Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using semantic web technologies.

ABSTRACT:

Motivation

Molecular complexes play a major role in the regulation of biological pathways. The Biological Pathway Exchange format (BioPAX) facilitates the integration of data sources describing interactions some of which involving complexes. The BioPAX specification explicitly prevents complexes to have any component that is another complex (unless this component is a black-box complex whose composition is unknown). However, we observed that the well-curated Reactome pathway database contains such recursive complexes of complexes. We propose reproductible and semantically rich SPARQL queries for identifying and fixing invalid complexes in BioPAX databases, and evaluate the consequences of fixing these nonconformities in the Reactome database.

Results

For the Homo sapiens ver

SUBMITTER: Juigne C 

PROVIDER: S-EPMC10168583 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature