SPARClink: an interactive tool to visualize the impact of the SPARC program [version 1; peer review: 2 approved, 1 approved with reservations]
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 n...
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| Published in: | F1000 research Vol. 11; p. 124 |
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| Main Authors: | , , , , |
| Format: | Journal Article |
| Language: | English |
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England
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2022
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| ISSN: | 2046-1402, 2046-1402 |
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| Abstract | 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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| AbstractList | 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.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. 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. |
| Author | Kuruppu, Sachira Singh, Ashutosh Achalla, Monalisa Kim, Jongchan Soundarajan, Sanjay |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36816808$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1145/3130348.3130369 10.1101/2021.02.10.430563v2.abstract 10.1096/fasebj.2020.34.s1.02483 10.1101/2021.08.08.455581.abstract 10.3389/fphys.2021.693735 10.1038/sdata.2016.18 |
| ContentType | Journal Article |
| Copyright | Copyright: © 2022 Soundarajan S et al. Copyright: © 2022 Soundarajan S et al. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Copyright: © 2022 Soundarajan S et al. 2022 |
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| References | (ref1) 2014 cited 2021 Oct 22 S Soundarajan (ref13) 2021 cited 2021 Oct 22 M Wilkinson (ref7) 2016 Mar 15; 3 R Quey (ref3) 2021 cited 2021 Oct 22 A Bandrowski (ref4) 2021 cited 2021 Oct 22 B Patel (ref5) 2020 Apr; 34 (ref2) cited 2021 Oct 22 (ref11) cited 2021 Oct 22 (ref12) cited 2021 Oct 22 (ref10) cited 2021 Oct 22 M Osanlouy (ref6) 2021 Jun 24; 12 (ref9) cited 2021 Oct 22 J Carbinell (ref16) 2017; 51 (ref8) cited 2021 Oct 22 |
| References_xml | – year: cited 2021 Oct 22 ident: ref9 article-title: 2021 SPARC FAIR Codeathon. SPARC Portal. – volume: 51 start-page: 209-210 year: 2017 ident: ref16 publication-title: The Use of MMR, Diversity-Based Reranking for Reordering Documents and Producing Summaries. doi: 10.1145/3130348.3130369 – start-page: 2021.02.10.430563 year: 2021 cited 2021 Oct 22 ident: ref4 article-title: SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data. publication-title: bioRxiv. doi: 10.1101/2021.02.10.430563v2.abstract – volume: 34 start-page: 1-1 year: 2020 Apr ident: ref5 article-title: SPARC: SODA, an interactive software for curating SPARC datasets. publication-title: FASEB J. doi: 10.1096/fasebj.2020.34.s1.02483 – year: cited 2021 Oct 22 ident: ref8 article-title: Pennsieve Discover. – year: 2014 cited 2021 Oct 22 ident: ref1 article-title: Stimulating Peripheral Activity to Relieve Conditions (SPARC). – year: cited 2021 Oct 22 ident: ref10 article-title: Pennsieve API. – year: 2021 cited 2021 Oct 22 ident: ref13 article-title: SPARClink Portal. – year: cited 2021 Oct 22 ident: ref12 article-title: NIH RePORTER API. – year: cited 2021 Oct 22 ident: ref2 article-title: SPARC Portal. – start-page: 2021.08.08.455581 year: 2021 cited 2021 Oct 22 ident: ref3 article-title: KnowMore: An Automated Knowledge Discovery Tool for the FAIR SPARC Datasets. publication-title: bioRxiv. doi: 10.1101/2021.08.08.455581.abstract – volume: 12 start-page: 693735 year: 2021 Jun 24 ident: ref6 article-title: The SPARC DRC: Building a Resource for the Autonomic Nervous System Community. publication-title: Front Physiol. doi: 10.3389/fphys.2021.693735 – volume: 3 start-page: 160018 year: 2016 Mar 15 ident: ref7 article-title: The FAIR Guiding Principles for scientific data management and stewardship. publication-title: Sci Data. doi: 10.1038/sdata.2016.18 – year: cited 2021 Oct 22 ident: ref11 article-title: Protocols.io for developers. |
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| SubjectTerms | Algorithms Biotechnology Citations Data Curation data sharing Databases, Factual Datasets eng FAIR Funding Interfaces Keywords Machine learning Medical research Metadata Nerves Neuromodulation Osteonectin Researchers Software Software Tool User experience Visualization |
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| Title | SPARClink: an interactive tool to visualize the impact of the SPARC program [version 1; peer review: 2 approved, 1 approved with reservations] |
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