How to onboard to Level 2 using the VP-API Specification
Transitioning to Level 2 involves seamlessly integrating resources with the EJP RD VP API Specification, a gateway to further unlock the capabilities of the Virtual Platform. This integration is facilitated by a suite of optional tools that pave the way for a comprehensive resource discovery experience. We offer five solutions for onboarding, which are described in the following sections. Figure 7 depicts the steps of the Level 2 onboarding process.
Figure 7 – Level 2 onboarding process overview
Level 2 onboarding solutions
Solution |
Description |
Capabilities |
Licensing |
Support Offered |
Supports Level 1? |
Supports Level 2? |
|---|---|---|---|---|---|---|
RD-Nexus is a convenient data discovery tool that adapts to many use cases and diverse datatypes. It utilises graph-based technologies to leverage semantic similarity and ontology mapping standards and is compatible with any input data format. Compliant with all major RD standards. |
API support for Any/All EJP RD Beacon v2 queries; Storage and Query of Metadata; Storage and Query of safe (or rich) demographic, sample, phenotypic and other data (omics, tabular, images); Ingest/Use any data format; Real-time query execution; Powerful similarity searching (phenotypes and disease); Enforce ontologies or controlled vocabularies; Dockerised & Non-Dockerised Install options; Inbuilt modular query & admin interfaces; Supports federated AuthN/AuthZ (inc LS AAI); Secure operation across firewall (via polling); Create/Manage secure custom networks. |
RD-Nexus is free to use under the MIT License. |
Yes: Installation and hosting support. Demo and customisation support. Guidance on setting up private networks. |
Yes |
Yes |
|
MOLGENIS (MOLecular GENetics Information Systems), is an open-source platform designed for managing and analyzing complex biomedical and genetic data. It supports the creation of RD registries, including discovery functions. |
Supports EJP RD Beacon v2 queries; Structured Data Management; FAIR data sharing; secure access; Scripting & visualisation; Harmonization and integration; Task automation; High-performance computing. |
MOLGENIS is free to use under LGPLv3 License. |
Yes. Helpdesk available for any developer or user questions. Additional services offered for hosted installations and backups at a low fee. |
Yes |
Yes |
|
Specialised version of the GA4GH Beacon adapted to enable easy setup of EJP-RD Level-2 services. |
Beacon deployment for /catalogs & /individuals endpoint; Docker & Docker-less deployment. |
Beacon is free to use under the Apache License 2.0. |
Yes |
No |
No |
|
FAIR-in-a-Box software enables the setup of a local Fair Data Point that holds your data in an accessible triple-store, with EJP RD Beacon v2 services. |
Supports EJP RD Beacon v2 queries for both the /catalogs & /individuals endpoints; Dockerized installation. |
FAIR-in-a-box is free to use; individual components have distinct licenses selected by their (third-party) authors. |
Yes |
Yes |
Yes |
|
A custom solution can be created by any developer comfortable with Python/Flask or similar backend technologies (support and guidance on this is available). |
|
Licensing will depend on the technologies chosen for your custom solution. |
No |