We are planning to create a listing of vocabularies used in Europe for medical coding. Typically they differ from country to country, also some of them are already OMOPed and some of them are not. Typically, we can find a lot of them on Ministry of Health web pages, if we can understand a word they are saying:slightly_smiling_face:. But many of them are not official.
If you have a vocabulary you know or think would need to be covered by the OMOP Standardized Vocabularies in Europe please let us know.
I know a lot about vocabularies used in Czechia. Send me email to follow up.
We have a few procedure code vocabularies available for a few countries in Europe.
What are they?
Do you need them to be added to OMOP Vocabulary?
In France, there are mainly :
- Classification Commune des Actes Médicaux (CCAM) for medical procedures
- CIP13 and UCD for drug administrations (mapping to RxNorm is feasible through the ATC codes)
- Affections Longue Durée (ALD) is a classification of chronic diseases
- CIM10, a French version of the ICD10
- LPP for medical devices
Hello! Thanks for the reply
We’ve collected the information regarding European coding vocabularies from open source resources. The result of our work has been presented at OHDSI Symposium ‘The Journey from Data to Evidence’ 2019 March 29th, and you can find it here.
You can see the status of each vocabulary: OMOPed; OMOPed but review / slightly changes are needed; partially OMOPed; not OMOPed, etc.
@mattiaskyhlstedt, @AntoineLamer, you can help us with providing necessary information regarding any non-mentioned vocabulary, describing it right here at the forum with a small note why do you think it is necessary to OMOP this particular vocab.
As for France, we did not include Affections Longue Durée (ALD) and both CIP13 and UCD. As far as I know, BDPM is currently used in France as a drug vocabulary and CIP13 is just a packing coding system. Am I wrong?
The UCD code represents, for each dosage form, the smallest dispensing unit (tablet, vial,…) unlike drugs dispensed in a city pharmacy, which have a CIP code corresponding to the brand and presentation of the drug (packaging).
This is these codes which are stored in the French Healthcare Database (SNDS).
We also have :
- hospital admission/discharge modes (emergency admission, transfer, etc.).
- GHM (Groupes Homogènes de Malades – French classification of diagnosis-related groups for acute hospital admissions)
- GHS (Groupes Homogènes de Séjours – costs associated with diagnosis-related groups)
- GME (Groupes Médico-Economiques - French classification of diagnosis-related groups for post-acute care and rehabilitation)
- Indication for “hospital at home” care (Mode de prise en charge)
- Medical and paramedical specialities
- Indication of cost for the outpatient visit (Nature de la prestation)
What is ACPC in the slide ?
In France, concerning the French Healthcare Database (SNDS), I would add the NABM used for outpatient biology acts (available here)
For Affection-longue-durée, there is a many-to-one correspondance between CIM10 and ALD codes that could help. The correspondance variable is called
ald_030_codin the nomenclature table IR_CIM_V. A nomenclature on the source labels of the ALDs can be found here too
For the CIP13 codes, we search trough the French Healthcare Database and try to make a mapping between cip13 codes in the database and the BDPM nomenclature given by ohdsi and managed to map 15000 codes. We mapped to ATC 3000 more codes not found in the BDPM. This mapping covered 99.725 codes present in the system. We should have a concept table available soon that summarize this information and could be of some help.
You can ask me abot vocabularies in Germany: ICD, DRG, OPS, ATC …
Hi Sergey. I am very curious about German vocabularies as we are doing a feasibility study to transform our clinical data into OMOP CDM. I read in “Towards Implementation of OMOP in a German University Hospital Consortium” that mapping the procedure codes (OPS) and ICD-10-GM proved to be difficult and might require substantial manual work.
Do you have more information on this or potentially mapping files (OPS)?
OPS has been added to OMOP Vocabulary as non-standard vocabulary, without mapping but with the internal hierarchy.
ICD10GM has been added to OMOP Vocabulary as non-standard vocabulary with mappings to standard concepts.
Thus, when converting your clinical data to OMOP CDM, it’s easy to populate CONDITION_OCCURRENCE with standard concepts,
but when you populate PROCEDURE_OCCURRENCE, you’ll might fill the procedure_source_concept_id, but procedure_concept_Id ==0,
once mappings would be developed, you can update your dataset with standard concepts.
@mik whom should we ask about the OPS mappings?
Hi Fabian, the OMOP Germany community is growing and so are the vocabularies.
In collaboration with the Dresden University, ICD10GM and OPS have been brought to Athena as freely available standardized vocabularies.
Because of time and budget constraints, both are not yet 100% mapped, with OPS lacking quite some in numbers. However, OPS mappings were built using material provided by TriNetX covering 2000 of the most frequently used procedure codes. It would be quite interesting to hear, what the coverage in your dataset would be. Feel free to query about more background. I am based in Berlin, Germany.
Kind regards - Mik