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Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project
The stimulating peripheral activity to relieve conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system (ANS) in support of bioelectronic medicine. As part of this effort, the SPARC project is...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9449460/ https://www.ncbi.nlm.nih.gov/pubmed/36090663 http://dx.doi.org/10.3389/fninf.2022.819198 |
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author | Surles-Zeigler, Monique C. Sincomb, Troy Gillespie, Thomas H. de Bono, Bernard Bresnahan, Jacqueline Mawe, Gary M. Grethe, Jeffrey S. Tappan, Susan Heal, Maci Martone, Maryann E. |
author_facet | Surles-Zeigler, Monique C. Sincomb, Troy Gillespie, Thomas H. de Bono, Bernard Bresnahan, Jacqueline Mawe, Gary M. Grethe, Jeffrey S. Tappan, Susan Heal, Maci Martone, Maryann E. |
author_sort | Surles-Zeigler, Monique C. |
collection | PubMed |
description | The stimulating peripheral activity to relieve conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system (ANS) in support of bioelectronic medicine. As part of this effort, the SPARC project is generating multi-species, multimodal data, models, simulations, and anatomical maps supported by a comprehensive knowledge base of autonomic circuitry. To facilitate the organization of and integration across multi-faceted SPARC data and models, SPARC is implementing the findable, accessible, interoperable, and reusable (FAIR) data principles to ensure that all SPARC products are findable, accessible, interoperable, and reusable. We are therefore annotating and describing all products with a common FAIR vocabulary. The SPARC Vocabulary is built from a set of community ontologies covering major domains relevant to SPARC, including anatomy, physiology, experimental techniques, and molecules. The SPARC Vocabulary is incorporated into tools researchers use to segment and annotate their data, facilitating the application of these ontologies for annotation of research data. However, since investigators perform deep annotations on experimental data, not all terms and relationships are available in community ontologies. We therefore implemented a term management and vocabulary extension pipeline where SPARC researchers may extend the SPARC Vocabulary using InterLex, an online vocabulary management system. To ensure the quality of contributed terms, we have set up a curated term request and review pipeline specifically for anatomical terms involving expert review. Accepted terms are added to the SPARC Vocabulary and, when appropriate, contributed back to community ontologies to enhance ANS coverage. Here, we provide an overview of the SPARC Vocabulary, the infrastructure and process for implementing the term management and review pipeline. In an analysis of >300 anatomical contributed terms, the majority represented composite terms that necessitated combining terms within and across existing ontologies. Although these terms are not good candidates for community ontologies, they can be linked to structures contained within these ontologies. We conclude that the term request pipeline serves as a useful adjunct to community ontologies for annotating experimental data and increases the FAIRness of SPARC data. |
format | Online Article Text |
id | pubmed-9449460 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-94494602022-09-08 Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project Surles-Zeigler, Monique C. Sincomb, Troy Gillespie, Thomas H. de Bono, Bernard Bresnahan, Jacqueline Mawe, Gary M. Grethe, Jeffrey S. Tappan, Susan Heal, Maci Martone, Maryann E. Front Neuroinform Neuroscience The stimulating peripheral activity to relieve conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system (ANS) in support of bioelectronic medicine. As part of this effort, the SPARC project is generating multi-species, multimodal data, models, simulations, and anatomical maps supported by a comprehensive knowledge base of autonomic circuitry. To facilitate the organization of and integration across multi-faceted SPARC data and models, SPARC is implementing the findable, accessible, interoperable, and reusable (FAIR) data principles to ensure that all SPARC products are findable, accessible, interoperable, and reusable. We are therefore annotating and describing all products with a common FAIR vocabulary. The SPARC Vocabulary is built from a set of community ontologies covering major domains relevant to SPARC, including anatomy, physiology, experimental techniques, and molecules. The SPARC Vocabulary is incorporated into tools researchers use to segment and annotate their data, facilitating the application of these ontologies for annotation of research data. However, since investigators perform deep annotations on experimental data, not all terms and relationships are available in community ontologies. We therefore implemented a term management and vocabulary extension pipeline where SPARC researchers may extend the SPARC Vocabulary using InterLex, an online vocabulary management system. To ensure the quality of contributed terms, we have set up a curated term request and review pipeline specifically for anatomical terms involving expert review. Accepted terms are added to the SPARC Vocabulary and, when appropriate, contributed back to community ontologies to enhance ANS coverage. Here, we provide an overview of the SPARC Vocabulary, the infrastructure and process for implementing the term management and review pipeline. In an analysis of >300 anatomical contributed terms, the majority represented composite terms that necessitated combining terms within and across existing ontologies. Although these terms are not good candidates for community ontologies, they can be linked to structures contained within these ontologies. We conclude that the term request pipeline serves as a useful adjunct to community ontologies for annotating experimental data and increases the FAIRness of SPARC data. Frontiers Media S.A. 2022-08-24 /pmc/articles/PMC9449460/ /pubmed/36090663 http://dx.doi.org/10.3389/fninf.2022.819198 Text en Copyright © 2022 Surles-Zeigler, Sincomb, Gillespie, de Bono, Bresnahan, Mawe, Grethe, Tappan, Heal and Martone. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Neuroscience Surles-Zeigler, Monique C. Sincomb, Troy Gillespie, Thomas H. de Bono, Bernard Bresnahan, Jacqueline Mawe, Gary M. Grethe, Jeffrey S. Tappan, Susan Heal, Maci Martone, Maryann E. Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project |
title | Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project |
title_full | Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project |
title_fullStr | Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project |
title_full_unstemmed | Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project |
title_short | Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project |
title_sort | extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project |
topic | Neuroscience |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9449460/ https://www.ncbi.nlm.nih.gov/pubmed/36090663 http://dx.doi.org/10.3389/fninf.2022.819198 |
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