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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...

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Autores principales: de Bono, Bernard, Gillespie, Tom, Surles-Zeigler, Monique C., Kokash, Natallia, Grethe, Jeff S., Martone, Maryann
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
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.
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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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