ICD-O Mapping

Overview

Documentation on the ICD-O mapping project.

Information on the ICDO mapping project.

ModuleId: 900000000000207008
RefsetId: 446608001

Helpful Admin Commands

Remove

cd ~/code/admin/remover
mvn install -PMapRecords -D$rc -Drefset.id=446608001
mvn install -PTerminology -D$rc -Dterminology=ICDO -Dversion=16_1

Load

Get maintenance window

cd ~/code/admin/loader
mvn install -PICDO -Dinput.dir=/home/ihtsdo/data/ICDO -Dterminology=ICDO -Dversion=16_1 -D$rc
cd ~/code/admin/loader
set file = /home/ihtsdo/data/ICDO/der2_sRefset_IcdoMorphSimpleMapSnapshot_INT_20170131.txt
/bin/rm -f /tmp/x.txt
# Keep only morphology codes (with '/')
perl -ne '@_=split/\t/; print if $_[4] eq "446608001"' $file | grep '/' > /tmp/x.txt
mvn install -PSimpleMapRecords -D$rc -Dinput.file=/tmp/x.txt -Dmember.flag=true -Drecord.flag=false

Compute

cd ~/code/admin/loader
mvn install -PComputeWorkflow -D$rc -Drefset.id=446608001

Release

cd ~/code/admin/release
mvn install -PBeginRelease -D$rc -Drefset.id=446608001 -Dtest.mode.flag=true
mvn install -PRelease -D$rc -Drefset.id=446608001 -Doutput.dir=. -Dtime=20170731 -Dmodule.id=900000000000207008 -Dtest.mode.flag=true
mvn install -PFinishRelease -D$rc -Drefset.id=446608001
mvn install -PBeginEditingCycle -D$rc -Drefset.id=446608001

Release with Alpha/Beta Iteration

Reloading Snomed is typically being done on prod-mapping now before the clone-over, so steps 2-5 should be skipped on alpha iteration.

1.) Take server down. Check RAM allocated to MAVEN_OPTS with export command. Adjust server size and RAM allocated with this command if necessary:

export MAVEN_OPTS="-XX:MaxPermSize=512m -Xmx3000M -Xmx7000M"
2.) cd ~/code/admin/remover
3.) mvn install -PTerminology -Drun.config=/home/ihtsdo/config/config.properties -Dterminology=SNOMEDCT -Dversion=latest
4.) cd ~/code/admin/loader
5.) mvn install -PRF2-snapshot -Drun.config=/home/ihtsdo/config/config.properties -Dterminology=SNOMEDCT -Dinput.dir=/home/ihstdo/data/xSnomedCT_InternationalRF2_ALPHA_20170731T120000Z/Snapshot

6.) DELETE from simple_map_refset_members where refsetId = 446608001;

7.) set file = /home/ihtsdo/data/ICDO/der2_sRefset_SimpleMapSnapshot_INT_20170131.txt

# Keep only morphology codes (with '/')
perl -ne '@_=split/\t/; print if $_[4] eq "446608001"' $file | grep '/' > /tmp/icdo.txt
mvn install -PSimpleMapRecords -Drun.config=/opt/mapping-rest/config.properties -Dinput.file=/tmp/icdo.txt -Dmember.flag=true -Drecord.flag=false

8.) bring server back up

9.) rerun compute workflow, begin, and process release steps

Loading "Human Readable" View

TBD

Updating Published Project

Similar approach to ICD10 but using the "simple" map loader. e.g.

cd /opt/mapping-admin/remover
mvn install -PMapRecords -Drun.config=/opt/mapping-rest/config.properties -Drefset.id=P446608001

cd /opt/mapping-admin/loader
grep 446608001 /opt/mapping-data/doc/release/SNOMEDCT_to_ICDO_446608001/20200731/der2_sRefset_SimpleMapActiveSnapshot_INT_20200731.txt | perl -pe 's/446608001/P446608001/;' > x.txt
mvn install -PSimpleMapRecords -Drun.config=/opt/mapping-rest/config.properties -Dinput.file=x.txt -Dmember.flag=false -Drecord.flag=true >&! mvn.log

Meeting Notes

20160617 ICD-O Scope Definition Meeting

Dev Requested

Ability to export map (suggestion is to support export from search resutls - there should be a ticket for this already)
Auto-mapping capability (as part of compute workflow?)
- exact match handler → e.g. support auto mapping where strings exactly match (e.g. without semantic tag)
Support feedback from Resovled→Editing in workflows (e.g. REVIEW_RESOLVED to REVIEW_IN_PROGRESS) via SAVE_FOR_LATER
Support for optional codes after the slash, e.g. things not explicitly in ICDO terminology but allowed ,e.g. /6 where only /3 exist

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

Load the ICDO-3-1 data
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.
Load the prior version ICDO map (as starting point) - both records and members.
Begin editing cycle
Compute workfow
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

References/Links

Initial files for ICDO load can be found in https://uat-mapping.ihtsdotools.org/doc/ICDO.zip

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