A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance
As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2023.1197310/full |
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| author | Alexander Mazein Marcio Luis Acencio Irina Balaur Adrien Rougny Danielle Welter Anna Niarakis Anna Niarakis Diana Ramirez Ardila Ugur Dogrusoz Piotr Gawron Venkata Satagopam Venkata Satagopam Wei Gu Wei Gu Andreas Kremer Reinhard Schneider Reinhard Schneider Marek Ostaszewski Marek Ostaszewski |
| author_facet | Alexander Mazein Marcio Luis Acencio Irina Balaur Adrien Rougny Danielle Welter Anna Niarakis Anna Niarakis Diana Ramirez Ardila Ugur Dogrusoz Piotr Gawron Venkata Satagopam Venkata Satagopam Wei Gu Wei Gu Andreas Kremer Reinhard Schneider Reinhard Schneider Marek Ostaszewski Marek Ostaszewski |
| author_sort | Alexander Mazein |
| collection | DOAJ |
| description | As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods. In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. We also describe how the Neo4j graph database environment can be used for managing and querying efficiently such a resource. For assessing the interoperability and reproducibility we apply FAIR principles. |
| format | Article |
| id | doaj-art-f0f445384bda413f8afbd1d17acb3009 |
| institution | Kabale University |
| issn | 2673-7647 |
| language | English |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj-art-f0f445384bda413f8afbd1d17acb30092025-02-06T11:04:14ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472023-06-01310.3389/fbinf.2023.11973101197310A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenanceAlexander Mazein0Marcio Luis Acencio1Irina Balaur2Adrien Rougny3Danielle Welter4Anna Niarakis5Anna Niarakis6Diana Ramirez Ardila7Ugur Dogrusoz8Piotr Gawron9Venkata Satagopam10Venkata Satagopam11Wei Gu12Wei Gu13Andreas Kremer14Reinhard Schneider15Reinhard Schneider16Marek Ostaszewski17Marek Ostaszewski18Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgIndependent Researcher, Massy, FranceLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgUniversité Paris-Saclay, Laboratoire Européen de Recherche Pour la Polyarthrite Rhumatoïde–Genhotel, University Evry, Evry, FranceLifeware Group, Inria Saclay-Ile de France, Palaiseau, FranceITTM Information Technology for Translational Medicine, Esch-sur-Alzette, LuxemburgComputer Engineering Department, Bilkent University, Ankara, TürkiyeLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgELIXIR Luxembourg, Belvaux, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgELIXIR Luxembourg, Belvaux, LuxembourgITTM Information Technology for Translational Medicine, Esch-sur-Alzette, LuxemburgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgELIXIR Luxembourg, Belvaux, LuxembourgLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, LuxembourgELIXIR Luxembourg, Belvaux, LuxembourgAs a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods. In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. We also describe how the Neo4j graph database environment can be used for managing and querying efficiently such a resource. For assessing the interoperability and reproducibility we apply FAIR principles.https://www.frontiersin.org/articles/10.3389/fbinf.2023.1197310/fulldisease mechanismscurationpathway biologysystems biologytranslational research |
| spellingShingle | Alexander Mazein Marcio Luis Acencio Irina Balaur Adrien Rougny Danielle Welter Anna Niarakis Anna Niarakis Diana Ramirez Ardila Ugur Dogrusoz Piotr Gawron Venkata Satagopam Venkata Satagopam Wei Gu Wei Gu Andreas Kremer Reinhard Schneider Reinhard Schneider Marek Ostaszewski Marek Ostaszewski A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance Frontiers in Bioinformatics disease mechanisms curation pathway biology systems biology translational research |
| title | A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance |
| title_full | A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance |
| title_fullStr | A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance |
| title_full_unstemmed | A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance |
| title_short | A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance |
| title_sort | guide for developing comprehensive systems biology maps of disease mechanisms planning construction and maintenance |
| topic | disease mechanisms curation pathway biology systems biology translational research |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2023.1197310/full |
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