Biobank data into OMOP CDM
Nobody has claimed this yet.
- Dominant language
- HTML
- Stars
- 1.1k
- Forks
- 508
- Avg merge
- 1h 30m
- Merged PRs (30d)
- 3
Description
Hello, our hospital already has the EHR data transformed into OMOP CDM, and now we are in the process of enriching our OMOP CDM with new source data. The hospital has an associated biobank with information on available specimens (from patients that are already included in our OMOP), but we haven’t found any official guidelines on how to map this information into OMOP.
We figured we could use the concept_id 46235133 (Biobank specimens are stored and available for research) in the Observation table to point to the specimen sample. Then, we thought of using concept_id 3018323 (Volume of Specimen) in the Measurement table to capture the quantity of specimen left.
Is there an official way to represent this information? Has anyone already included biobank data in OMOP so we could follow the same approach?
Thanks in advance for any insights or guidance!
Carlos
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No repository files or tests are identified. Start by reviewing the OMOP CDM Observation and Measurement tables and the cited concept IDs; done would require an agreed, documented official mapping for biobank specimen availability and remaining volume.
Written by the indexing model from the issue text.
Assessment
- Domain
- databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100