Proposed Updates for CLIF 2.0 Labs Table

[kaveriC]

While setting up the CLIF 2.0 labs table, @08wparker and I would like to propose the following updates:

1. Add New Labs: Incorporate the following labs into the lab_category: RDW, Beta-hydroxybutyrate, and Lipase.
2. Include LOINC Codes: Introduce a new variable to record LOINC codes for better standardization.
3. Urinalysis Inclusion: Add Urinalysis to the lab_order_category and include relevant labs under lab_category, such as pH_urine and creatinine_urine.
4. Remove Redundant Variable: Eliminate the lab_type_name variable, as it has become redundant in the CLIF 2.0 version after adding lab_order and lab_order_category.

[chochbe1]

Agree with the above

[clif-consortium]

@cloverbunny - revisit post-ATS

[08wparker]

@cloverbunny can we agree to drop lab_type_name from the data dictionary and leave the other items as "to-dos" post ATS?

[08wparker]

I think we also need to have lab_order_name and lab_order_category in order to distinguish blood and urine labs (e.g. creatinine)

[08wparker]

@cloverbunny looking through all the "Proc_names" we currently have mapped to lab_order_name I think categorizing all the lab orders (e.g. CBC w/diff, CMP, etc.) is something we should do post-ATS.

But maybe we should replace lab_type_name with lab_specimen_category which will have levels c(blood/plasma/serum, urine, csf, other).

There will be a mapping of lab_order_name to lab_specimen_category . The point of this is so you can quickly filter down to just blood tests and avoid using a urinalysis creatinine or a CSF WBC in a prediction model

[cloverbunny]

I know we (NU) did pre-CLIF filtering out of urine and CSF labs of things like protein, and think others probably also did? We can include a lab_specimen_category to make this more explicit, but think this can be done post-ATS? Where were the examples again of what is lab_type_name vs lab_order_name?

[08wparker]

lab_type_name was never well defined and lab_order_name is the actual "procedure name", e.g. "URINALYSIS CHEMISTRY SCREEN".

Overall I think we should try to make CLIF LOINC compatible https://loinc.org/get-started/loinc-term-basics/, which is why I'm suggesting the lab_specimen_category to correspond to the "system(specimen)" part of the LOINC code which represents "The specimen or thing upon which the observation was made"

lab_name and lab_category correspond to LOINC's "component (analyte)", defined as "The substance or entity being measured or observed."

[cloverbunny]

So an example would be like: If we drop lab_type_name, how else would we define standard vs POC? Isn't that what it was originally intended for? lab_order_name: total_bilirubin lab_order_category: blood/plasma/serum, urine, csf, other [do we have a list of all categories we want such as tissue, synovial, etc?] I think we also need to think of some better way of naming these as it's confusing what's lab_order and what's lab_category heh.

Reference from website of current format Variable Name	Data Type	Definition	Permissible Values
hospitalization_id	VARCHAR	ID variable for each patient encounter.	No restriction
lab_order_dttm	DATETIME	Date and time when the lab is ordered.	Datetime format should be %Y-%m-%d %H:%M:%S
lab_collect_dttm	DATETIME	Date and time when the specimen is collected.	Datetime format should be %Y-%m-%d %H:%M:%S
lab_result_dttm	DATETIME	Date and time when the lab results are available.	Datetime format should be %Y-%m-%d %H:%M:%S
lab_order_name	VARCHAR	Procedure name for the lab. This field is not used for analysis.	No restriction
lab_order_category	VARCHAR	Permissible CDE values for lab order names.	CDE under development
lab_name	VARCHAR	Original lab name string recorded in the raw data. This field is not used for analysis.	No restriction
lab_category	VARCHAR	Limited labs identified by the CLIF consortium as minimum necessary labs for the study of critical illness.	List of lab categories in CLIF
lab_value	VARCHAR	Recorded value corresponding to a lab. Lab values are often strings that can contain non-numeric results (e.g. “> upper limit of detection”).	No restriction
lab_value_numeric	DOUBLE	Parse out numeric part of the lab_value variable.	Numeric
reference_unit	VARCHAR	Unit of measurement for that lab.	Permissible reference values for each lab_category listed here
lab_type_name	VARCHAR	Type of lab. (e.g. standard, POC)	No restrictions
lab_loinc_code	VARCHAR	LOINC code corresponding to the lab_name.	No restrictions

Variable Name Data Type Definition Permissible Values hospitalization_id VARCHAR ID variable for each patient encounter. No restriction lab_order_dttm DATETIME Date and time when the lab is ordered. Datetime format should be %Y-%m-%d %H:%M:%S lab_collect_dttm DATETIME Date and time when the specimen is collected. Datetime format should be %Y-%m-%d %H:%M:%S lab_result_dttm DATETIME Date and time when the lab results are available. Datetime format should be %Y-%m-%d %H:%M:%S lab_order_name VARCHAR Procedure name for the lab. This field is not used for analysis. No restriction lab_order_category VARCHAR Permissible CDE values for lab order names. CDE under development lab_name VARCHAR Original lab name string recorded in the raw data. This field is not used for analysis. No restriction lab_category VARCHAR Limited labs identified by the CLIF consortium as minimum necessary labs for the study of critical illness. List of lab categories in CLIF lab_value VARCHAR Recorded value corresponding to a lab. Lab values are often strings that can contain non-numeric results (e.g. “> upper limit of detection”). No restriction lab_value_numeric DOUBLE Parse out numeric part of the lab_value variable. Numeric reference_unit VARCHAR Unit of measurement for that lab. Permissible reference values for each lab_category listed here lab_type_name VARCHAR Type of lab. (e.g. standard, POC) No restrictions lab_loinc_code VARCHAR LOINC code corresponding to the lab_name. No restrictions

[clif-consortium]

Not required for ATS (only map blood to lab categories): @08wparker Add lab_speciman_name to the data-dictionary.