vocabulary tables this is great as I can then work with them like with other vocabularly tables. But then I´m struggling to understand how I can know whether the concepts in concept_recommended are from the same vocabulary version as the concept table itself?
In the longer term, will concept_recommended become another vocabulary table, or would these be appended to concept relationship as I see they are in a similar format and that would probably make it even easier to incorporate into tools?
My understanding was that this table would be generated and produced as part of the vocabulary download. This is why we decided to instruct users to pulace this table in the CDM schema (with the other vocab tables)
Thanks @Chris_Knoll. I and @MaximMoinat can ask data partners we work with to upload the concept_recommended.csv into the database as is.
For the longer term, what I’m a bit confused about is whether:
- phoebe is like any other vocabulary table provided by ohdsi which the data partner uploads (and then it seems like it could indeed be provided from athena with the others and maybe the code used to generate could live in https://github.com/OHDSI/Vocabulary-v5.0 for transparency), or
- phoebe is more like achilles in that it is derived from the cdm data somebody has mapped, in which case maybe the code for it could even be added to achilles to increase uptake (as that is something people are used to running as they map a data source).
More than anything, the problem we currently have is that if a data partner does upload the concept_recommended.csv how can we know that the results are consistent with the other vocabulary tables they have? And how would we know whether the data from that data partner was used to generate the recommendations?
Any thoughts @aostropolets @Christian_Reich @Patrick_Ryan @Frank ?
There are several types of recommendations that are dependent on the vocabulary version. For example, ontology-parent and ontology-descendant are derived based on the concept_ancestor of a given vocabulary release (the recent Phoebe update uses the most recent version of the vocabs). So to be fully consistent they want to be on the Feb 2024 vocabulary release.
The source currently is the aggregated data from 22 CDMs collected in the OHDSI Concept Prevalence study from a couple of years ago.
Unfortunately, we did not have many EU partners contributing to the study and would be very happy to expand the coverage. Would be happy to discuss 