The SPARC DRC: Building a resource for the autonomic nervous system community

Osanlouy, Mahyar; Bandrowski, Anita; Bono, Bernard de; Brooks, David J.; Cassarà, Antonio M.; Christie, Richard; Ebrahimi, Nazanin; Gillespie, Tom; Grethe, Jeffrey S.; Guercio, Leonardo A.; Heal, Maci; Lin, Mabelle; Kuster, Niels; Martone, Maryann E.; Neufeld, Esra; Nickerson, David; Soltani, Elias G.; Tappan, Susan; Wagenaar, Joost B.; Zhuang, Katie Z.; Hunter, Peter

doi:10.1101/2021.04.01.438136

Cited by 8 publications

(19 citation statements)

References 26 publications

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“…These resources include the Pennsieve API 13 , the Scicrunch Elasticsearch API 14 , the protocols.io API 15 , and the Biolucida API 16 . We refer to the paper on the SPARC Data Resource Center (DRC) for more details about these resources and their role in the SPARC data ecosystem 6 . Details about each of the visualization items are provided below.…”

Section: Data Processing and Outputsmentioning

confidence: 99%

“…To ensure SPARC datasets are Findable, Accessible, Interoperable, and Reusable (FAIR), they are curated according to the SPARC Data Structure (SDS), the data standards designed by the SPARC Data Curation Team to capture the large variety of data generated by SPARC investigators 3,4 . Accordingly, many resources are made available to SPARC researchers for making their data FAIR 5,6 . As a result, the SPARC program provides a wealth of open and well-curated datasets that are accessible via the SPARC Data Portal.…”

Section: Introductionmentioning

confidence: 99%

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KnowMore: an automated knowledge discovery tool for the FAIR SPARC datasets

Quey¹,

Schiefer

Kiran

et al. 2021

Preprint

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This manuscript provides the methods and outcomes of KnowMore, the Grand Prize winning automated knowledge discovery tool developed by our team during the 2021 NIH SPARC FAIR Data Codeathon. The NIH SPARC program generates rich datasets from neuromodulation researches, curated according to the Findable, Accessible, Interoperable, and Reusable (FAIR) SPARC data standards. These datasets are publicly available through the SPARC Data Portal at sparc.science. Currently, the process of simultaneously comparing and analyzing multiple SPARC datasets is tedious because it requires investigating each dataset of interest individually and downloading all of them to conduct cross-analyses. It is crucial to enhance this process to enable rapid discoveries across SPARC datasets. To fill this need, we created KnowMore, a tool integrated into the SPARC Portal that only requires the user to select their datasets of interest to launch an automated discovery process. KnowMore uses several SPARC resources (Pennsieve, o2S2PARC, SciCrunch, protocols.io, Biolucida), data science methods, and Machine Learning algorithms in the back end to generate various visualizations in the front end intended to help the user identify potential similarities, differences, and relations across the datasets. These visualizations can lead to a new discovery, new hypothesis, or simply guide the user to the next logical step in their discovery process. The outcome of this project is a SPARC portal-ready code architecture that helps researchers to use SPARC datasets more efficiently and fully leverages their FAIR characteristics. The tool has been built and documented such that more data analysis methods and visualization items could be easily added. The potential for automated discoveries from SPARC datasets is huge given the unique SPARC data ecosystem promoting FAIR data practices, and KnowMore has only demonstrated a small highlight of what could be achieved to speed up discoveries from SPARC datasets.

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Section: Data Processing and Outputsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

KnowMore: an automated knowledge discovery tool for the FAIR SPARC datasets

Quey¹,

Schiefer

Kiran

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…All SPARC datasets are curated by the researchers according to the SPARC Data Standards (SDS), a data and metadata structure derived from the Brain Imaging Data Structure (BIDS) (4). Several resources are made available to SPARC researchers for making their data FAIR, such as the cloud data platform Pennsieve, the curated vocabulary selector and annotation platform SciCrunch, the open-source computational modeling platform o²S²PARC, the online microscopy image viewer Biolucida, and the data curation software SODA (4)(5)(6). The datasets submitted by researchers also follow an extensive curation process where teams from the SPARC Data Resource Center (DRC) examine the submitted data and work with the researchers to ensure all aspects of the FAIR data principles are being followed (4,6,7).…”

Section: Introductionmentioning

confidence: 99%

SPARClink: an interactive tool to visualize the impact of the SPARC program

Soundarajan

Kuruppu

Singh

et al. 2021

Preprint

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The NIH SPARC program seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. SPARC-funded researchers are generating rich datasets from neuromodulation research that are curated and shared according to FAIR (Findable, Accessible, Interoperable, and Reusable) guidelines and are accessible to the public on the SPARC data portal. Keeping track of the utilization of these datasets within the larger research community is a feature that will benefit data generating researchers in showcasing the impact of their SPARC outcomes. This will also allow the SPARC program to display the impact of the FAIR data curation and sharing practices that have been implemented. This manuscript provides the methods and outcomes of SPARClink, our web tool for visualizing the impact of SPARC, which won the 2nd prize at the 2021 SPARC FAIR Codeathon. With SPARClink, we built a system that automatically and continuously finds new published SPARC scientific outputs (datasets, publications, protocols) and the external resources referring to them. SPARC datasets and protocols are queried using publicly accessible REST APIs (provided by Pennsieve and Protocols.io) and stored in a publicly accessible database. Citation information for these resources is retrieved using the NIH reporter API and NCBI Entrez system. A novel knowledge-graph-based structure was created to visualize the results of these queries and showcase the impact that the FAIR data principles can have on the research landscape when they are adopted by a consortium.

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“…The authors would like to gratefully acknowledge all of their SPARC colleagues for their contributions to the SPARC DRC program, including the SPARC experimental groups and the SPARC NIH program officers, all of whom have contributed to the work presented here. We would also like to acknowledge BioRxiv for hosting a preprint of this manuscript (Osanlouy et al, 2021 ), and we thank Frontiers for its supportive preprint policy.…”

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confidence: 99%

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

et al. 2021

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The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons. We discuss examples that illustrate the data pipeline, which includes data upload, curation, segmentation (for image data), registration against the flatmaps and scaffolds, and finally display via the web portal, including the link to freely available online computational facilities that will enable neuromodulation hypotheses to be investigated by the autonomic neuroscience community and device manufacturers.

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The SPARC DRC: Building a resource for the autonomic nervous system community

Cited by 8 publications

References 26 publications

KnowMore: an automated knowledge discovery tool for the FAIR SPARC datasets

KnowMore: an automated knowledge discovery tool for the FAIR SPARC datasets

SPARClink: an interactive tool to visualize the impact of the SPARC program

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

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