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Jan 05, 2024;52 (D1): D1121-D1130.

BioKA: a curated and integrated biomarker knowledgebase for animals.

Yibo Wang, Yihao Lin, Sicheng Wu, Jiani Sun, Yuyan Meng, Enhui Jin, Demian Kong, Guangya Duan, Shaoqi Bei, Zhuojing Fan, Gangao Wu, Lili Hao, Shuhui Song, Bixia Tang, Wenming Zhao
Author Information
  1. Yibo Wang: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  2. Yihao Lin: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  3. Sicheng Wu: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  4. Jiani Sun: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  5. Yuyan Meng: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  6. Enhui Jin: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  7. Demian Kong: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  8. Guangya Duan: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  9. Shaoqi Bei: Qilu University of Technology (Shandong Academy of Sciences), Shandong 250353, China.
  10. Zhuojing Fan: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  11. Gangao Wu: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  12. Lili Hao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  13. Shuhui Song: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  14. Bixia Tang: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  15. Wenming Zhao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
PMID: 37843156 DOI: 10.1093/nar/gkad873

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.

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Grants

  1. 32100506/National Natural Science Foundation of China

MeSH Term

Animals
Biomarkers
Knowledge Bases
MicroRNAs
Proteins
RNA, Circular
RNA, Long Noncoding

Chemicals

Biomarkers
MicroRNAs
Proteins
RNA, Circular
RNA, Long Noncoding
Journal Article
Article has an altmetric score of 17

Word Cloud

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