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 SnoLyzeexecute()executes an expressiongetTransitiveClosure()returns the initialized transitive closure file
# 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")libv8-3.14-dev (deb), v8-314-devel (rpm), v8-3.14 (arch), [email protected] (homebrew)
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)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 |