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uc-0007: Compiling datasets of movement related disorders

Completion Date: ✅ September 2020

Tutorial walkthrough of this use case

NIH Goal:

Enhance the ability to ask scientific questions across data sets


p-001: Clinical Researcher


obj-0001: Multi DCC Comparison


Movement-related disorders affect the neuromuscular system, disrupting the ability of the nervous and muscular systems to work together. There are several known movement-related disorders, including Amyotrophic Lateral Sclerosis (ALS) or Lou Gehrig’s disease, Parkinson's disease, Spinal Muscular Atrophy (SMA) and Multiple Sclerosis (MS). A few common features of these neuromuscular disorders are that they all involve the brain, share many symptoms, and are all difficult to diagnose in their early stages. Natasha is interested in scanning what data already exists that may help in identifying key genomic, transcriptomic and/or proteomic differences between these conditions along with potential biomarkers that may aide in early diagnosis and/or targeted drug development.

Natasha navigates to the CFDE portal, and searches by collection. They start by searching all columns for "IPSC" (induced pluripotent stem cell) lines, which gives a manageable 19 records. Natasha browses the descriptions for the these results, and the uses the "Part of Collection" filter to select only the 9 that best fit their plan. Natasha exports this list of desirable data sets to save.

Natasha then decides that they would also like to include neural stem cells in their experimental design. They click 'clear all filters' and then repeat their search with "stem cell neu", and export that list as well. Since the CFDE portal uses a single standardized export format, Natasha easily combines the two exported files into a single cohort with datasets from LINCS and Metabolomics. Natasha can then use the persistent_id to go actually obtain the data files (or request access to them) at their parent portal.

Tasks for this use case:

Requirements for this use case: