Explore @aehrc Open Source projects

The Australian e-Health Research Centre (@aehrc)

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VariantSpark

machine learning for genomic variants

pathling

Tools that make it easier to use FHIR® and clinical terminology within data analytics, built on Apache Spark.

LAAT

A Label Attention Model for ICD Coding from Clinical Text

cvt2distilgpt2

Improving Chest X-Ray Report Generation by Leveraging Warm-Starting

smart-forms

React-based form renderer implementing Structured Data Capture (SDC) FHIR specification

Mirorr

Mirorr: Multimodal Image Registration using blOck-matching and Robust Regression

snorocket

The Snorocket Description Logic classifier for EL++ with concrete domains support

fhir-owl

Transforms OWL ontologies into FHIR code systems.

ontoserver-deploy

Sample deployment project for Ontoserver

fhir-claml

Transforms ClaML classifications into FHIR code systems.

cxrmate

CXRMate: Longitudinal Data and a Semantic Similarity Reward for Chest X-Ray Report Generation

TRIBES

Finding cryptic relationships to boost disease gene detection

redmatch

A rules-based transformation engine that allows exporting data in REDCap as FHIR resources.

terraform-aws-serverless-beacon

Serverless implementation of Beacon V2 protocol, to enable cheaper and faster exchange of genomic and phenotypic information

INSIDER

Detecting foreign inserted DNA segments in the genome

redcap_fhir_ontology_provider

REDCap external module provides support for referencing an external Fhir based ontology server to lookup values.

fhir-tx-encoder

A tool for encoding FHIR terminology concepts for machine learning applications.

COVID-sBeacon

redcap_pedigree_editor

Redcap External Module to allow the entry of a pedigree diagram, storing the result as a FHIR resource

PEPS

Polygenic EpiStatic Phenotype Simulation

tx-analytics-fhir

An example analytic workflow describing some techniques for working with FHIR and SNOMED CT data.

Jupyter Notebook

BitEpi

spia-to-fhir

A Maven plugin for converting terminology from the Standards for Pathology Informatics in Australia (SPIA) into a set of FHIR terminology resources.

fhir-analytics-pipeline

An example of how to build a pipeline for extracting, transforming and analyzing FHIR data.

ontology-core

Internal model to represent ontologies and utilities to import ontologies from different formats.

redcap_simple_ontology_provider

REDCap external module provides simple implementation of the ontology provider mechanism.

isling

A tool for detection of viral integrations

Ontoserver

Ontoserver puts SNOMED CT, AMT, LOINC, and FHIR-based CodeSystems at your fingertips.

parquet-on-fhir

A specification for representing FHIR data within the Apache Parquet format.

sVEP

smart-forms-ig

fhir-bulk-java

A Java client for the Bulk Data Export operation within the FHIR Bulk Data Access IG.

VIGWAS

Interactive notebook for quality control and Spark-based genome wide association analysis using HAIL and VariantSpark.

primary-care-data-technical

labcodeset-fhir-transform

Application which transforms Nederlandse Labcodeset from its native XML file format to a collection of FHIR terminology resources.

real-time-fhir

A simulated FHIR data source that can write resources into a remote FHIR server in real time.

fhir-ts-exemplars

jre-docker

Docker images for building base images capable of running Java applications.

redcap_advanced_fhir_ontology

REDCap External Module to give autocomplete using a FHIR terminology server with advanced options.

fhir-tx-transforms

Transformations of various code systems to FHIR.

vector-integration-simulation-pipeline

A pipeline for simulating viral or vector integration into a host genome

fhir-phenopackets-ig

Phenopackets on FHIR Implementation Guide

SMART-EHR-Launcher

An EHR simulator dashboard testing tool to launch SMART on FHIR apps

openmrs-module-terminologysearch

A module for OpenMRS to search a FHIR terminology server for concepts.

EpiExplorer

imageclefmedical_caption_23

MedICap: Code for the participation of team CSIRO at the ImageCLEFmedical Caption task of 2023.

Jupyter Notebook

fhir-hgnc

Transforms HGNC source files into FHIR code systems.

sct-historical-analytics

Data Analytics with historical SNOMED CT data - SNOMED CT Expo 2021

fhircap

FHIRCap is a tool designed to transform REDCap forms into FHIR resources.

genomator

Privacy-hardened, hallucination-resistant synthetic data generator.

cxrmate-ed

Jupyter Notebook

primary-care-data-technical-stu3

COVID-GenomeMap

snomio

An integration with Snomed International's Authoring Platform that extends functionality to improve authoring of medicinal terminology.

fhir-phenopackets

primary-care-phase2

semantic-search

A deep learning based approach for semantic search over large clinical terminology system

antlr-generator

COVID19_TBED

Jupyter Notebook

CRISPR-diagnostics

CRISPR-diagnostics

Jupyter Notebook

VariantSpark_Gigascience

Scripts for the GigaScience publication

clinicaltrialsearch

A search engine for retrieving clinical trials.

OCT_Denoising_pix2pix

Employing Texture Loss to Denoise OCT Images using Generative Adversarial Networks

genclipr-fhir-ig

FHIR implementation guide for the Genomics Clinical Picture Repository standard developed as part of the Standardised Clinical Phenotypes project in Australian Genomics.

ecl-builder

UI components that help you build SNOMED CT ECL expressions.

fhir-validator-spark

A tool for executing FHIR validation over a set of resources using Apache Spark.