Technical Implementation
The services, standards and public endpoints that make up the Irish node of the European Genomic Data Infrastructure.
The node is built on the Genomic Data Infrastructure starter kit and GA4GH standards. Together its services let a researcher discover a dataset, sign in with their home institution, apply for access, and retrieve or stream encrypted data, while metadata is published in a form the wider European infrastructure can harvest.
A FAIR Data Point publishes DCAT-AP metadata using the GDI profile, for the GDI User Portal to harvest into its searchable catalogue. Two Beacon v2 services answer variant queries: one for aggregate allele frequencies, one for a subject-level cohort.
Keycloak provides sign-in by brokering to Life Science AAI, so users authenticate at their own institution. REMS manages data-access applications and records approved entitlements as GA4GH visas.
The Sensitive Data Archive stores files encrypted with Crypt4GH. Approved users retrieve whole files through the download API, or a single genomic region through htsget, re-encrypted to their own key.
A GA4GH Task Execution Service is deployed to run analysis next to the data. It is not open for public job submission until it runs on isolated compute with authentication.
These endpoints form the current test stack, used to validate the infrastructure end to end. It holds synthetic and openly available reference data only, and no sensitive or identifiable personal data. The GDI project combines node components, which each national node deploys and operates for its own data, with central components, which serve all nodes.
Deployed and operated by GDI Ireland. These services hold and serve the node's data, and each of them will be redeployed in the staging and production environments.
| Service | Endpoint | Standard | Access |
|---|---|---|---|
| Discovery and metadata | |||
| FAIR Data Point | fdp-gdi.ul.ie | DCAT-AP, HealthDCAT-AP | Open |
| Allele Frequency Beacon | beacon.ul.ie/af API beacon.ul.ie/af/api | GA4GH Beacon v2 | Open |
| Subject-level Beacon | beacon.ul.ie API beacon.ul.ie/api | GA4GH Beacon v2 | Open, counts only |
| Identity and access | |||
| Identity provider | beacon.ul.ie/auth | OpenID Connect, Life Science AAI | Open |
| Access management | daam.genomicdata.ie | REMS, GA4GH Passports | Sign-in |
| Storage and retrieval | |||
| Data download | https://download.genomicdata.ie |
Sensitive Data Archive, Crypt4GH | Token |
| Region streaming | https://htsget.genomicdata.ie |
GA4GH htsget | Token |
| Upload inbox | https://inbox.genomicdata.ie |
S3 API, Crypt4GH | Token |
| Compute | |||
| Task execution | https://funnel.genomicdata.ie |
GA4GH TES | Closed |
Central components serve the whole GDI infrastructure rather than a single node. A copy of the User Portal is included in this test stack to understand how it works and to support the node's technical documentation. It will not be part of staging or production, where the node instead publishes its metadata to the central GDI User Portal, connects its Beacons to the Beacon Network, and signs users in through Life Science AAI.
| Service | Endpoint | Standard | Access |
|---|---|---|---|
| User Portal | |||
| Portal | portal.genomicdata.ie | GDI User Portal | Open |
| Catalogue | catalogue.genomicdata.ie | CKAN, harvesting the FAIR Data Point | Open |
| API gateway | https://api.genomicdata.ie |
Dataset discovery API | Open |
Addresses shown in monospace are API base URLs for clients and scripts rather than pages to open in a browser.
A secure deployment of the staging environment is underway at the University of Limerick. It will run the node components of the test stack and connect to the central GDI services for the catalogue, the Beacon Network and sign-in. It will be available soon.
Staging endpoints will be listed on this page once the environment is open.
