CERNER-TOOLS

Code and scripts for interacting with Cerner Health Facts.

Dependencies

• unm_biocomp_util

Compiling

mvn clean install

Usage

java -classpath unm_biocomp_cerner-0.0.1-SNAPSHOT-jar-with-dependencies.jar edu.unm.health.biocomp.cerner.hf.hf_query

hf_query - HealthFacts query application
usage: hf_query [options]
  operations:
    -test .................. test connection
    -info .................. db metadata
    -list_tables ........... 
    -query ................. query db
  i/o:
    -sqlfile SQLFILE ....... 
    -sql SQL ............... 
    -o OFILE ............... output file (CSV)
  options:
    -dbhost DBHOST ......... [localhost]
    -dbport DBPORT ......... [5432] 
    -dbname DBNAME ......... [healthfacts] 
    -dbusr DBUSR ........... [jjyang] 
    -dbpw DBPW ............. [********]
    -v[v] .................. verbose [very]
    -h ..................... this help

java -classpath unm_biocomp_cerner-0.0.1-SNAPSHOT-jar-with-dependencies.jar edu.unm.health.biocomp.cerner.hf.hf_patients

hf_patients - HealthFacts patient facts app
Select patients and get all facts of specified type.
usage: hf_patients [options]

  i/o:
    -o OFILE ............... output file (CSV)

  patient selection:
    -nmax NMAX ............. patient limit [None]
    -skip SKIP ............. skip 1st SKIP patients (from input file only)
    -random ................ random selection (from db only)
    -skfile SKFILE ......... input SK IDs (else sample all)
    -sk SK ................. input SK ID
    -id ID ................. input patient ID (mapped to SK)
    -idfile IDFILE ......... input patient IDs (mapped to SK)

  fact selection:
    -ftype FTYPE ........... [all]

  options:
    -dbhost DBHOST ......... [localhost]
    -dbport DBPORT ......... [5432] 
    -dbname DBNAME ......... [healthfacts] 
    -dbusr DBUSR ........... [jjyang] 
    -dbpw DBPW ............. [********]
    -v[v[v]] ............... verbose [very [very]]
    -h ..................... this help

FTYPES:
	diagnosis
	medication
	med_history
	surgery
	lab
	clinical_event
	discharge
	procedure

Documentation

mvn javadoc:javadoc

• JavaDoc (API docs)

UNM Cerner HealthFacts paper:

• Low serum sodium levels at hospital admission: Outcomes among 2.3 million hospitalized patients, Saleem Al Mawed, V. Shane Pankratz, Kelly Chong, Matthew Sandoval, Maria-Eleni Roumelioti, Mark Unruh, Published: March 22, 2018https://doi.org/10.1371/journal.pone.0194379