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Molecular cartooning with knowledge graphs

Molecular “cartoons,” such as pathway diagrams, provide a visual summary of biomedical research results and hypotheses. Their ubiquitous appearance within the literature indicates their universal application in mechanistic communication. A recent survey of pathway diagrams identified 64,643 pathway...

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Detalles Bibliográficos
Autores principales: Santangelo, Brook E., Gillenwater, Lucas A., Salem, Nourah M., Hunter, Lawrence E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9772836/
https://www.ncbi.nlm.nih.gov/pubmed/36568701
http://dx.doi.org/10.3389/fbinf.2022.1054578
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author Santangelo, Brook E.
Gillenwater, Lucas A.
Salem, Nourah M.
Hunter, Lawrence E.
author_facet Santangelo, Brook E.
Gillenwater, Lucas A.
Salem, Nourah M.
Hunter, Lawrence E.
author_sort Santangelo, Brook E.
collection PubMed
description Molecular “cartoons,” such as pathway diagrams, provide a visual summary of biomedical research results and hypotheses. Their ubiquitous appearance within the literature indicates their universal application in mechanistic communication. A recent survey of pathway diagrams identified 64,643 pathway figures published between 1995 and 2019 with 1,112,551 mentions of 13,464 unique human genes participating in a wide variety of biological processes. Researchers generally create these diagrams using generic diagram editing software that does not itself embody any biomedical knowledge. Biomedical knowledge graphs (KGs) integrate and represent knowledge in a semantically consistent way, systematically capturing biomedical knowledge similar to that in molecular cartoons. KGs have the potential to provide context and precise details useful in drawing such figures. However, KGs cannot generally be translated directly into figures. They include substantial material irrelevant to the scientific point of a given figure and are often more detailed than is appropriate. How could KGs be used to facilitate the creation of molecular diagrams? Here we present a new approach towards cartoon image creation that utilizes the semantic structure of knowledge graphs to aid the production of molecular diagrams. We introduce a set of “semantic graphical actions” that select and transform the relational information between heterogeneous entities (e.g., genes, proteins, pathways, diseases) in a KG to produce diagram schematics that meet the scientific communication needs of the user. These semantic actions search, select, filter, transform, group, arrange, connect and extract relevant subgraphs from KGs based on meaning in biological terms, e.g., a protein upstream of a target in a pathway. To demonstrate the utility of this approach, we show how semantic graphical actions on KGs could have been used to produce three existing pathway diagrams in diverse biomedical domains: Down Syndrome, COVID-19, and neuroinflammation. Our focus is on recapitulating the semantic content of the figures, not the layout, glyphs, or other aesthetic aspects. Our results suggest that the use of KGs and semantic graphical actions to produce biomedical diagrams will reduce the effort required and improve the quality of this visual form of scientific communication.
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spelling pubmed-97728362022-12-23 Molecular cartooning with knowledge graphs Santangelo, Brook E. Gillenwater, Lucas A. Salem, Nourah M. Hunter, Lawrence E. Front Bioinform Bioinformatics Molecular “cartoons,” such as pathway diagrams, provide a visual summary of biomedical research results and hypotheses. Their ubiquitous appearance within the literature indicates their universal application in mechanistic communication. A recent survey of pathway diagrams identified 64,643 pathway figures published between 1995 and 2019 with 1,112,551 mentions of 13,464 unique human genes participating in a wide variety of biological processes. Researchers generally create these diagrams using generic diagram editing software that does not itself embody any biomedical knowledge. Biomedical knowledge graphs (KGs) integrate and represent knowledge in a semantically consistent way, systematically capturing biomedical knowledge similar to that in molecular cartoons. KGs have the potential to provide context and precise details useful in drawing such figures. However, KGs cannot generally be translated directly into figures. They include substantial material irrelevant to the scientific point of a given figure and are often more detailed than is appropriate. How could KGs be used to facilitate the creation of molecular diagrams? Here we present a new approach towards cartoon image creation that utilizes the semantic structure of knowledge graphs to aid the production of molecular diagrams. We introduce a set of “semantic graphical actions” that select and transform the relational information between heterogeneous entities (e.g., genes, proteins, pathways, diseases) in a KG to produce diagram schematics that meet the scientific communication needs of the user. These semantic actions search, select, filter, transform, group, arrange, connect and extract relevant subgraphs from KGs based on meaning in biological terms, e.g., a protein upstream of a target in a pathway. To demonstrate the utility of this approach, we show how semantic graphical actions on KGs could have been used to produce three existing pathway diagrams in diverse biomedical domains: Down Syndrome, COVID-19, and neuroinflammation. Our focus is on recapitulating the semantic content of the figures, not the layout, glyphs, or other aesthetic aspects. Our results suggest that the use of KGs and semantic graphical actions to produce biomedical diagrams will reduce the effort required and improve the quality of this visual form of scientific communication. Frontiers Media S.A. 2022-12-08 /pmc/articles/PMC9772836/ /pubmed/36568701 http://dx.doi.org/10.3389/fbinf.2022.1054578 Text en Copyright © 2022 Santangelo, Gillenwater, Salem and Hunter. 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 Bioinformatics
Santangelo, Brook E.
Gillenwater, Lucas A.
Salem, Nourah M.
Hunter, Lawrence E.
Molecular cartooning with knowledge graphs
title Molecular cartooning with knowledge graphs
title_full Molecular cartooning with knowledge graphs
title_fullStr Molecular cartooning with knowledge graphs
title_full_unstemmed Molecular cartooning with knowledge graphs
title_short Molecular cartooning with knowledge graphs
title_sort molecular cartooning with knowledge graphs
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9772836/
https://www.ncbi.nlm.nih.gov/pubmed/36568701
http://dx.doi.org/10.3389/fbinf.2022.1054578
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