The Arthritis, Autoimmune and Related Knowledge (ARK) Portal

Le résumé fourni par la source

Rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are relatively common, severe autoimmune disorders that can last a lifetime, cause severe disability, greatly affect quality of life, and are associated with increased risk of death. The Arthritis and Autoimmune-Related Diseases Knowledge (ARK) Portal was created to publicly disseminate data from the Accelerating Medicines Partnership (AMP) RA/SLE program which used novel technologies to deconstruct and analyze gene expression and signaling in subsets of immune and resident tissue cells across cohorts of RA, SLE, and healthy subjects. Starting with ~50 TB of uncurated, structured and unstructured data, Sage Bionetworks has collaborated with AMP RA/SLE to develop a flexible and comprehensive model of metadata standards that accommodates a broad range of data types, including epigenomic, transcriptomic, proteomic, imaging, cytometry, and clinical data. These standards facilitate the discovery and reuse of AMP RA/SLE data by diverse communities of researchers through faceted data queries and data summarizations. Development of this data model encountered many of the common challenges facing similar biomedical metadata standards efforts, including challenges specific to multimodal single-cell, spatial transcriptomics, and imaging data types. Our model design also includes mappings to standards currently in development for the AMP Autoimmune and Immune-Mediated Diseases (AMP AIM) program, a successor of AMP RA/SLE, which will host data on the ARK Portal. Future ARK Portal work includes creating a structured AMP RA/SLE publications database and implementing natural language processing and large language model-based pipelines to extract key findings, experimental details, and major scientific impacts from these papers. This database will be an annotated knowledge layer that directly links impactful research findings to the underlying data hosted in the portal and is an important step towards creating a significant resource for the autoimmune research community supported by state-of-the-art biocuration and annotation efforts.

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