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

Osanlouy, Mahyar; Bandrowski, Anita; Bono, Bernard de; Brooks, David J.; Cassarà, Antonino 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:10.3389/fphys.2021.693735

Cited by 38 publications

(28 citation statements)

References 31 publications

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“…The degree to which these spatially distributed regions of heterogeneous action potential and conduction velocity can contribute to providing suitable arrhythmogenic substrates can only be fully realised by upscaling the modelling and simulation efforts of β-ARS to multiscale whole-ventricular, whole-atria, or whole-organ levels. In particular, the resources provided by the "Stimulating Peripheral Activity to Relieve Conditions" (SPARC) programme, including tools and curated and annotated high-resolution datasets in different species for investigations on autonomic nervous stimulation (Figure 4), may prove fundamental in understanding the role of a heterogeneous innervation in heart function [105]. However, there is a lack of computational studies to date implementing β-ARS models in 3D geometries.…”

Section: β-Ars and 3d Modellingmentioning

confidence: 99%

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Multiscale Modelling of β-Adrenergic Stimulation in Cardiac Electromechanical Function

Doste

Bueno‐Orovio

2021

Mathematics

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β-adrenergic receptor stimulation (β-ARS) is a physiological mechanism that regulates cardiovascular function under stress conditions or physical exercise. Triggered during the so-called “fight-or-flight” response, the activation of the β-adrenergic receptors located on the cardiomyocyte membrane initiates a phosphorylation cascade of multiple ion channel targets that regulate both cellular excitability and recovery and of different proteins involved in intracellular calcium handling. As a result, β-ARS impacts both the electrophysiological and the mechanical response of the cardiomyocyte. β-ARS also plays a crucial role in several cardiac pathologies, greatly modifying cardiac output and potentially causing arrhythmogenic events. Mathematical patient-specific models are nowadays envisioned as an important tool for the personalised study of cardiac disease, the design of tailored treatments, or to inform risk assessment. Despite that, only a reduced number of computational studies of heart disease have incorporated β-ARS modelling. In this review, we describe the main existing multiscale frameworks to equip cellular models of cardiac electrophysiology with a β-ARS response. We also outline various applications of these multiscale frameworks in the study of cardiac pathology. We end with a discussion of the main current limitations and the future steps that need to be taken to adapt these models to a clinical environment and to incorporate them in organ-level simulations.

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Section: β-Ars and 3d Modellingmentioning

confidence: 99%

“…Connectivity diagrams of autonomic nervous systems for individual species, available through the SPARC portal (https://sparc.science/maps) (accessed on 4 July 2021). Reproduced from[105] under Creative Commons Attribution (CC BY 4.0) license.…”

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confidence: 99%

Multiscale Modelling of β-Adrenergic Stimulation in Cardiac Electromechanical Function

Doste

Bueno‐Orovio

2021

Mathematics

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“…The NIH Common Fund’s effort, Stimulating Peripheral Activity to Relieve Conditions (SPARC) (SPARC, 2014 ), is targeting medical conditions through the development and application of electroceuticals: electronic devices that stimulate peripheral nerves to rectify diseased organ function ( Osanlouy et al, 2021 ). To this end, SPARC has set out to build ApiNATOMY connectivity maps representing routes relevant to central autonomic control of the viscera, and to semantically imbue these maps with annotations that describe organ structure, function and disease involvement.…”

Section: Apinatomy Infrastructurementioning

confidence: 99%

Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY

et al. 2022

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We present (i) the ApiNATOMY workflow to build knowledge models of biological connectivity, as well as (ii) the ApiNATOMY TOO map, a topological scaffold to organize and visually inspect these connectivity models in the context of a canonical architecture of body compartments. In this work, we outline the implementation of ApiNATOMY’s knowledge representation in the context of a large-scale effort, SPARC, to map the autonomic nervous system. Within SPARC, the ApiNATOMY modeling effort has generated the SCKAN knowledge graph that combines connectivity models and TOO map. This knowledge graph models flow routes for a number of normal and disease scenarios in physiology. Calculations over SCKAN to infer routes are being leveraged to classify, navigate and search for semantically-linked metadata of multimodal experimental datasets for a number of cross-scale, cross-disciplinary projects.

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“…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 o 2 S 2 PARC, 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 Once these datasets are made public, access to them is provided through the Pennsieve Discover service and sparc.science, the official access point of the SPARC Portal.…”

Section: Introductionmentioning

confidence: 99%

“…[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 Once these datasets are made public, access to them is provided through the Pennsieve Discover service and sparc.science, the official access point of the SPARC Portal. 8 While the submission and curation of data are simplified by such tools, one of the greater benefits of the FAIR guidelines is the ability to reuse data in other studies by other researchers around the world.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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The National Institutes of Health (NIH) Stimulating Peripheral Activity to Relieve Conditions (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 Second 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 application programming interfaces (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 National Center for Biotechnology Information (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 SPARC DRC: Building a Resource for the Autonomic Nervous System Community

Cited by 38 publications

References 31 publications

Multiscale Modelling of β-Adrenergic Stimulation in Cardiac Electromechanical Function

Multiscale Modelling of β-Adrenergic Stimulation in Cardiac Electromechanical Function

Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY

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

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