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Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY
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 outli...
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/PMC9083405/ https://www.ncbi.nlm.nih.gov/pubmed/35547570 http://dx.doi.org/10.3389/fphys.2022.795303 |
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author | de Bono, Bernard Gillespie, Tom Surles-Zeigler, Monique C. Kokash, Natallia Grethe, Jeff S. Martone, Maryann |
author_facet | de Bono, Bernard Gillespie, Tom Surles-Zeigler, Monique C. Kokash, Natallia Grethe, Jeff S. Martone, Maryann |
author_sort | de Bono, Bernard |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9083405 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-90834052022-05-10 Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY de Bono, Bernard Gillespie, Tom Surles-Zeigler, Monique C. Kokash, Natallia Grethe, Jeff S. Martone, Maryann Front Physiol Physiology 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. Frontiers Media S.A. 2022-04-25 /pmc/articles/PMC9083405/ /pubmed/35547570 http://dx.doi.org/10.3389/fphys.2022.795303 Text en Copyright © 2022 de Bono, Gillespie, Surles-Zeigler, Kokash, Grethe 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 | Physiology de Bono, Bernard Gillespie, Tom Surles-Zeigler, Monique C. Kokash, Natallia Grethe, Jeff S. Martone, Maryann Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY |
title | Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY |
title_full | Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY |
title_fullStr | Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY |
title_full_unstemmed | Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY |
title_short | Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY |
title_sort | representing normal and abnormal physiology as routes of flow in apinatomy |
topic | Physiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9083405/ https://www.ncbi.nlm.nih.gov/pubmed/35547570 http://dx.doi.org/10.3389/fphys.2022.795303 |
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