Visualization of automatically combined disease maps and pathway diagrams for rare diseases
Introduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mec...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2023.1101505/full |
| _version_ | 1827902959833317376 |
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| author | Piotr Gawron David Hoksza David Hoksza Janet Piñero Janet Piñero Janet Piñero Maria Peña-Chilet Maria Peña-Chilet Marina Esteban-Medina Jose Luis Fernandez-Rueda Vincenza Colonna Vincenza Colonna Ewa Smula Laurent Heirendt François Ancien Valentin Groues Venkata P. Satagopam Reinhard Schneider Joaquin Dopazo Joaquin Dopazo Laura I. Furlong Laura I. Furlong Laura I. Furlong Marek Ostaszewski |
| author_facet | Piotr Gawron David Hoksza David Hoksza Janet Piñero Janet Piñero Janet Piñero Maria Peña-Chilet Maria Peña-Chilet Marina Esteban-Medina Jose Luis Fernandez-Rueda Vincenza Colonna Vincenza Colonna Ewa Smula Laurent Heirendt François Ancien Valentin Groues Venkata P. Satagopam Reinhard Schneider Joaquin Dopazo Joaquin Dopazo Laura I. Furlong Laura I. Furlong Laura I. Furlong Marek Ostaszewski |
| author_sort | Piotr Gawron |
| collection | DOAJ |
| description | Introduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower.Methods: In this article we present an automated workflow for construction of maps of molecular mechanisms for rare diseases. The workflow requires a standardized definition of a disease using Orphanet or HPO identifiers to collect relevant genes and variants, and to assemble a functional, visual repository of related mechanisms, including data overlays. The diagrams composing the final map are unified to a common systems biology format from CellDesigner SBML, GPML and SBML+layout+render. The constructed resource contains disease-relevant genes and variants as data overlays for immediate visual exploration, including embedded genetic variant browser and protein structure viewer.Results: We demonstrate the functionality of our workflow on two examples of rare diseases: Kawasaki disease and retinitis pigmentosa. Two maps are constructed based on their corresponding identifiers. Moreover, for the retinitis pigmentosa use-case, we include a list of differentially expressed genes to demonstrate how to tailor the workflow using omics datasets.Discussion: In summary, our work allows for an ad-hoc construction of molecular diagrams combined from different sources, preserving their layout and graphical style, but integrating them into a single resource. This allows to reduce time consuming tasks of prototyping of a molecular disease map, enabling visual exploration, hypothesis building, data visualization and further refinement. The code of the workflow is open and accessible at https://gitlab.lcsb.uni.lu/minerva/automap/. |
| first_indexed | 2024-03-13T00:06:33Z |
| format | Article |
| id | doaj.art-2a8ecff469be48179eb1a3911ed85df0 |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-03-13T00:06:33Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj.art-2a8ecff469be48179eb1a3911ed85df02023-07-12T23:41:35ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472023-07-01310.3389/fbinf.2023.11015051101505Visualization of automatically combined disease maps and pathway diagrams for rare diseasesPiotr Gawron0David Hoksza1David Hoksza2Janet Piñero3Janet Piñero4Janet Piñero5Maria Peña-Chilet6Maria Peña-Chilet7Marina Esteban-Medina8Jose Luis Fernandez-Rueda9Vincenza Colonna10Vincenza Colonna11Ewa Smula12Laurent Heirendt13François Ancien14Valentin Groues15Venkata P. Satagopam16Reinhard Schneider17Joaquin Dopazo18Joaquin Dopazo19Laura I. Furlong20Laura I. Furlong21Laura I. Furlong22Marek Ostaszewski23Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgFaculty of Mathematics and Physics, Charles University, Prague, CzechiaResearch Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, SpainDepartment of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, SpainMedBioinformatics Solutions SL, Barcelona, SpainComputational Medicine Platform, Fundacion Progreso y Salud, Sevilla, SpainSpanish Network of Research in Rare Diseases (CIBERER), Sevilla, SpainComputational Medicine Platform, Fundacion Progreso y Salud, Sevilla, SpainComputational Medicine Platform, Fundacion Progreso y Salud, Sevilla, SpainInstitute of Genetics and Biophysics, National Research Council of Italy, Naples, RomeDepartment of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United StatesLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgComputational Medicine Platform, Fundacion Progreso y Salud, Sevilla, SpainSpanish Network of Research in Rare Diseases (CIBERER), Sevilla, SpainResearch Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, SpainDepartment of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, SpainMedBioinformatics Solutions SL, Barcelona, SpainLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, LuxembourgIntroduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower.Methods: In this article we present an automated workflow for construction of maps of molecular mechanisms for rare diseases. The workflow requires a standardized definition of a disease using Orphanet or HPO identifiers to collect relevant genes and variants, and to assemble a functional, visual repository of related mechanisms, including data overlays. The diagrams composing the final map are unified to a common systems biology format from CellDesigner SBML, GPML and SBML+layout+render. The constructed resource contains disease-relevant genes and variants as data overlays for immediate visual exploration, including embedded genetic variant browser and protein structure viewer.Results: We demonstrate the functionality of our workflow on two examples of rare diseases: Kawasaki disease and retinitis pigmentosa. Two maps are constructed based on their corresponding identifiers. Moreover, for the retinitis pigmentosa use-case, we include a list of differentially expressed genes to demonstrate how to tailor the workflow using omics datasets.Discussion: In summary, our work allows for an ad-hoc construction of molecular diagrams combined from different sources, preserving their layout and graphical style, but integrating them into a single resource. This allows to reduce time consuming tasks of prototyping of a molecular disease map, enabling visual exploration, hypothesis building, data visualization and further refinement. The code of the workflow is open and accessible at https://gitlab.lcsb.uni.lu/minerva/automap/.https://www.frontiersin.org/articles/10.3389/fbinf.2023.1101505/fullpathway diagramssystems biomedicinerare diseases (RD)disease mapsgene-disease association |
| spellingShingle | Piotr Gawron David Hoksza David Hoksza Janet Piñero Janet Piñero Janet Piñero Maria Peña-Chilet Maria Peña-Chilet Marina Esteban-Medina Jose Luis Fernandez-Rueda Vincenza Colonna Vincenza Colonna Ewa Smula Laurent Heirendt François Ancien Valentin Groues Venkata P. Satagopam Reinhard Schneider Joaquin Dopazo Joaquin Dopazo Laura I. Furlong Laura I. Furlong Laura I. Furlong Marek Ostaszewski Visualization of automatically combined disease maps and pathway diagrams for rare diseases Frontiers in Bioinformatics pathway diagrams systems biomedicine rare diseases (RD) disease maps gene-disease association |
| title | Visualization of automatically combined disease maps and pathway diagrams for rare diseases |
| title_full | Visualization of automatically combined disease maps and pathway diagrams for rare diseases |
| title_fullStr | Visualization of automatically combined disease maps and pathway diagrams for rare diseases |
| title_full_unstemmed | Visualization of automatically combined disease maps and pathway diagrams for rare diseases |
| title_short | Visualization of automatically combined disease maps and pathway diagrams for rare diseases |
| title_sort | visualization of automatically combined disease maps and pathway diagrams for rare diseases |
| topic | pathway diagrams systems biomedicine rare diseases (RD) disease maps gene-disease association |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2023.1101505/full |
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