---
title: "Labs"
author: "<a href=mailto:anobel.odisho@ucsf.edu>Anobel Odisho, MD MPH </a><br>"
subtitle: "Epi 231 - EHR Data for Clinical Research"
output: 
  ioslides_presentation: 
    css: aocustom.css
    self_contained: yes
    incremental: false
    output: ioslides_presentation
    widescreen: true
    smaller: true
    transition: faster
    code_folding: true
    
---

```{r, include=FALSE}
# baseline knitr options
knitr::opts_chunk$set(echo = F, warning = F, message = F, cache = F)

library(odbc)         # Loads the ODBC drivers
library(DBI)          # Allows you to pass SQL to database
library(dbplyr)       # use dplyr style commands to extract data from SQL databases
library(tidyverse)    # data cleaning
library(knitr)        # Rmarkdown and table display
library(DT)           # Interactive tables in markdown
library(ggplot2)      # making charts
library(ggthemes)
library(htmlwidgets)
library(ucsftheme)
```

```{r}
source("connect_deidcdw.R")
```

## Intro
- Ontology: LOINC 
- Key Challenges


## LOINC
- Logical Observation Identifiers Names and Codes (loinc.org)
- Ontology for labs and clinical measurements
  + Laboratory LOINC
  + Clinical LOINC
- Goal is interoperability
- Uniquely identify every possible lab

## LOINC
- Component (analyte): substance or entity measured or observed
- Property: e.g., mass concentration, numeric fraction
- Time: point in time
- Specimen (system): e.g., blood, cerebrospinal fluid
- Scale: e.g., qualitative, quantitative, ordinal, nominal
- Method: optional, procedure used to make observation

## LOINC - CBC
![](images/loinc_cbc.png)

## LOINC - Creatinine
![](images/loinc_creatinine.png){width=60%}

## LOINC - PSA
![](images/loinc_psa.png)

## LOINC - Prostate
![](images/loinc_gleason.png)

## Lab Lifecycle
![](images/lifeoflab.png)

## Key Challenges
- Same lab, different name
- Same test, different body fluid
- Different labs, different reference ranges
- per-hospital variation in devices used
- Consistency in units and normal ranges
- Calculated values that require other clinical data (eGFR)
- Lack of good groupers

## Key Challenges
- Erroneous results
- Results change over time
  + micro: may be negative at first, but subsequently positive
  + erroneous corrected

## Key Lab Tables
- LabDim: Info about the laboratories themselves
- LabComponentDim: info about the lab tests
- LabTestFact: data about the test itself
- LabComponentResultFact: actual test results
- LabTestComponentResultMappingFact: linking LabTestFact to LabComponentResultFact

![](images/lab_bridge.png)