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. 2023 Jun 1;39(6):btad368.
doi: 10.1093/bioinformatics/btad368.

The NanoFlow Repository

Jessie E Arce  1 , Joshua A Welsh  2 , Sean Cook  2 , John Tigges  3 , Ionita Ghiran  3 , Jennifer C Jones  2 , Andrew Jackson  1 , Matthew Roth  1 , Aleksandar Milosavljevic  1
Affiliations

The NanoFlow Repository

Jessie E Arce et al. Bioinformatics. .

Abstract

Motivation: Extracellular particles (EPs) are the focus of a rapidly growing area of exploration due to the widespread interest in understanding their roles in health and disease. However, despite the general need for EP data sharing and established community standards for data reporting, no standard repository for EP flow cytometry data captures rigor and minimum reporting standards such as those defined by MIFlowCyt-EV (https://doi.org/10.1080/20013078.2020.1713526). We sought to address this unmet need by developing the NanoFlow Repository.

Results: We have developed The NanoFlow Repository to provide the first implementation of the MIFlowCyt-EV framework.

Availability and implementation: The NanoFlow Repository is freely available and accessible online at https://genboree.org/nano-ui/. Public datasets can be explored and downloaded at https://genboree.org/nano-ui/ld/datasets. The NanoFlow Repository's backend is built using the Genboree software stack that powers the ClinGen Resource, specifically the Linked Data Hub (LDH), a REST API framework written in Node.js, developed initially to aggregate data within ClinGen (https://ldh.clinicalgenome.org/ldh/ui/about). NanoFlow's LDH (NanoAPI) is available at https://genboree.org/nano-api/srvc. NanoAPI is supported by a Node.js Genboree authentication and authorization service (GbAuth), a graph database called ArangoDB, and an Apache Pulsar message queue (NanoMQ) to manage data inflows into NanoAPI. The website for NanoFlow Repository is built with Vue.js and Node.js (NanoUI) and supports all major browsers.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
The data submission steps. Scientists can easily share and publish their nanoparticle datasets in simple steps. The data submitter, the user, creates a team. Acting on behalf of the team, the user made a resource that can have multiple datasets uploaded to it. A dataset comprises one or many FCS files generated from the same flow cytometer. File metadata is extracted, validated, transformed, and saved to the NanoFlow database.
Figure 2.
Figure 2.
The graph entity data model. Each rounded rectangle represents a type of entity, e.g. Team, DataSet, or Sample; each entity is assigned the following roles: subject and linked data. Arrows represent edges that link entities to one another. The model is based on LDH’s subject and linked data entity roles to model data sources. Subject entities are related to linked data entities. For example, an entity of the type Team is a subject entity with user-linked data entities (members). Whereas an entity of the type DataSet is both a subject and linked data entity such that it is a linked data entity to a Team entity (the owners of the dataset) but a subject entity to a SampleSource entity.
Figure 3.
Figure 3.
User interface listing publicly available NanoFlow datasets.
See this image and copyright information in PMC

References

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