scholarly journals Marking 15 years of the Genetic and Rare Diseases Information Center

2017 ◽  
Vol 2 (1-2) ◽  
pp. 77-88 ◽  
Author(s):  
Janine Lewis ◽  
Michelle Snyder ◽  
Henrietta Hyatt-Knorr
Keyword(s):  
Rare Diseases ◽  
Information Center

scholarly journals An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD)

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Qian Zhu ◽  
Dac-Trung Nguyen ◽  
Ivan Grishagin ◽  
Noel Southall ◽  
Eric Sid ◽  
...  
Keyword(s):  
Health Information ◽  
Rare Diseases ◽  
Consumer Health Information ◽  
Scientific Understanding ◽  
Knowledge Graph ◽  
Biomedical Data ◽  
Translational Science ◽  
Consumer Health ◽  
Disease Characteristics ◽  
Information Center

Abstract Background The Genetic and Rare Diseases (GARD) Information Center was established by the National Institutes of Health (NIH) to provide freely accessible consumer health information on over 6500 genetic and rare diseases. As the cumulative scientific understanding and underlying evidence for these diseases have expanded over time, existing practices to generate knowledge from these publications and resources have not been able to keep pace. Through determining the applicability of computational approaches to enhance or replace manual curation tasks, we aim to both improve the sustainability and relevance of consumer health information, but also to develop a foundational database, from which translational science researchers may start to unravel disease characteristics that are vital to the research process. Results We developed a meta-ontology based integrative knowledge graph for rare diseases in Neo4j. This integrative knowledge graph includes a total of 3,819,623 nodes and 84,223,681 relations from 34 different biomedical data resources, including curated drug and rare disease associations. Semi-automatic mappings were generated for 2154 unique FDA orphan designations to 776 unique GARD diseases, and 3322 unique FDA designated drugs to UNII, as well as 180,363 associations between drug and indication from Inxight Drugs, which were integrated into the knowledge graph. We conducted four case studies to demonstrate the capabilities of this integrative knowledge graph in accelerating the curation of scientific understanding on rare diseases through the generation of disease mappings/profiles and pathogenesis associations. Conclusions By integrating well-established database resources, we developed an integrative knowledge graph containing a large volume of biomedical and research data. Demonstration of several immediate use cases and limitations of this process reveal both the potential feasibility and barriers of utilizing graph-based resources and approaches to support their use by providers of consumer health information, such as GARD, that may struggle with the needs of maintaining knowledge reliant on an evolving and growing evidence-base. Finally, the successful integration of these datasets into a freely accessible knowledge graph highlights an opportunity to take a translational science view on the field of rare diseases by enabling researchers to identify disease characteristics, which may play a role in the translation of discover across different research domains.

The Collaborative Network Approach: a model for advancing patient-centric research for Castleman disease and other rare diseases

2019 ◽  
Vol 3 (1) ◽  
pp. 97-105
Author(s):  
Mary Zuccato ◽  
Dustin Shilling ◽  
David C. Fajgenbaum
Keyword(s):  
Rare Diseases ◽  
Treatment Options ◽  
Castleman Disease ◽  
High Impact ◽  
Collaborative Network ◽  
Network Approach ◽  
Grant Applications ◽  
Research Questions ◽  
Novel Strategy ◽  
Patient Centric

Abstract There are ∼7000 rare diseases affecting 30 000 000 individuals in the U.S.A. 95% of these rare diseases do not have a single Food and Drug Administration-approved therapy. Relatively, limited progress has been made to develop new or repurpose existing therapies for these disorders, in part because traditional funding models are not as effective when applied to rare diseases. Due to the suboptimal research infrastructure and treatment options for Castleman disease, the Castleman Disease Collaborative Network (CDCN), founded in 2012, spearheaded a novel strategy for advancing biomedical research, the ‘Collaborative Network Approach’. At its heart, the Collaborative Network Approach leverages and integrates the entire community of stakeholders — patients, physicians and researchers — to identify and prioritize high-impact research questions. It then recruits the most qualified researchers to conduct these studies. In parallel, patients are empowered to fight back by supporting research through fundraising and providing their biospecimens and clinical data. This approach democratizes research, allowing the entire community to identify the most clinically relevant and pressing questions; any idea can be translated into a study rather than limiting research to the ideas proposed by researchers in grant applications. Preliminary results from the CDCN and other organizations that have followed its Collaborative Network Approach suggest that this model is generalizable across rare diseases.

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