Discover aehrc/BitEpi Open Source project

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

139

pathling

A Label Attention Model for ICD Coding from Clinical Text

LAAT

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

cvt2distilgpt2

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

smart-forms

TypeScript

Mirorr

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

C++

snorocket

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

Transforms OWL ontologies into FHIR code systems.

fhir-owl

Sample deployment project for Ontoserver

ontoserver-deploy

HCL

fhir-claml

Transforms ClaML classifications into FHIR code systems.

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

cxrmate

Finding cryptic relationships to boost disease gene detection

TRIBES

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

redmatch

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

terraform-aws-serverless-beacon

Detecting foreign inserted DNA segments in the genome

INSIDER

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

redcap_fhir_ontology_provider

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

fhir-tx-encoder

COVID-sBeacon

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

redcap_pedigree_editor

Polygenic EpiStatic Phenotype Simulation

PEPS

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

tx-analytics-fhir

Jupyter Notebook

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.

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

fhir-analytics-pipeline

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

ontology-core

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

redcap_simple_ontology_provider

A tool for detection of viral integrations

isling

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

Ontoserver

parquet-on-fhir

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

sVEP

Perl

smart-forms-ig

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

fhir-bulk-java

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

VIGWAS

primary-care-data-technical

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

labcodeset-fhir-transform

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

real-time-fhir

fhir-ts-exemplars

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

jre-docker

Dockerfile

redcap_advanced_fhir_ontology

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

Transformations of various code systems to FHIR.

fhir-tx-transforms

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

vector-integration-simulation-pipeline

Phenopackets on FHIR Implementation Guide

fhir-phenopackets-ig

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

SMART-EHR-Launcher

TypeScript

openmrs-module-terminologysearch

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

EpiExplorer

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

imageclefmedical_caption_23

Jupyter Notebook

fhir-hgnc

Transforms HGNC source files into FHIR code systems.

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

sct-historical-analytics

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

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

COVID-GenomeMap

CSS

snomio

TypeScript

fhir-phenopackets

primary-care-phase2

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

semantic-search

antlr-generator

COVID19_TBED

CRISPR-diagnostics

VariantSpark_Gigascience

Scripts for the GigaScience publication

A search engine for retrieving clinical trials.

clinicaltrialsearch

Employing Texture Loss to Denoise OCT Images using Generative Adversarial Networks

OCT_Denoising_pix2pix

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

genclipr-fhir-ig

UI components that help you build SNOMED CT ECL expressions.

ecl-builder

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

fhir-validator-spark