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Open Source Science

https://github.com/aehrc/fhir-tx-transforms

Transformations of various code systems to FHIR.

https://github.com/aehrc/fhir-tx-transforms

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 10 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary

Keywords from Contributors

interactive projection archival sequences standards packaging versions tracing charts network-simulation
Last synced: 10 months ago · JSON representation

Repository

Transformations of various code systems to FHIR.

Basic Info
  • Host: GitHub
  • Owner: aehrc
  • License: other
  • Language: Java
  • Default Branch: master
  • Size: 638 KB
Statistics
  • Stars: 5
  • Watchers: 8
  • Forks: 6
  • Open Issues: 4
  • Releases: 0
Created almost 6 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

FHIR Terminology Transforms

A stand-alone command-line tool transfers various clinical terminology and code set resources into FHIR codes systems and concept maps.

Build

mvn clean package

RUN

java -jar "target\fhir-tx-transforms-jar-with-dependencies.jar" CONFIG-FILE-PATH

Configuration file

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 famp23080420.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

Supported Resources

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

Required resources for processing

The resources are hosted on the Technology Reference data Update Distribution (NHS TRUD) web site. The resource files need to be prepared before transformation.

Read code (CTV) V3

Read code V2

NICIP

ODS

OPCS-4

ICD-UK-10

DM+D

  • 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.

Owner

  • Name: The Australian e-Health Research Centre
  • Login: aehrc
  • Kind: organization

The Australian e-Health Research Centre (AEHRC) is CSIRO’s digital health research program.

GitHub Events

Total
  • Watch event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 56
  • Total Committers: 10
  • Avg Commits per committer: 5.6
  • Development Distribution Score (DDS): 0.464
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zhang, Ming (H&B, Marsfield) M****2@c****u 30
lwalsh7 l****2@d****m 8
Michael Lawley m****y@c****u 6
dionmcm d****e@g****m 4
Dougal Fleming d****9@d****p 2
Ming Zhang m****2@c****u 2
dependabot[bot] 4****] 1
Roger Jane r****g@r****c 1
zha12j z****j@M****u 1
Bill Lush b****h@n****t 1
Committer Domains (Top 20 + Academic)
csiro.au: 3 nhs.net: 1 modely-wd.nexus.csiro.au: 1 rog.cc: 1 dedalus.group: 1 dxc.com: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 15
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 months
  • Total issue authors: 0
  • Total pull request authors: 6
  • Average comments per issue: 0
  • Average comments per pull request: 0.2
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (8)
  • dionmcm (4)
  • lwdedalus (4)
  • MingZhang111 (2)
  • dfleming9 (1)
  • rogerjane-nhs (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (8) enhancement (1)

Dependencies

pom.xml maven
  • ca.uhn.hapi.fhir:hapi-fhir-base 4.1.0
  • ca.uhn.hapi.fhir:hapi-fhir-client 4.1.0
  • ca.uhn.hapi.fhir:hapi-fhir-structures-r4 4.1.0
  • com.fasterxml.jackson.core:jackson-databind 2.11.0
  • com.sun.xml.bind:jaxb-core 2.3.0
  • com.sun.xml.bind:jaxb-impl 2.3.0
  • commons-io:commons-io 2.6
  • javax.activation:activation 1.1.1
  • javax.xml.bind:jaxb-api 2.3.0
  • org.apache.poi:poi-ooxml 3.13
  • org.codehaus.mojo:exec-maven-plugin 1.6.0
  • org.glassfish.jersey.core:jersey-client 2.25.1
  • org.glassfish.jersey.media:jersey-media-multipart 2.25.1
  • org.javatuples:javatuples 1.2
  • junit:junit 4.12 test