Questions tagged [ohdsi-omop]
11 questions
0
votes
0 answers
Why am I getting ROLLBACK_COMPLETE when trying to install OHDSI?
I get the error message ROLLBACK_COMPLETE when I tried to install OHDSI-in-a-box from https://github.com/OHDSI/OHDSI-in-a-Box according to the video https://www.youtube.com/watch?v=9JbgyE4rW2w.
I tried twice and both times I got ROLLBACK_COMPLETE…
Salma
- 1
- 1
0
votes
1 answer
ETL Mapping LOINC vocabulary on OMOP Common Data Model
I am working on the lab test values mapping (MEASUREMENT table of the OMOP CDM).
My local mapping table (handmade) has my measurement name (in French) and the associated LOINC code.
The LOINC vocabulary has been loaded from Athena (OHDSI community…
MF_
- 36
- 4
0
votes
0 answers
Project with gmaven-plugin in POM compiles at command line but fails to compile in Eclipse
I'm trying to get a project that uses gmaven-plugin to compile in Eclipse. When I import the project into Eclipse using the Maven Import I get the error shown below.
After the project finishes importing, I'm left with these Java compile errors…
John
- 3,458
- 4
- 33
- 54
0
votes
1 answer
How to fix connection error seen when running Synthea ETL tool but not seen running DQD?
I can run DQD using the connection parameters shown below but I get an SSL error if I try to use connect() and I get the same error trying to use the synthea etl tool.
Full script is below.
Any help would be greatly appreciated.
Connection…
John
- 3,458
- 4
- 33
- 54
0
votes
1 answer
How can I pass the results of a query/subquery to another query, and UNION the results together?
ANSWERED! CTE is the best method, using descriptive dummyvariable names
I have two relevant tables concept which describes all of the database wide concepts (concept_code) from different vocabularies (vocabulary_id), and relates them to a unique,…
Moss_and_Bones
- 5
- 2
0
votes
2 answers
What resources are (typically|supposed |required) to be in a /Patient/[ID]/$everything FHIR resource?
The short version is this:
The /Patient/[ID]/$everything for the example patient shown below has a reference to a procedure that is not also included in the /Patient/$everything resource.
Specifically:
This example is from synthea. Synthea is an…
John
- 3,458
- 4
- 33
- 54
0
votes
1 answer
FHIR to OMOP Mapping Question: Blood pressure systolic and diastolic with unmapped, not valid code (55284-4)
There is a LOINC concept 55284-4 that appears in some FHIR resources, for example:
https://syntheticmass.mitre.org/v1/fhir/Patient/0000aa42-c235-4447-8389-8a2640f44466/$everything
This code is for "Blood pressure systolic and diastolic" and is in…
John
- 3,458
- 4
- 33
- 54
0
votes
1 answer
Discrepancy between representation of codes for UCUM in FHIR v OMOP
I’m seeing some differences between what I’m getting in FHIR messages from synthea v. codes in OMOP for UCUM vocabulary. Most of these seem to be around punctuation for lack of a better word (things like _, {, }, [, ], /,. etc.). Examples include…
John
- 3,458
- 4
- 33
- 54
0
votes
1 answer
Are FHIR code systems available in OMOP from Athena?
FHIR seems to have implemented their own coding systems. For example, this was found in a Synthea patient:
"valueCoding": {
"code": "2106-3",
"system": "urn:oid:2.16.840.1.113883.6.238",
"display":…
John
- 3,458
- 4
- 33
- 54
-1
votes
1 answer
Is there a mapping of FHIR Systems to OMOP Vocabularies?
Is there a mapping of FHIR systems to OMOP vocabularies?
The FHIR messages I’m working with are using things like this:
SNOMED http://snomed.info/sct
RxNorm http://www.nlm.nih.gov/research/umls/rxnorm
…and OMOP uses things like…
John
- 3,458
- 4
- 33
- 54
-2
votes
2 answers
How to improve "select min(my_col)" query in MySQL without adding and index
The query below takes about a minute to run on my MySQL instance (running on a fairly beefy machine with 64G memory, 2T disc, 2.30Ghz CPU with 8 cores and 16 logical, and the query is running on localhost). This same query runs in less than a…
John
- 3,458
- 4
- 33
- 54