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Workflows and tools for phenomic and multi-omics analysis, integration, and sharing, aiding in diagnostic
acceleration, were also further developed [28-31] and are being connected to the VP. Additionally, resources for
systems biology research on rare diseases have been updated and expanded. This approach mitigates the
challenge of limited RD patient and sample numbers for data analysis by incorporating prior knowledge
from known molecular interactions and annotated multi-omics data. Various methods have been developed
for hypothesis generation relating to diagnostics, drug repurposing, and identifying potential toxic
interactions in rare diseases [32-34] . In collaboration with the ELIXIR rare disease community, a
comprehensive systems biology service bundle was created, including guides and tutorials on tools and
methods for systems biology in rare diseases .
[35]

Looking ahead, the VP will expand to include new resources that address the ongoing and emerging needs
of rare disease research.

Training and empowerment
A significant impact on the RD landscape was achieved through EJP RD support activities, which primarily
[37]
[36]
include training and project mentoring . Stakeholders from widening countries have shown active
participation in these initiatives. In data management and quality training, they represented 12% to 50% of
the attendees . Moreover, research mobility fellowships and ERN Research training workshops
[40]
[39]
[38]
beneficiaries from these countries constituted 20% and 10%, respectively . The Massive Open Online
[38]
Course (MOOC) on “Diagnosing Rare Diseases” has drawn over 5,800 participants from 150 countries since
April 2021, illustrating EJP RD’s extensive global influence beyond the EU .
[41]
The programme has also been instrumental in accompanying researchers by providing highly specialised
knowledge. In 2020, 15 projects from 8 countries benefited from EJP RD mentoring services (confidential
EJP RD deliverable No 19.1). From 2021 to 2022, this expanded to include a total of 32 projects with
Principal Investigators from 12 countries (confidential EJP RD deliverable No 19.2). Mentoring support is
essential to accelerate the translation of research results as it empowers researchers with expertise on
regulatory, biostatistical, or business development aspects that are key to increasing the success rate of the
uptake and follow-on funding. Furthermore, EJP RD implemented the “train the trainers” concept on an
international scale, standardizing and disseminating high-quality education programmes. An example of
this was the training dedicated to Orphanet nomenclature and RD ontologies, which was adapted in five
[42]
different countries . The EJP RD training and capacity-building activities helped promote interdisciplinary
collaboration among scientists, clinicians, and patient representatives, further enhancing the EJP RD's
impact on the RD research field.

EXPANDING BEYOND EJP RD
Avoiding duplication and optimizing resource use in synergy with other initiatives has been a cornerstone
of the EJP RD. The sustained collaboration with the European Rare Disease Research Coordination and
Support Action consortium (ERICA) has bolstered RD research with ERNs, focusing on patient registries,
biobanking, translational research, and clinical trials. The EJP RD plays a pivotal role in the Global Alliance
for Genomics and Health (GA4GH), driving the development of standards, products, and policies for
genomic data sharing and interoperability . Particularly, EJP RD's contributions to data processing
[43]
through its RD use-case have been instrumental in contributing to the establishment of the federated
ecosystem for genomic data in Europe, as part of the 1 + Million Genomes (1 + MG) initiative .
[44]

In collaboration with the Critical Path Institute, EJP RD is advancing data standards and ontologies,
mapping and transforming data, and developing semantic models for rare diseases [45,46] . Additionally,