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. 2022 Jan 7;50(D1):D956-D961.
doi: 10.1093/nar/gkab1116.

Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services

Zhi-Liang Hu  1 , Carissa A Park  1 , James M Reecy  1
Affiliations

Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services

Zhi-Liang Hu et al. Nucleic Acids Res. .

Abstract

The Animal QTLdb (https://www.animalgenome.org/QTLdb) and CorrDB (https://www.animalgenome.org/CorrDB) are unique resources for livestock animal genetics and genomics research which have been used extensively by the international livestock genome research community. This is largely due to the active development of the databases over the years to keep up with the rapid advancement of genome sciences. The ongoing development has ensured that these databases provide researchers not only with continually updated data but also with new web tools to disseminate the data. Through our continued efforts, the databases have evolved from the original Pig QTLdb for cross-experiment QTL data comparisons to an Animal QTLdb hosting 220 401 QTL, SNP association and eQTL data linking phenotype to genotype for 2210 traits. In addition, there are 23 552 correlations for 866 traits and 4273 heritability data on 1069 traits in CorrDB. All these data were curated from 3157 publications that cover seven livestock species. Along with the continued data curation, new species, additional genome builds, and new functions and features have been built into the databases as well. Standardized procedures to support data mapping on multiple species/genome builds and the ability to browse data based on linked ontology terms are highlights of the recent developments.

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Figures

Figure 1.
Figure 1.
Cumulative curated data increase in all seven species hosted at the Animal QTLdb/CorrDB (according to database release records; data transformation was performed on data counts in order for small counts to be visible).
Figure 2.
Figure 2.
A stacked column plot showing a significant increase of curated data by data types in recent years (Notes: (i) the data for 2021 are mid-year counts; (ii) counts for all data types are transformed for small values to be visible; (iii) prior to 2009, the database did not have a full-time curator).
Figure 3.
Figure 3.
Two trait ontology hierarchy browser views showing the partially expanded QTLdb trait hierarchy (A) and Vertebrate Trait Ontology hierarchy (B), with QTL/association data links marked where found.
Figure 4.
Figure 4.
Simplified web portal structure to minimize unnecessary steps for improved access to data while providing tools for various types of data discovery, formatting, and visualization.
See this image and copyright information in PMC

References

    1. Bai Y., Sartor M., Cavalcoli J.. Current status and future perspectives for sequencing livestock genomes. J. Anim. Sci. Biotechnol. 2012; 3:8. - PMC - PubMed
    1. Sayers E.W., Beck J., Brister J.R., Bolton E.E., Canese K., Comeau D.C., Funk K., Ketter A., Kim S., Kimchi A.et al. .. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2020; 48:D9–D16. - PMC - PubMed
    1. Uffelmann E., Huang Q.Q., Munung N.S., de Vries J., Okada Y., Martin A.R., Martin H.C., Lappalainen T., Posthuma D.. Genome-wide association studies. Nat. Rev. Methods Primers. 2021; 1:59.
    1. Clark E.L., Archibald A.L., Daetwyler H.D., Groenen M.A.M., Harrison P.W., Houston R.D., Kühn C., Lien S., Macqueen D.J., Reecy J.M.et al. .. From FAANG to fork: application of highly annotated genomes to improve farmed animal production. Genome Biol. 2020; 21:285. - PMC - PubMed
    1. Hu Z.L., Park C.A., Reecy J.M.. Developmental progress and current status of the Animal QTLdb. Nucleic Acids Res. 2016; 44:D827–D833. - PMC - PubMed

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