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OHDSI / Themis

Repository for OMOP CDM conventions as defined by THEMIS. These can be reference lists of concepts, pieces of standardized code for data generation or quality certification, and debates.
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Convention for storing result of culture and microbiology susceptibility #58

Open chandryou opened 5 years ago

chandryou commented 5 years ago
TYPE MEASUREMENT
ITEM Result of Culture and Microbiology Susceptibility
FORUM POST http://forums.ohdsi.org/t/mapping-microbiology-susceptibility-into-omop-cdm4-observations/167
SOLUTION For the microbiology susceptibility, various information should be stored such as specimen, culture (which culture method and when), grown infectious organism, and susceptibility result to each antibiotics
NEXT STEPS Currently nothing comes up with me. Does anyone have a solution for this?
dimshitc commented 5 years ago

Let's take an example: Source: stool specimen, Rahnella aquatilis, grow = "+++", Gentamicin Susceptible. CDM: MEASUREMENT: 1st row: MEASUREMENT_concept_id = 3025941 (Bacteria identified in Stool by Culture) 2nd row: MEASUREMENT_concept_id = 3035007 (Gentamicin [Susceptibility]), value_as_concept_id = 4038110 Susceptible OBSERVATION: Observation_concept_id = 4001253 (Rahnella aquatilis), value_as_concept_id = 4125547 (+++) SPECIMEN: SPECIMEN_concept_id = 4002879 Stool specimen

These are connected via FACT_Relationship: OBSERVATION_id is connected to other entries mentioned. @aostropolets , right?

don-torok commented 5 years ago

@dimshitc I think your response belongs in the forum post, http://forums.ohdsi.org/t/mapping-microbiology-susceptibility-into-omop-cdm4-observations/167, not in Themis github issues.

dimshitc commented 5 years ago

@don-torok , you're right, so, I copied the message to the forum. Thanks

cukarthik commented 5 years ago

@chandryou I just created a proposal for a new table to handle microbiology results and other results.

tbanokina commented 4 years ago

Hi @chandryou , I just posted a solution on forum related to your question: https://forums.ohdsi.org/t/mapping-microbiology-susceptibility-into-omop-cdm4-observations/167/30 Please have a look at it. Maybe it will help to resolve your case.

MelaniePhilofsky commented 12 months ago

@cukarthik and @clairblacketer Is this issue closed? Or is it in the hands of the CDM WG? Karthik's post from May 31, 2019 points to another proposal in the CDM WG

cukarthik commented 12 months ago

not to my knowledge.

AbeckCO commented 9 months ago

Hello @cukarthik,

My name is Alyssa, and I'm a PhD student in Epidemiology at the University of Colorado. I am reaching out regarding mapping microbiology results to OMOP CDM. I've been in touch with @MelaniePhilofsky and @clairblacketer on this matter. Myself and Dr. Lisa Schilling have a use case at the University of Colorado to support public health surveillance efforts.

Would others be interested in working on standardizing microbiology results at this time? We are particularly interested in bacterial cultures and antibiotic susceptibility testing, and would be very interested to meet and discuss next steps. Thank you!