OHDSI Home | Forums | Wiki | Github

Genomic Data in the CDM

CDM Builders
#84

Can I also join the discussion group, please?
Thanks

#85

Hi @Christian_Reich. We are working on the integration of the genetic data and the clinical data in our hospital (Parc de Salut Mar (FIMIM-IMASIS) in Barcelona) and we are very interested in knowing the current point in which the development of G-CDM is, with the idea to use it. We are interested in being involved in this working group. So please, could you tell me how to have more details about the G-CDM for the development of this module and its integration in our EHR in OMOP-CDM of our hospital?
By the way, we are collaborating with you in the E-CORE initiative :grinning:

#86

@mmayer:

Yes, yes, I know who you are. :slight_smile:

@shilpa is running the show in the Oncology WG, which also is now the foster parent for the genomic OMOP. She’ll help you in. Do you have mostly data from cancer data or other therapeutic areas as well?

#87

Thanks a lot @Christian_Reich for your quick reply. Currently we are focused on two use cases to begin with (lung and colon cancers) but the idea is to work on other cancers, rare diseases and also inherited genetic disorders and finally any kind of therapeutic area in which genetic information is required or available.

#88

Got it. Just want to make sure you are not confused:

  1. The G-CDM is a model proposed by the original Genomics WG. It is an Open World model, meaning, it doesn’t use pre-specified OMOP Vocabulary Concepts, but introduced new tables and fields. It is more similar to a generic NGS pipeline representation.

  2. The Oncology WG created a Closed World (hence OMOP CDM type) model, using predefined Genetic Variant concepts, but no new structure. Those concepts live in the MEASUREMENT table. Those Concepts define somatic mutations found in cancers.

  3. If you want to use predefined Genetic variants for germ line mutations in syndromic conditions or pharmacogenetics we don’t have that today.

Makes sense?

1 Like
#89

Yes it does. As I understand the last version of the genomic module of the CDM with all the current variables included is at:
https://github.com/OHDSI/Genomic-CDM Is that right?

#90

Right. That is 1. above.

#91

how can i join this effort?

#92

hi, I would like to join the genomic data WG. Could u let me know how?

best

1 Like
#93

Hello every body. Greeting from Germany-Dresden.
we have a Question and be happy to get help here.
what is the neu version of genomic-cdm ? which Tables are be used for storing Genomic Date in OMOP? MEASUREMENT Tabel? or 4 Tables from Genomic-CDM (GENOMIC_Test, TARGET_GENE, VARIANT_OCCURRENCE, and VARIANT_ANNOTATION)? we have seen that These 4 Tables are published in 2019 and we don’t hear about more updates? are they still to be used?
many Thanks

1 Like
#94

Dear @clairblacketer, could you please add me to the group meetings?

#95

hi @clairbacketer can you add me to the group meetings as well?

t