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Creating, curating and querying computer models of biological pathways for Inherited Metabolic Disorders

D. Slenter,E. Willighagen

Published 2023 in bioRxiv

ABSTRACT

Collecting knowledge about Inherited Metabolic Disorders (IMDs) has the potential to support early diagnosis as well as foster research into treatment options. Biological pathway databases can be used to create an overview of relevant articles and books describing IMDs and collect, curate, and summarize knowledge about these disorders. Reuse of the information captured in these databases in research requires the knowledge to be accurate but also machine-readable. WikiPathways is a community-driven project to establish a machinereadable knowledge base of biological processes. We here describe how pathways models from WikiPathways were used to represent the underlying biological mechanisms of many IMDs collected by domain experts over a period of six years. This paper describes a standardized approach to depict IMDs in WikiPathways, shows the current limitations in creating machine-readable disease information, and introduces an approach to support data curation based on these machine-readable biological pathways. Furthermore, several SPARQL-queries were developed to analyze the biological content created in these models. Using this approach, 47 pathways were collected about 345 diseases, involving 877 metabolites, 421 annotated metabolic interactions, 262 genes, and 587 proteins related to these disorders.

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