Implementations

Browse implementations of GA4GH products. Learn how they solve real problems for organisations around the world.

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All of Us Researcher Workbench

The Researcher Workbench is a cloud-based platform where registered researchers can access Registered and Controlled Tier data. Its powerful tools support data analysis and collaboration. Integrated help and educational resources are provided through the Workbench User Support Hub.

Products Used
Data Repository Service (DRS), Data Use Ontology (DUO), CRAM, Genetic Data Encryption (Crypt4GH), htsget
Implementing Organisation
All of Us Research Program

ARGO Data Platform

The International Cancer Genome Consortium Accelerating Research in Genomic Oncology (ICGC ARGO) aims to uniformly analyse specimens from 100,000 donors with high-quality clinical data in order to address outstanding questions that are vital to the quest to defeat cancer.

Products Used
Workflow Execution Service (WES), Beacon, Framework for responsible sharing of genomic and health-related data, Tool Registry Service (TRS), CRAM, Framework for Involving and Engaging Participants, Patients, and Publics in Genomics Research and Health Implementation
Implementing Organisation
ICGC ARGO

Australian Genomics Data Management Systems

Australian Genomics has tools to support storage, access, and sharing of its genomic datasets for secondary research use. They include a web-based platform for dynamic consent and data sharing preferences (CTRL), a cloud-based Genomic Data Repository (GDR) that ingests, stores, and provides access to data, and a data release coordinator system (Elsa) to streamline data sharing.

Products Used
Data Use Ontology (DUO), SAM/BAM, htsget, Passports, Beacon, Genetic Variation Formats (VCF)
Implementing Organisation
Australian Genomics

BioBank Japan (BBJ)

BBJ is of the three major biobanks in Japan managed by the AMED BioBank Japan Project for Genomic and Clinical Research. It has collected DNA, serum, and clinical information from more than 270,000 patients nationwide, and thus is regarded as one of the largest disease biobanks in the world.

Products Used
Data Use Ontology (DUO), CRAM
Implementing Organisation
Japan Agency for Medical Research and Development (AMED)

BRCA Exchange

Information drawn from multiple databases — which have been intelligently merged together — provides researchers with a set of BRCA variations and annotations that is as comprehensive as possible.

Products Used
Workflow Execution Service (WES), Beacon, Variation Representation (VRS)
Implementing Organisation
BRCA Challenge

CanDIG V2

The CanDIG v2 project is a collection of heterogeneous services designed to work together to facilitate end-to-end data flow for genomic data.

Products Used
Phenopackets, Data Repository Service (DRS), Data Security Infrastructure Policy (DSIP), Beacon, Data Use Ontology (DUO), CRAM, htsget, RNAget, Framework for responsible sharing of genomic and health-related data
Implementing Organisation
Canadian Distributed Infrastructure for Genomics (CanDIG)

ClinGen Knowledge-base

Funded by the National Institutes of Health (NIH), ClinGen is dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

Products Used
Variation Representation (VRS)
Implementing Organisation
Clinical Genome Resource (ClinGen)

cwl-WES

cwl-WES (formerly: WES-ELIXIR) is a Flask/Gunicorn application that makes use of Connexion to implement the GA4GH WES OpenAPI specification. cwl-WES enables clients and users to execute CWL workflows in the cloud via an execution backend that is compatible with the GA4GH Task Execution Service (TES) — for example, TESK or Funnel. Workflows can be sent for execution, previous runs can be listed, and the status and run information of individual runs can be queried. The service leverages cwl-tes to interpret CWL workflows, break them down into individual tasks, and emit GA4GH TES-compatible HTTP requests to a configured TES instance. Access to endpoints can be configured to require JSON Web Token-based access tokens, such as those issued by ELIXIR AAI. Run information is stored in a MongoDB database.

Products Used
Workflow Execution Service (WES)
Implementing Organisation
ELIXIR, ELIXIR Cloud and AAI

EJP-RD Beacon-in-a-Box

This stand-alone Beacon instance was designed to allow for the sharing of metadata of datasets.

Products Used
Beacon
Implementing Organisation
European Joint Programme on Rare Disease (EJP RD)

EJP-RD Virtual Platform

The platform is a federated ecosystem in which resources are enhanced to be amenable to rare disease research, and made FAIR: findable, accessible, interoperable, and reusable. Data stay at the source level but can be queried remotely. As an ecosystem, multiple query points will be possible, allowing for sending interrogations from one resource to others. Thus, federated discovery, query, and analysis are made possible, preserving patient privacy and respecting access conditions of each resource.

Products Used
Phenopackets, Service Info, Service Registry, Variant Annotation (VA), CRAM, Genetic Data Encryption (Crypt4GH), htsget, refget, Framework for responsible sharing of genomic and health-related data
Implementing Organisation
European Joint Programme on Rare Disease (EJP RD)

ELIXIR BioContainers

BioContainers is based on the popular frameworks Conda, Docker, and Singularity. This community-driven project provides the infrastructure and basic guidelines to create, manage, and distribute bioinformatics packages (e.g Conda) and containers (e.g Docker, Singularity).

Products Used
Tool Registry Service (TRS), Phenopackets, Task Execution Service (TES)
Implementing Organisation
ELIXIR

ELIXIR Cloud & AAI

A multi-cloud computing infrastructure allows life scientists within and beyond the ELIXIR network to run large-scale data analysis workloads in a federated network of ELIXIR compute and storage nodes.

Products Used
Workflow Execution Service (WES), Service Registry, Data Repository Service (DRS), Tool Registry Service (TRS), Task Execution Service (TES)
Implementing Organisation
ELIXIR Cloud and AAI, ELIXIR

ELIXIR European Genome-phenome Archive (EGA)

The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of personally-identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems.

Products Used
Authorisation and Authentication Infrastructure (AAI), Data Use Ontology (DUO), Passports, Genetic Data Encryption (Crypt4GH), htsget, Phenopackets, Beacon
Implementing Organisation
ENA / EVA / EGA, ELIXIR

ELIXIR-Beacon

The Beacon Network search bar is a simple form with two options: assembly and variant. The assembly can be selected from the dropdown menu on the left side. The search bar then takes the desired variant information as a search term which will be sent to Beacons in a structured manner.

Products Used
Phenopackets, Data Repository Service (DRS), Tool Registry Service (TRS), Task Execution Service (TES), Workflow Execution Service (WES), Authorisation and Authentication Infrastructure (AAI), Beacon, Service Registry, Passports, Data Use Ontology (DUO), Genetic Data Encryption (Crypt4GH), htsget, refget, RNAget
Implementing Organisation
ELIXIR, ELIXIR Beacon

ENCODE RNAExpression report

This ENCODE Portal hosts data produced by members of the Encyclopedia of DNA Elements (ENCODE) Consortium and also provides the wider scientific community with access to these data.

Products Used
RNAget
Implementing Organisation
The Encyclopedia of DNA Elements (ENCODE)

EpiShare Platform

The EpiShare Platform builds GA4GH tools and standards and other online resources. It aims to create a web resource to make epigenomic data more easily discoverable and to enable the launch of multi-omics analyses on these controlled-access datasets at their storage locations.

Products Used
Phenopackets, Data Repository Service (DRS), Workflow Execution Service (WES), Service Registry, Data Use Ontology (DUO), Genetic Data Encryption (Crypt4GH), RNAget
Implementing Organisation
EpiShare

Federated EGA

The Federated EGA provides a network of connected resources to enable transnational discovery of and access to human data for research while also respecting jurisdictional data protection regulations. By providing a solution to emerging challenges around secure and efficient management of human “omics” and associated data, the Federated EGA fosters data reuse, enables reproducibility, and accelerates biomedical research.

Products Used
Beacon, Genetic Data Encryption (Crypt4GH), Data Use Ontology (DUO), htsget, refget, Passports
Implementing Organisation
ENA / EVA / EGA, EMBL's European Bioinformatics Institute (EBI), Centre for Genomic Regulation

Funnel

Funnel is a toolkit for distributed task execution via a simple, standard API.

Products Used
Task Execution Service (TES)
Implementing Organisation
Oregon Health & Science University

GA4GH TES on Azure

This implementation of the GA4GH TES API provides distributed batch task execution on Microsoft Azure.

Products Used
Task Execution Service (TES)
Implementing Organisation
Microsoft

Genomics England Research Environment

The secure Research Environment provides approved researchers with a range of open source tools, shared storage drives, databases, and research platforms linking genomic data to a rich set of clinical, phenotypic, and longitudinal data.

Products Used
CRAM, htsget
Implementing Organisation
Genomics England

GTEx RNAget

This is an implementation of GA4GH’s RNAget API for the Genotype Tissue Expression Project (GTEx).

Products Used
RNAget
Implementing Organisation
Broad Institute of MIT and Harvard

H3ABionet

H3ABioNet is a pan-African bioinformatics network for the Human Heredity and Health in Africa (H3Africa) consortium.

Products Used
Beacon, Data Use Ontology (DUO), CRAM, Genetic Data Encryption (Crypt4GH)
Implementing Organisation
Human Heredity and Health in Africa (H3Africa)

Human Cell Atlas (HCA) Data Portal

The HCA Data Portal stores and provides single-cell data contributed by labs around the world. Anyone can contribute data, find data, or access community tools and applications.

Products Used
Task Execution Service (TES), Tool Registry Service (TRS), Workflow Execution Service (WES), Data Repository Service (DRS), Authorisation and Authentication Infrastructure (AAI), Data Use Ontology (DUO)
Implementing Organisation
Human Cell Atlas

Life Science AAI

The Life Science Login enables researchers to use their home organisation credentials or community or other identities (e.g. Google, Linkedin, LS ID) to sign in and access data and services they need. It also allows service providers (both in academia and industry) to control and manage access rights of their users and create different access levels for research groups or international projects.

Products Used
Authorisation and Authentication Infrastructure (AAI), Passports
Implementing Organisation
ELIXIR, ELIXIR Cloud and AAI

Medical Genomics Japan Variant Database (MGeND)

Medical Genomics Japan Variant Database (MGeND) aims to provide integrated information about genomic variations and clinical characteristics, and improve clinical interpretation by cross-sectional studies on cancer, rare/intractable disease, infectious disease, dementia, and hearing loss. This database contains genetic variations and their frequencies with supporting evidence and clinical information that have been provided from research institutions and cooperating hospitals, which were selected for the Integrated Database of Clinical and Genomic Information programme supported by the Japan Agency for Medical Research and Development (AMED).

Products Used
CRAM, Data Use Ontology (DUO)
Implementing Organisation
Japan Agency for Medical Research and Development (AMED)

MSSNG Genetics Application System

MSSNG (pronounced “missing”) is a groundbreaking collaboration between Autism Speaks, Verily, DNAstack, Hospital for Sick Children (SickKids), and the research community to create the world’s largest whole-genome-sequencing database on autism with deep phenotyping.

Products Used
Service Registry, Data Connect
Implementing Organisation
Autism Speaks, Autism Sharing Initiative

National Genomic Information System (NGIS)

NGIS provides systems to enable the full end-to-end path from test ordering to interpretation and reporting for the whole-genome-sequencing component of the Genomic Medicine Service for England.

Products Used
CRAM, htsget
Implementing Organisation
Genomics England

NCI Data Commons Framework

The vision of the Data Commons Framework is to make it easier to develop, operate, and interoperate data commons, data clouds, knowledge-bases, and other resources for managing, analysing, and sharing research data that can be part of a large data commons ecosystem.

Products Used
Data Repository Service (DRS)
Implementing Organisation
NIH National Cancer Institute (NCI)

NHLBI TOPMed BioData Catalyst

This is a full implementation of the DRS v1.1 standard with support for persistent identifiers. The open-source DRS server follows the Gen3 implementation. Gen3 is a GA4GH-compliant, open-source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org

Products Used
Tool Registry Service (TRS), Workflow Execution Service (WES), Data Use Ontology (DUO), CRAM, Data Repository Service (DRS)
Implementing Organisation
Trans-Omics for Precision Medicine (TOPMed)

TESK

This is an implementation of a task execution engine based on the TES standard, running on Kubernetes.

Products Used
Task Execution Service (TES)
Implementing Organisation
ELIXIR, ELIXIR Cloud and AAI

The Exomiser

The Exomiser is a Java program that functionally annotates variants from whole-exome-sequencing data in VCF v4.0 format. The functional annotation is performed with Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates.

Products Used
Phenopackets, Variation Representation (VRS)
Implementing Organisation
Monarch Initiative

TogoVar

TogoVar is a comprehensive Japanese genetic variation database that has collected and organised genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.

Products Used
Data Use Ontology (DUO), CRAM
Implementing Organisation
GEnome Medical alliance Japan (GEM Japan)

Tohoku Medical Megabank Project (ToMMo)

The project conducts a long-term health study of 150,000 residents living in communities which suffered major damage from the Great East Japan Earthquake and reports the findings to the respective residents with their personal information. It also establishes a system of dispatching physicians on a rotation basis to healthcare providers in the region.

Products Used
Data Use Ontology (DUO), CRAM
Implementing Organisation
Japan Agency for Medical Research and Development (AMED)

Variant Interpretation for Cancer Consortium (VICC) Meta-Knowledgebase (v1)

This search interface for cancer variant interpretations is assembled by aggregating and harmonising across multiple cancer variant interpretation knowledge-bases.

Products Used
Beacon, Variation Representation (VRS), Service Info, Service Registry
Implementing Organisation
Variant Interpretation for Cancer Consortium (VICC)

See also

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