A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

Mazein, Alexander; Acencio, Márcio Luís; Balaur, Irina; Rougny, Adrien; Welter, Danielle; Niarakis, Anna; Ardila, Diana Ramirez; Doğrusöz, Uğur; Gawron, Piotr; Satagopam, Venkata; Gu, Wanyi; Kremer, Andreas E.; Schneider, Reinhard; Ostaszewski, Marek

doi:10.3389/fbinf.2023.1197310

Cited by 5 publications

(2 citation statements)

References 83 publications

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“…Disease maps are human- and computer-readable repositories containing manually curated interactions following the SBML format, organized into diagrams according to the SBGN notation. The process of map development ( 39 ) involves intensive biocuration work over a selected body of literature. Importantly, interactions of disease maps reference the source literature.…”

Section: Resultsmentioning

confidence: 99%

BioKC: a collaborative platform for curation and annotation of molecular interactions

Vega,

Ostaszewski,

Grouès

et al. 2024

Database

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Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in a format suitable for systems biology applications. Importantly, curation should capture the complexity of molecular interactions in such a format together with annotations of the involved elements and support stable identifiers and versioning. This challenge calls for novel collaborative tools and platforms allowing to improve the quality and the output of the curation process. In particular, community-based curation, an important source of curated knowledge, requires support in role management, reviewing features and versioning. Here, we present Biological Knowledge Curation (BioKC), a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML). BioKC offers a graphical user interface for curation of complex molecular interactions and their annotation with stable identifiers and supporting sentences. With the support of collaborative curation and review, it allows to construct building blocks for systems biology diagrams and computational models. These building blocks can be published under stable identifiers and versioned and used as annotations, supporting knowledge building for modelling activities.

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Section: Resultsmentioning

confidence: 99%

BioKC: a collaborative platform for curation and annotation of molecular interactions

Vega,

Ostaszewski,

Grouès

et al. 2024

Database

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“…The SYSCID map was constructed by following most of the recommendations in the recently published guidelines for disease maps construction (18). At first, we manually curated reviews and original peer-reviewed research papers suggested by domain experts from the SYSCID consortium.…”

Section: Capturing Ibd- Ra-and Sle-related Causal Interactions From L...mentioning

confidence: 99%

The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease

Acencio,

Ostaszewski,

Mazein

et al. 2023

Front. Immunol.

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Chronic inflammatory diseases (CIDs), including inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are thought to emerge from an impaired complex network of inter- and intracellular biochemical interactions among several proteins and small chemical compounds under strong influence of genetic and environmental factors. CIDs are characterised by shared and disease-specific processes, which is reflected by partially overlapping genetic risk maps and pathogenic cells (e.g., T cells). Their pathogenesis involves a plethora of intracellular pathways. The translation of the research findings on CIDs molecular mechanisms into effective treatments is challenging and may explain the low remission rates despite modern targeted therapies. Modelling CID-related causal interactions as networks allows us to tackle the complexity at a systems level and improve our understanding of the interplay of key pathways. Here we report the construction, description, and initial applications of the SYSCID map (https://syscid.elixir-luxembourg.org/), a mechanistic causal interaction network covering the molecular crosstalk between IBD, RA and SLE. We demonstrate that the map serves as an interactive, graphical review of IBD, RA and SLE molecular mechanisms, and helps to understand the complexity of omics data. Examples of such application are illustrated using transcriptome data from time-series gene expression profiles following anti-TNF treatment and data from genome-wide associations studies that enable us to suggest potential effects to altered pathways and propose possible mechanistic biomarkers of treatment response.

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Advancing radiation therapy safety in cancer-care: Leveraging AI for adverse reaction prediction

Barki,

Alsufyani,

Softah

et al. 2024

Journal of Radiation Research and Applied Sciences

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A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

Cited by 5 publications

References 83 publications

BioKC: a collaborative platform for curation and annotation of molecular interactions

BioKC: a collaborative platform for curation and annotation of molecular interactions

The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease

Advancing radiation therapy safety in cancer-care: Leveraging AI for adverse reaction prediction

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