SNOMED International Mapping Tool

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Overview

Documentation on the ICD-O mapping project.

Meeting Notes

Details

Computing Scope

Use the attached transitive_closure.pl script.  The file icdoScope.txt is attached (1558 entries).  A file of those unmapped codes is also attached.

cd Snapshot/Refset/Map
grep 446608001 *Simple* | grep '/' | perl -ne '@_=split/\t/; print if $_[2];' | cut -f 6 | sort -u -o icdo.txt
./transitive_closure.pl ../../Terminology/*_Relationships*txt out.txt
sort -t\ 	 -k 1,1 -o out.txt out.txt
join -j 1 -o 2.2. icdo.txt out.txt > scope.txt
sort -u -o icdoScope.txt scope.txt icdo.txt
/bin/rm f icdo.txt out.txt scope.txt

 

Preparing the Data

In Lieu of obtaining offical ICD-O-3.1 files from WHO, we proceeded with ICDO morphology data from NCI Metathesaurus (available from NCI in the US).  As we understand it, this is the correct ICDO version to map to and contains the real data.

Steps for processing the data:

  • in the /home/ihtsdo/data/ICDO directory (on PROD or UAT) are the files containing just morphology code data.

    • icdo3.txt (see format below)

      Code|Level|Term|Note|Code reference|obs|See also|See note|Includes|Excludes|Other text|comment_April_Fritz
|1|MORPHOLOGY|||||||||
800|2|Neoplasms, NOS|||||||||
801-804|2|Epithelial neoplasms, NOS|||||||||

    • chdPar.txt (sample entries below, it's a child → parent code list).

      800|MORPHOLOGY
801-804|MORPHOLOGY
805-808|MORPHOLOGY
809-811|MORPHOLOGY
  • The same directory has a conversion script (icdo3.pl) that produces a valid ClaML representation of the morphology codes (icdo-3-1.xml).
  • This file can be loaded using the standard ClaML loader.
  • In the same directory is a subset of the ICDO mapping file containing just the morphology entries. 
    • der2_sRefset_IcdoMorphSimpleMapSnapshot_INT_20160131.txt
  • The mapping tool is loaded with just morphology terminology and just morphology mappings.  Thus, RF2 release output from the tool can be simply applied to the previous full as it will only indicate modifications to morphology codes.  Thus, it is not necessary to load all of ICD-O in order to make this work.

 

At such time as official files are obtained from WHO and are in a different format, work will be done (as part of warranty/maintenance) to either convert that format into suitable ClaML or a new loader will be created for the native data format.

Production Deployment

  1. Load the ICDO-3-1 data
  2. Create and configure the project (with scope definition based on icdoScope.txt "plus descendants".
    1. Use "REVIEW" workflow
    2. Configure Nicki/Donna as users
    3. Add basic productivity reports.
  3. Load the prior version ICDO map (as starting point)  - both records and members.
  4. Begin editing cycle
  5. Compute workfow
  6. Create a "published" form of the project as well

Here's the process in code:

service tomcat7 stop
# 1. load ICDO-3-1 data
cd ~/code/admin/loader
set file = ~/data/ICDO/icdo-3-1.xml
mvn install -PClaML -D$rc -Dterminology=ICDO -Dversion=3_1 -Dinput.file=$file >&! mvn.log
 
# 2. do in mapping tool
service tomcat7 start
...
service tomcat7 stop



# 3. Load the prior version ICDO map
cd ~/code/admin/loader
set file = ~/data/ICDO/der2_sRefset_IcdoMorphSimpleMapSnapshot_INT_20160131.txt
mvn install -PSimpleMapRecords -D$rc -Dinput.file=$file -Dmember.flag=true -Drecord.flag=true >&! mvn.log
 
# 4. Begin editing cycle
cd ~/code/admin/release
mvn install -PBeginEditingCycle -D$rc -Drefset.id=446608001 >&! mvn.log


# 5. Compute workflow
cd ~/code/admin/loader
mvn install -PComputeWorkflow -D$rc -Drefset.id=446608001 >&! mvn.log
 
# load published project data
cd ~/code/admin/loader
set file = ~/data/ICDO/der2_sRefset_IcdoMorphSimpleMapSnapshot_INT_20160131.txt
perl -pe 's/446608001/P446608001/;' $file >! x.txt
mvn install -PSimpleMapRecords -Drun.config=/home/ihtsdo/config/config.properties -Dinput.file=x.txt -Dmember.flag=false -Drecord.flag=true >&! mvn.log

service tomcat7 start

Publishing ICD-O

TBD (copy from GMDN and replace refset id)