NIMP: Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation (RRID:SCR_024684)
NIMP is developed under NIH BRAIN Initiative's BICAN U24MH130988 award as a part of the coordinating unit for biostatistics, informatics, and engagement (CUBIE) for the BRAIN Initiative Cell Atlas Network (BICAN) program.
NIMP consists of two portals for BICAN collaborative data generation: the Specimen Portal and the Sequence Library (SeqLib) Portal. The Specimen Portal focuses on tissue management from donors to brain slabs and annotated brain samples. The SeqLib Portal manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent, data-modality-specific archives. Both portals work in tandem to generate multimodal genomic data that can be traced back to their anatomical origins using the Allen Brain Atlas.
The portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. All of the underlying functionalities are achieved through a robust agile development strategy using NHash resource identifiers, metadata standardization, active combinatorial dashboarding, resource provenance linkage and rendering (e.g. Sankey diagrams), and dedicated interfaces with NIH Neuro Biobank, sequencing centers, NeMO, and the larger BICAN data ecosystem.
Frequently Asked Questions
Please click the “Sign-up” button on the top-right of the landing page to start the sign-up process.
To request a specific user role such as Brain Bank Personnel or Library Submitter, you need to indicate this in the "Message" text box on the sign-up page. If you have already signed up, please email Shiqiang Tao ([email protected]) what user role you need.
Contact the user who is the manager of the Lab in the portal to have you added to the Lab.
The User Guide contain a glossary of terms describing the meanings of the terms used in the portal.
Yes, the portal has an API for data access. More information can be found in the Swagger page and the User Guide.
Refer the User Guide for detailed information. If you still have questions, email Rashmie Abeysinghe ([email protected])
Data Ecosystem Upstream Components (Blue Diagram)
The upstream BICAN data ecosystem workflow diagram shows how Specimen Portal facilitates data transfer across different ecosystem components.
Sequencing Library Workflow (Purple Diagram)
The sequencing library workflow diagram shows the detailed dataflow from Specimen Portal to Sequencing Portal, then to Seq Core and NeMO.
Resource Provenance Tracking (Sankey Diagram)
The BICAN resource-provenance visualization engine uses NHash identifier to identify, link, and track BICAN resource items from their source-point inception all the way to output data files. It uses the Sankey rendering library to visualize flow from donor ancestors to library aliquot descendants, through tissue region of interests (ROIs) as the intermediary, from any ancestor to any descendant and vice versa. It provides seamless linkage from resources in the Specimen Portal to those in the Sequencing Library Portal, whereby integrates the functional components of NIMP.
API Specification
The NIMP API suite, following the RESTful structure, allows users and systems to lookup various structured data, slab images, and annotations with API lookup calls. All BICAN resource types with NHash identifiers can be looked-up and retrieved using APIs, including, but not limited to: donor, slab, ROI, library, library pool, library aliquot, as well as all data elements (variable names) used in the implementation of NIMP (and mapped to other standardized codes and terms).
API Documentation