In case it helps…maybe a little window into how this works in a clinical setting will help. Sorry if this is repetitive.
Morphology and other characteristics
Microbiology testing is done in stages- in the direction of increasing specificity. Historically this has been because the full identification usually takes days. So initially the lab report will say something like “gram positive cocci in clusters” or “ gram negative rod oxidase negative”. So doctors can change/adapt antibiotics if needed quickly before the final ID arrives. But this is superseded by the final ID when it arrives. So if the final ID says Staphylococcus aureus- we know the morphology was gram positive cocci in clusters or if it says E.coli we know it is oxidase negative. So in most situations, the final ID/ susceptibilities are all you need. The one place where this could be relevant is for that small group of organisms where the culture takes a long time to grow (e.g. ,months). Tuberculosis is a classic example – where you could have an initial result “AFB smear positive” and it will take weeks to months for the culture to finalize. But again with the kind of mostly long term retrospective studies that are planned this should not be that big an issue.
Abundance
Most times, the micro lab will not quantify the amount of bacteria that grows. An important exception is urine cultures where depending on how the urine specimen is collected ( via catherization or asking the patient to pee in a cup)- the lab does a rough estimate of how much bacteria was there ( expressed as colony counts). There are specific thresholds (10K, 50K , 100K etc) and depending on the value you adjudicate whether this is a real infection vs just contamination of the specimen that occurred during collection. So if this is available, specially for urine cultures this is useful information to include. In Karthik’s proposal this would be a row in the measurement table tagged to the specific organism( if I understand it correctly).
Antibiotic susceptibility results outside of Sensitive/Resistant and MIC values
Antibiotic susceptibility is usually tested using methods where different concentrations of antibiotics are tested against the organism. There are pre-specified cut offs used by each lab to classify a specific bug as sensitive vs. resistant. But occasionally the lab will test for other specific resistance mechanisms to groups of antibiotics-using a gene probe, PCR or other methods. In the example above, the beta-lactamase test will identify whether the organism produces enzymes that can destroy penicillins or related drug classes. So the clinician knows that this means that a specific class of antibiotics should not be used. In real life, one can guess if some of these resistance mechanisms are present, by looking at the specific drugs being R vs S in the antibiotic susceptibility panel which arrives later. And there is a lot of diversity in whether laboratories choose to do these tests. But if included these will need to be linked to the specific organism that is identified.
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, but I think I get it. I do agree we need to keep a standard naming convention for these references. I’m not opposed to an additional column in the measurement table that’s either a GUID or a reference measurement id. From a query point of view, I suppose it would be a self-join on the measurement table, which somewhat similar to joining to a new measurement_attribute or measurement group table. If you go the route as mention by