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 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.

[1]  A. Mazein,et al.  StonPy: a tool to parse and query collections of SBGN maps in a graph database , 2023, Bioinformatics.

[2]  C. Auffray,et al.  GraphML-SBGN bidirectional converter for metabolic networks , 2022, J. Integr. Bioinform..

[3]  S. Soliman,et al.  Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach , 2022, bioRxiv.

[4]  F. Augé,et al.  A Mechanistic Cellular Atlas of the Rheumatic Joint , 2022, Frontiers in Systems Biology.

[5]  Sarah M. Keating,et al.  Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology , 2022, Briefings Bioinform..

[6]  A. O. Falcão,et al.  CyFi-MAP: an interactive pathway-based resource for cystic fibrosis , 2021, Scientific Reports.

[7]  Gary D Bader,et al.  The reactome pathway knowledgebase 2022 , 2021, Nucleic Acids Res..

[8]  H. Hermjakob,et al.  Complex Portal 2022: new curation frontiers , 2021, Nucleic Acids Res..

[9]  Alexander R. Pico,et al.  COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms , 2021, Molecular systems biology.

[10]  K. Hanspers,et al.  Ten simple rules for creating reusable pathway models for computational analysis and visualization , 2021, PLoS Comput. Biol..

[11]  U. Dogrusoz,et al.  fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support , 2021, IEEE Transactions on Visualization and Computer Graphics.

[12]  Jonathan R. Karr,et al.  Reusability and composability in process description maps: RAS–RAF–MEK–ERK signalling , 2021, Briefings Bioinform..

[13]  M. Elati,et al.  Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map , 2021, bioRxiv.

[14]  Anna Niarakis,et al.  The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling , 2020, Briefings Bioinform..

[15]  Anushya Muruganujan,et al.  The Gene Ontology resource: enriching a GOld mine , 2020, Nucleic Acids Res..

[16]  Thomas S. Ligon,et al.  AsthmaMap: an interactive knowledge repository for mechanisms of asthma. , 2020, The Journal of allergy and clinical immunology.

[17]  Gary D. Bader,et al.  SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks , 2020, bioRxiv.

[18]  J. Mcentyre,et al.  Europe PMC in 2020 , 2020, Nucleic Acids Res..

[19]  Benjamin A. Shoemaker,et al.  PubChem in 2021: new data content and improved web interfaces , 2020, Nucleic Acids Res..

[20]  Jonathan R. Karr,et al.  SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems , 2020, Bioinform..

[21]  E. Barillot,et al.  cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. , 2020, Bioinformatics.

[22]  Ugur Dogrusoz,et al.  Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps , 2020, Bioinform..

[23]  Hiroaki Kitano,et al.  SBML Level 3: an extensible format for the exchange and reuse of biological models , 2020, Molecular systems biology.

[24]  Thawfeek M. Varusai,et al.  Using Reactome to build an autophagy mechanism knowledgebase , 2020, Autophagy.

[25]  Ugur Dogrusoz,et al.  Systems biology graphical notation markup language (SBGNML) version 0.3 , 2020, J. Integr. Bioinform..

[26]  Anna Niarakis,et al.  Automated inference of Boolean models from molecular interaction maps using CaSQ , 2020, Bioinform..

[27]  Charles Tapley Hoyt,et al.  The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST) , 2020, Bioinform..

[28]  Aurélien Naldi,et al.  Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop , 2020, Briefings Bioinform..

[29]  Inna Kuperstein,et al.  Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases , 2020, Cancers.

[30]  Andrei Zinovyev,et al.  cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats , 2020, Bioinform..

[31]  Piotr Gawron,et al.  RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis , 2020, Database J. Biol. Databases Curation.

[32]  Livia Perfetto,et al.  SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update , 2019, Nucleic Acids Res..

[33]  Marek Ostaszewski,et al.  Closing the gap between formats for storing layout information in systems biology , 2019, Briefings Bioinform..

[34]  Ugur Dogrusoz,et al.  Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 , 2019, J. Integr. Bioinform..

[35]  James Malone,et al.  Ten quick tips for biocuration , 2019, PLoS Comput. Biol..

[36]  Piotr Gawron,et al.  MINERVA API and plugins: opening molecular network analysis and visualization to the community , 2019, Bioinform..

[37]  Victoria McGilligan,et al.  New models of atherosclerosis and multi-drug therapeutic interventions , 2018, Bioinform..

[38]  Anushya Muruganujan,et al.  PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools , 2018, Nucleic Acids Res..

[39]  Charles Auffray,et al.  Human-like layout algorithms for signalling hypergraphs: outlining requirements , 2018, Briefings Bioinform..

[40]  C. Auffray,et al.  Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms , 2018, npj Systems Biology and Applications.

[41]  Marek Ostaszewski,et al.  Community-driven roadmap for integrated disease maps , 2018, Briefings Bioinform..

[42]  Inna Kuperstein,et al.  Signalling maps in cancer research: construction and data analysis , 2018, Database J. Biol. Databases Curation.

[43]  Henning Hermjakob,et al.  Reactome graph database: Efficient access to complex pathway data , 2018, PLoS Comput. Biol..

[44]  Inna Kuperstein,et al.  Application of Atlas of Cancer Signalling Network in pre-clinical studies , 2017, bioRxiv.

[45]  David S. Wishart,et al.  DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..

[46]  Christopher J. Rawlings,et al.  Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks , 2016, Bioinform..

[47]  Peter J Hunter,et al.  Modular modelling with Physiome standards , 2016, The Journal of physiology.

[48]  Julio Saez-Rodriguez,et al.  OmniPath: guidelines and gateway for literature-curated signaling pathway resources , 2016, Nature Methods.

[49]  Piotr Gawron,et al.  ReconMap: an interactive visualization of human metabolism , 2016, Bioinform..

[50]  Piotr Gawron,et al.  MINERVA—a platform for visualization and curation of molecular interaction networks , 2016, npj Systems Biology and Applications.

[51]  Inna Kuperstein,et al.  Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors , 2016, Clinical Cancer Research.

[52]  Christopher J. Rawlings,et al.  Representing and querying disease networks using graph databases , 2016, BioData Mining.

[53]  Marek Ostaszewski,et al.  Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases , 2016, Big Data.

[54]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[55]  Jing Chen,et al.  NDEx, the Network Data Exchange. , 2015, Cell systems.

[56]  Christoph Steinbeck,et al.  ChEBI in 2016: Improved services and an expanding collection of metabolites , 2015, Nucleic Acids Res..

[57]  E. Barillot,et al.  Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps , 2015, Oncogenesis.

[58]  Inna Kuperstein,et al.  NaviCell Web Service for network-based data visualization , 2015, Nucleic Acids Res..

[59]  E. Barillot,et al.  The shortest path is not the one you know: application of biological network resources in precision oncology research. , 2015, Mutagenesis.

[60]  N. Novère.  Quantitative and logic modelling of molecular and gene networks , 2015, Nature Reviews Genetics.

[61]  Inna Kuperstein,et al.  Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut , 2014, Nature Communications.

[62]  George Papadatos,et al.  The ChEMBL bioactivity database: an update , 2013, Nucleic Acids Res..

[63]  Falk Schreiber,et al.  Translation of SBGN maps: Process Description to Activity Flow , 2013, BMC Systems Biology.

[64]  Samik Ghosh,et al.  A comprehensive map of the influenza A virus replication cycle , 2013, BMC Systems Biology.

[65]  H. Kitano,et al.  Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map , 2013, Molecular Neurobiology.

[66]  Ronan M. T. Fleming,et al.  A community-driven global reconstruction of human metabolism , 2013, Nature Biotechnology.

[67]  Inna Kuperstein,et al.  NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps , 2013, BMC Systems Biology.

[68]  Samik Ghosh,et al.  AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease , 2012, BMC Systems Biology.

[69]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[70]  Astrid Junker,et al.  SBGN-ED – a tool for editing, validating, and translating of SBGN maps , 2010 .

[71]  N. Novère,et al.  Systems Biology Graphical Notation: Process Description language Level 1 , 2009 .

[72]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Activity Flow language Level 1 , 2009 .

[73]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[74]  Maria J Grant,et al.  A typology of reviews: an analysis of 14 review types and associated methodologies. , 2009, Health information and libraries journal.

[75]  Ying Zhang,et al.  HMDB: the Human Metabolome Database , 2007, Nucleic Acids Res..

[76]  David W. Russell,et al.  LMSD: LIPID MAPS structure database , 2006, Nucleic Acids Res..

[77]  P. Shannon,et al.  Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks , 2003 .

[78]  OUP accepted manuscript , 2021, Nucleic Acids Research.

[79]  Hiroshi Tanaka,et al.  AlzPathway, an Updated Map of Curated Signaling Pathways: Towards Deciphering Alzheimer's Disease Pathogenesis. , 2016, Methods in molecular biology.

[80]  Gary D. Bader,et al.  Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative , 2015, Front. Bioeng. Biotechnol..

[81]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010, Nature Protocols.

[82]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..