A stand-alone command-line tool transfers various clinical terminology and code set resources into FHIR codes systems and concept maps.
mvn clean package
java -jar "target\fhir-tx-transforms-jar-with-dependencies.jar" CONFIG-FILE-PATH
Single configuration file for terminology resources transform. Each supported resources (list below) has individual controls and configuration.
FHIR Terminology Server URL
tx.server.url=TERMINOLOGY-SERVER-URL
Local output folder for FHIR resources
output.dir=PATH-TO-LOCAL-FOLDER
Control running of individual resource transform
process.ctv2=TRUE/FALSE
process.ctv3=TRUE/FALSE
process.icd=TRUE/FALSE
process.nicip=TRUE/FALSE
process.opcs=TRUE/FALSE
process.ods=TRUE/FALSE
process.dmd=TRUE/FALSE
READ V2
ctv2.coreFile=PATH-TO-LOCAL-FILE
ctv2.mapFile=PATH-TO-LOCAL-FILE
CTV 3
ctv3.version.VERSION.folder=PATH-TO-LOCAL-FOLDER
ICD-10-UK
icd10uk.version.VERSION.codeFile=PATH-TO-LOCAL-FILE
NICIP
nicip.version.VERSION.folder=PATH-TO-LOCAL-FOLDER
OPCS-4
opcs.version.VERSION.codeFile=PATH-TO-LOCAL-FILE
opcs.version.VERSION.validFile=PATH-TO-LOCAL-FILE
- Use number only for OPCS version, for example 4.9 will be 49 here.
ODS
ods.version.VERSION.zipfile=PATH-TO-LOCAL-FILE
DM+D
dmd.releaseFolder=PATH-TO-LOCAL-FOLDER
dmd.releaseSerial=Numeric value in DM+D file names
dmd.dmdReleaseNote=URL of dm+d release notes
dmd.gtinReleaseNote=URL of GTIN release notes
- The serial number used in dm+d file, example f_amp2_3080420.xml, the serial number should be 3080420
- The transform use an excel config file internally from NHS, it is in src/main/resources
Support multiple version
To add multiple version processing for single resource, separate the configuration lines for each version. For example. to add 2 versions for CTV 3, the version number is 20160401 and 20170401, use the lines below.
ctv3.version.20160401.folder=PATH-TO-LOCAL-FOLDER-20160401
ctv3.version.20170401.folder=PATH-TO-LOCAL-FOLDER-20170401
The FHIR Terminology Transforms project supports transforming the following terminologies into FHIR code systems.
- Read Code V2
- Read Code (CTV) V3
- NICIP
- ODS
- OPCS-4
- ICD-10-UK
- DM+D
The resources are hosted on the Technology Reference data Update Distribution (NHS TRUD) web site. The resource files need to be prepared before transformation.
- Resources URL :https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/9/subpack/19/releases
- Folder/File: EXTRACTED_FOLDER/V3
- Transformed Versions: 20170401, 20180702
- Resources URL : Need access the retired product from https://hscic.kahootz.com/connect.ti/t_c_home/grouphome
- Folder/File: EXTRACTED_FOLDER/Unified/Corev2.all, EXTRACTED_FOLDER/Unified/Uniicd10.xrf
- Transformed Versions: 20160401
- Resources URL :https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/2/subpack/14/releases
- Folder/File: EXTRACTED_FOLDER/SUBFOLDER
- Transformed Versions: 20171001, 20180401,20181001,20190601,20200401
- Resources URL :https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/5/subpack/341/releases
- Folder/File: EXTRACTED_FOLDER/fullfile.zip
- Transformed Versions: 26 monthly release since 20180427
- Resources URL : https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/10/subpack/119/releases
- Folder/File: EXTRACTED_FOLDER/OPCS_VERSION_CodesAndTitles_RELEASE_DATE V1.0.txt,EXTRACTED_FOLDER/OPCS_VERSION _Metadata_RELEASE_DATE V1.0.txt
- Transformed Versions: 4.8,4.9
- Resources URL : https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/28/subpack/259/releases
- Folder/File: EXTRACTED_FOLDER/Content/ICD10_Edition_VERSION_CodesAndTitlesAndMetadata_GB_DATE.txt
- Transformed Versions: 5th.4th
- Resources URL : [https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/6/subpack/24/releases]
- Folder/File: EXTRACTED_FOLDER/
- Transformed Versions: 202007.0.0,202004.1.0
Copyright © 2020, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230. Licensed under the CSIRO Open Source Software License Agreement.