BioKA: a curated and integrated biomarker knowledgebase for animals

Abstract

Biomarkers play an important role in various area such as personalized medicine, drug development, clinical care, and molecule breeding. However, existing animals’ biomarker resources predominantly focus on human diseases, leaving a significant gap in non-human animal disease understanding and breeding research. To address this limitation, we present BioKA (Biomarker Knowledgebase for Animals, https://ngdc.cncb.ac.cn/bioka), a curated and integrated knowledgebase encompassing multiple animal species, diseases/traits, and annotated resources. Currently, BioKA houses 16 296 biomarkers associated with 951 mapped diseases/traits across 31 species from 4747 references, including 11 925 gene/protein biomarkers, 1784 miRNA biomarkers, 1043 mutation biomarkers, 773 metabolic biomarkers, 357 circRNA biomarkers and 127 lncRNA biomarkers. Furthermore, BioKA integrates various annotations such as GOs, protein structures, protein–protein interaction networks, miRNA targets and so on, and constructs an interactive knowledge network of biomarkers including circRNA–miRNA–mRNA associations, lncRNA–miRNA associations and protein–protein associations, which is convenient for efficient data exploration. Moreover, BioKA provides detailed information on 308 breeds/strains of 13 species, and homologous annotations for 8784 biomarkers across 16 species, and offers three online application tools. The comprehensive knowledge provided by BioKA not only advances human disease research but also contributes to a deeper understanding of animal diseases and supports livestock breeding.

REMEMProt: a resource of membrane-enriched proteome profiles, their disease associations, and biomarker status

“…The current data-dependent analysis of the human protein–disease association indicated that most of the membrane proteins are associated with multiple types of cancers. To investigate the biomarker status of the REMEMProt protein data, a search against the biomarker database Biomarker Knowledgebase for Animals was carried out ( Wang et al, 2024 ). The data revealed the potential role of the membrane proteins in various disease conditions such as diagnostic, prognostic, predictive, and therapeutic factors.…”

“…The enlisted proteins from human, and mouse, can be distinctively subjected to disease ontology analysis to visualize their associated diseases. Similarly, the biomarker status of the proteins was fetched from the Biomarker Knowledgebase for Animals database ( Wang et al, 2024 ) Furthermore, the proteins were also enriched for the information on cellular markers using the CellMarker 2.0 database ( Zhang et al, 2019 ).…”