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Engagement through specimen and sequencing tracking portals

Specimen & sequencing portals

National Institute of Mental Health

Award #


CUBIE Specimen

Award PIs

Guo-Qiang Zhang, University of Texas Health Science Center
Hua Xu, University of Texas Health Science Center
Wenjin Jim Zheng, University of Texas Health Science Center

Project Description

As a part of BRAIN 2.0, the BRAIN Initiative Cell Atlas Network (BICAN) is expected to advance fundamental knowledge and enabling technology for classifying human brain cell types, understanding their organizational principles, and providing open-access digital brain cell reference atlases, emphasizing cell diversity in health and disease. Undertaking the grand challenge of BRAIN 2.0 requires the scientific community to collaborate and tap the tremendous skill and knowledge in a diverse set of disciplines outside of neuroscience. BICAN's Coordinating Unit for Biostatistics, Informatics, and Engagement (CUBIE) is designed to provide effective coordination benefits to the awardee network, the NIH, and the scientific community. Advancing the ambitious BICAN goals requires CUBIE to anticipate and address potential challenges in coordinating time-sensitive management activities, mitigating data complexity and tool scalability, and supporting diverse service needs. Our team is highly experienced in leading large consortia projects at national scale and we have the knowledge, skill set, and resources to launch the Engagement and Outreach element for CUBIE (CUBIE4) and work with the BICAN network in taming the structural and organizational complexity of data and driving a FAIR (Findable, Accessible, Interoperable, Reusable) data ecosystem through three specific components. The Specimen Portal is the most upstream system for BICAN which uses a common-data-modeled database to systematically link BICAN tissue resources prospectively to set the stage for achieving anatomical precision using CCFs longer term. The Specimen Portal will facilitate an environment which supports various activities regarding BICAN human specimens. It provides functionality for data capturing, dashboarding, linking to external data archives, specimen exploration, and specimen requesting and tracking. The Sequence Tracking Portal will serve as a nexus linking the data generation pipeline from tissue preparation by investigators to processing by sequencing centers and deposition of fastq files to NeMO. This will be a highly coordinated and collaborative effort that will facilitate sequencing data and metadata management for a variety of stakeholders. The data model and ontology component will engage the BICAN research network to standardize library metadata and extract common LIMS data models, as well as serving as a bridge to link BICAN terminology resources to external ontologies in general. We contribute to diversity in multidisciplinary knowledge, women and early-career investigators, neurological diseases and brain health perspectives, and institutional inclusivity resources. Therefore, the CUBIE4 team is uniquely well-positioned to advance the overarching goals of BICAN.

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