README.md

In slaverman/SnoLyze: SNOMED CT Expression Constraint Language (ECL) Execution Engine

SnoLyze

SnoLyze is a lightweight and fast SNOMED CT Expression Constraint Language Execution Engine in R to support data analytics over SNOMED CT enabled data.

SnoLyze consists of three functions: - launch() initializes SnoLyze - execute() executes an expression - getTransitiveClosure() returns the initialized transitive closure file

Installation

# requires devtools
# install.packages("devtools")
devtools::install_github("slaverman/SnoLyze")

#without devtools
install.packages("PATH_TO/SnoLyze_X.X.X.tar.gz", repo = NULL, type = "source")

Additional requirements for Linux and Mac OS X

libv8-3.14-dev (deb), v8-314-devel (rpm), v8-3.14 (arch), v8@3.15 (homebrew)

Usage

library(SnoLyze)

# without transitive closure file, takes around 70 seconds to read in the relationship file and create the transitive closure file
launch("PATH_TO_SNOMED_CT_SNAPSHOT_RELATIONSHIP_FILE")

# with transitive closure file, takes around 10 seconds to read in the relationship and transitive closure files
launch("PATH_TO_SNOMED_CT_SNAPSHOT_RELATIONSHIP_FILE", "PATH_TO_TRANSITIVE_CLOSURE_FILE")

# get transitive closure file, to save it with your favourite filewriter (example below uses fwrite of the data.table package)
transitive <- getTransitiveClosure()
fwrite(transitive, "transitive_closure_INT_20170131.txt")

# < 19829001 |Disorder of lung| : 116676008 |Associated morphology|  =  79654002 |Edema|
execute("< 19829001 |Disorder of lung| : 116676008 |Associated morphology|  =  79654002 |Edema|")
# integer64
#  [1] 11468004          19242006          67782005          89687005          95437004          162970000         196151000        
#  [8] 196152007         196153002         233705000         233707008         233708003         233712009         240629003        
# [15] 276637009         405276000         698638005         698640000         700458001         10674871000119105
# run time: 23 ms

# select all cases in 'data' with a type of 'Diabetes mellitus', 
# but not a type of 'Diabetes mellitus during pregnancy, childbirth and the puerperium'
result <- execute("<< 73211009 | Diabetes mellitus (disorder)| MINUS << 199223000 | Diabetes mellitus during pregnancy, childbirth and the puerperium (disorder)|")
data[sctid %in% result]
#    pid   date      sctid           fsn
#     1   2011-01-06 5969009         Diabetes mellitus associated with genetic syndrome (disorder)
#     1   2012-02-07 609572000       Maturity-onset diabetes of the young, type 5 (disorder)
#     3   2013-03-08 426875007       Latent autoimmune diabetes mellitus in adult (disorder)
#     4   2014-04-09 426875007       Latent autoimmune diabetes mellitus in adult (disorder)
#     5   2015-05-10 426875007       Latent autoimmune diabetes mellitus in adult (disorder)
#    ---
#   61154 2011-12-07 359642000       Diabetes mellitus type 2 in nonobese (disorder)
#   61155 2012-11-06 359642000       Diabetes mellitus type 2 in nonobese (disorder)
#   61156 2013-10-05 359642000       Diabetes mellitus type 2 in nonobese (disorder)
#   61157 2014-09-04 359642000       Diabetes mellitus type 2 in nonobese (disorder)
#   61158 2015-08-03 359642000       Diabetes mellitus type 2 in nonobese (disorder)

Supported features

SnoLyze currently supports the brief and long syntax of the Expression Constraint Language version 1.2 in combination with SNOMED CT Release Format 2.

Feature | Example | Supported ---------- | ----------------------- | -- Self | 404684003 \|Clinical finding\| | Yes Descendant of | < 404684003 \|Clinical finding\| | Yes Descendant or Self of | << 404684003 \|Clinical finding\| | Yes Child of | <! 404684003 \|Clinical finding\| | Yes Ancestor of | > 40541001 \|Acute pulmonary edema\| | Yes Ancestor or Self of | >> 40541001 \|Acute pulmonary edema\| | Yes Parent of | >! 40541001 \|Acute pulmonary edema\| | Yes Member of | ^ 700043003 \|Example problem list concepts reference set\| | No Any | * | Yes Attributes | < 19829001 \|Disorder of lung\| : 116676008 \|Associated morphology\| = 79654002 \|Edema\| | Yes Attribute Groups | < 404684003 \|Clinical finding\| : {363698007 \|Finding site\| = << 39057004 \|Pulmonary valve structure\| , 116676008 \|Associated morphology\| = << 415582006 \|Stenosis\| }, {363698007 \|Finding site\| = << 53085002 \|Right ventricular structure\| , 116676008 \|Associated morphology\| = << 56246009 \|Hypertrophy\| } | Yes Nested Attributes | < 404684003 \|Clinical finding\| 47429007 \|Associated with\| = (< 404684003 \|Clinical finding\| : 116676008 \|Associated morphology\| = << 55641003 \|Infarct\| ) | Yes Attribute Operators | << 404684003 \|Clinical finding\| : << 47429007 \|Associated with\| = << 267038008 \|Edema\| | Yes Concrete Values | < 373873005 \|Pharmaceutical / biologic product\| : 209999999104 \|Has trade name\| = "PANADOL"| No Reverse Attributes | < 91723000 \|Anatomical structure\| : R 363698007 \|Finding site\| = < 125605004 \|Fracture of bone\| | Yes Any Attribute Name and Value | < 404684003 \|Clinical finding\| : * = 79654002 \|Edema\| | Yes Attribute Cardinality | < 373873005 \|Pharmaceutical / biologic product\| : [1..3] 127489000 \|Has active ingredient\| = < 105590001 \|Substance\| | Yes Attribute Cardinality in Groups | < 373873005 \|Pharmaceutical / biologic product\| : [1..3] { 127489000 \|Has active ingredient\| = < 105590001 \|Substance\| } | Yes Simple Conjunction | < 19829001 \|Disorder of lung\| AND < 301867009 \|Edema of trunk\| | Yes Simple Disjunction | < 19829001 \|Disorder of lung\| OR < 301867009 \|Edema of trunk\| | Yes Attribute Conjunction | < 404684003 \|Clinical finding\| : 363698007 \|Finding site\| = << 39057004 \|Pulmonary valve structure\| , 116676008 \|Associated morphology\| = << 415582006 \|Stenosis\| | Yes Attribute Disjunction | < 404684003 \|Clinical finding\| : 116676008 \|Associated morphology\| = << 55641003 \|Infarct\| OR 42752001 \|Due to\| = << 22298006 \|Myocardial infarction\| | Yes Attribute Group Conjunction and Disjunction | < 404684003 \|Clinical finding\| : { 363698007 \|Finding site\| = << 39057004 \|Pulmonary valve structure\| , 116676008 \|Associated morphology\| = << 415582006 \|Stenosis\| } OR { 363698007 \|Finding site\| = << 53085002 \|Right ventricular structure\| , 116676008 \|Associated morphology\| = << 56246009 \|Hypertrophy\| } | Yes Attribute Value Conjunction | < 404684003 \|Clinical finding\| : 116676008 \|Associated morphology\| = (<< 56208002 \|Ulcer\| AND << 50960005 \|Hemorrhage\| ) | Yes Attribute Value Disjunction | < 404684003 \|Clinical finding\| : 116676008 \|Associated morphology\| = (<< 56208002 \|Ulcer\| OR << 50960005 \|Hemorrhage\| ) | Yes Exclusion of Simple Expressions | << 19829001 \|Disorder of lung\| MINUS << 301867009 \|Edema of trunk\| | Yes Exclusion of Attribute Values | < 404684003 \|Clinical finding\| : 116676008 \|Associated morphology\| = ((<< 56208002 \|Ulcer\| AND << 50960005 \|Hemorrhage\| ) MINUS << 26036001 \|Obstruction\| ) | Yes Not Equal to Attribute Value | < 404684003 \|Clinical finding\| : 116676008 \|Associated morphology\| != << 26036001 \|Obstruction\| | Yes

slaverman/SnoLyze documentation built on May 20, 2019, 4:07 p.m.