BioKA

BioKA compiles a curated, integrated knowledgebase of animal biomarkers to support biomarker discovery and cross-species comparative studies.

Key Features:

• Biomarker corpus: Contains 16,296 biomarkers associated with 951 distinct diseases or traits compiled from 4,747 literature references across 31 species (nine model animals, sixteen domestic animals, five other species, and humans).
• Biomarker types: Includes 11,925 gene/protein biomarkers, 1,784 miRNA biomarkers, 1,043 mutation biomarkers, 773 metabolic biomarkers, 357 circRNA biomarkers, and 127 lncRNA biomarkers.
• Functional and structural annotations: Integrates Gene Ontologies (GOs), protein structures, protein-protein interaction networks, miRNA targets, and related annotations.
• Network representations: Constructs networks elucidating circRNA-miRNA-mRNA, lncRNA-miRNA, and protein-protein interactions.
• Breed and strain metadata: Provides detailed information for 308 breeds or strains across 13 species.
• Homology annotations: Provides homologous annotations for 8,784 biomarkers across 16 species to enable cross-species comparison.
• Literature curation: Biomarkers and annotations are compiled from 4,747 literature references.

Scientific Applications:

• Personalized medicine: Enables translation of biomarker information for individualized veterinary diagnostics and treatment decisions.
• Drug development: Supports target identification and validation across animal species for therapeutics research.
• Clinical care: Informs diagnostic and prognostic biomarker selection in veterinary clinical contexts.
• Molecular breeding and livestock breeding: Supplies biomarker information applicable to molecular breeding strategies and livestock improvement.
• Comparative and translational research: Facilitates cross-species comparative studies of disease mechanisms and translational insights between animals and humans.

Methodology:

Curated biomarker collection from 4,747 literature references; integration of annotations including Gene Ontologies, protein structures, protein-protein interaction networks, and miRNA targets; construction of networks for circRNA-miRNA-mRNA, lncRNA-miRNA, and protein-protein interactions; homologous annotation across 16 species.