pbg-ld

pbg-ld integrates geno- and phenotypic data using a Linked Data approach to support ranking and identification of candidate causal genes underlying complex traits in Solanaceae species.

Key Features:

• Literature-based QTL extraction: Extracts QTLs from full-text articles in Europe PubMed Central (PMC) using QTLTableMiner++ (QTM).
• Genomic annotation sources: Incorporates genomic annotations from the Sol Genomics Network (SGN), UniProt, and Ensembl Plants.
• Linked Data transformation: Transforms integrated datasets into Linked Data graphs to enable interoperability with databases such as Gramene, Plant Reactome, InterPro, and KEGG Orthology (KO).
• Programmatic querying: Exposes integrated data via SPARQL endpoints and RESTful APIs for computational analysis.

Scientific Applications:

• Comparative genomics: Supports comparison of genetic mechanisms underlying fruit shape in tomato and tuber shape in potato within Solanaceae.
• Candidate gene prioritization: Enables integration of genomic data from knowledge graphs with prioritization pipelines to predict candidate genes within QTL regions associated with metabolic traits in tomato.

Methodology:

QTLs are extracted from Europe PMC full-text articles using QTLTableMiner++ (QTM); genomic annotations from SGN, UniProt, and Ensembl Plants are integrated and transformed into Linked Data graphs, and the integrated graphs are made available via SPARQL endpoints and RESTful APIs.