Hey @Christian_Reich. As I explore the drug concept diagram (also here: http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug) and its relationship to the actual vocabulary tables, I’m finding a number of puzzling discrepancies…I think. I’ll use the vocabulary tables from the Symposium tutorials in order to have a common reference, though I find somewhat different issues in the CDM I’m actually working with.
select vocabulary_id, domain_id, standard_concept, count(*)
from concept
where domain_id = 'Drug' and invalid_reason is null
group by 1,2,3 order by 3,2,1;
vocabulary_id | domain_id | standard_concept | count
------------------+-----------+------------------+--------
ATC | Drug | C | 1257
Cohort | Drug | C | 12
EphMRA ATC | Drug | C | 895
NDFRT | Drug | C | 18202
NFC | Drug | C | 692
RxNorm | Drug | C | 37595
SPL | Drug | C | 152392
VA Class | Drug | C | 486
DPD | Drug | S | 131946
HCPCS | Drug | S | 31
RxNorm | Drug | S | 145929
RxNorm Extension | Drug | S | 157720
ATC | Drug | | 4751
CIEL | Drug | | 7673
DPD | Drug | | 35492
GCN_SEQNO | Drug | | 28689
Gemscript | Drug | | 224408
HCPCS | Drug | | 790
MeSH | Drug | | 3991
Multum | Drug | | 9770
NDC | Drug | | 428374
NDFRT | Drug | | 7728
OXMIS | Drug | | 3
Read | Drug | | 20
RxNorm | Drug | | 18630
RxNorm Extension | Drug | | 6555
SNOMED | Drug | | 308214
SPL | Drug | | 14707
VA Product | Drug | | 17951
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CVX, NDFRTInd, and FDBInd appear on the diagram but not as vocabularies in the data at all (checking in my vocab tables and http://athena.ohdsi.org/). All of the boxes on this diagram are vocabularies, right?
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I don’t find ETC in my vocab tables but it does show up in ATHENA as License Required, so that’s probably fine.
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Four vocabularies show as having Drug/Classification concepts in my query but not on the diagram: Cohort, EphMRA ATC, NFC, RxNorm. Any explanation?
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SNOMED appears in the classification section in the diagram but in my query shows up as only have non-standard (source) concepts in the Drug domain.
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Based on the diagram (and other docs and discussion), I would expect that the only vocabulary with Standard concepts in the Drug domain would be from RxNorm and RxNormExtension. In my query I also see DPD and HCPCS (in the CDM I’m actually working with I also have CPT4 and don’t see RxNorm Extension at all).
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RxNorm, RxNorm Extension, ATC, NDC, NDFRT, SNOMED and SPL also show up in the query but not the diagram as having non-standard (source) concepts. Is that correct?
I also see some confusing relationships beyond what we already discussed here: Relationship.relationship_name != concept.concept_name, but I’ll post another message about those later.
Thanks!
Happy holidays!
Sigfried