Release 47
(Apr 25, 2022)
 

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped to livestock animal genomes, in order to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features such as annotated genes.

Many scientific journals require or recommend that any original QTL/association data be deposited into a public database before a paper may be accepted for publication. We provide user/curator accounts for direct data submission, and in return we supply users with a data summary link to facilitate the manuscript review process.

Database summary:
Publications:
Species:
Traits:
QTL/associations:
2,593
7
2,272
253,330

This graph is partly adopted from
the RGD with kind permission
Last 30 days visitor activities:
  • 651 visitors, who made
  • 9,019 hits, which generated
  • 124.09 MB data downloads
  • Cattle QTL  

    There are 192,925 QTL from 1,103 publications curated into the database. Those QTL represent 701 different traits (see data summary for details).

    Catfish QTL

    There are 0 QTL from 0 publications curated into the database. Those QTL represent 0 different traits (see data summary for details).

    Chicken QTL

    There are 16,637 QTL from 374 publications curated into the database. Those QTL represent 443 different traits (see data summary for details).

    Goat QTL

    There are 128 QTL from 6 publications curated into the database. Those QTL represent 25 different traits (see data summary for details).

    Horse QTL

    There are 2,636 QTL from 106 publications curated into the database. Those QTL represent 65 different traits (see data summary for details).

    Pig QTL

    There are 35,384 QTL from 762 publications curated into the database. Those QTL represent 716 different traits (see data summary for details).

    Rainbow Trout QTL

    There are 1,413 QTL from 21 publications curated into the database. Those QTL represent 41 different traits (see data summary for most recent updates).

    Sheep QTL

    There are 4,207 QTL from 221 publications curated into the database. Those QTL represent 281 different traits (see data summary for most recent updates).

    QTL on GBrowse / JBrowse: For species that have a genome sequence assembly, QTL/association data are also ported to GBrowse and JBrowse to view against respective map features on their most recent builds.
    Data Alliances: Newly released QTL/association data are exported to our data alliances: Ensembl, Monarch Project, NCBI Entrez GeneDB, Reuters Data Citation Index, and UCSC. Users can employ tools on these respective sites for information mining in relation to animal QTL and association data.
    Data Downloads: The QTLdb data is available for download at each species front page or at individual chromosome pages, where customized data search/download is possible. The data formats include "cM" mapping data in tab-delimited form and "bp" locations in GFF, BAM, and BED formats (FAQ #23).
    API and dbxref: We provide scriptable access to the Animal QTLdb using a REpresentational State Transfer (REST) protocol, and dbxref links into the database for information.
    Curator / Editor Tools: You can register for a free curator account to directly get your data into the database. Once your curator's account is granted, you can find a step-by-step curation guide to help you proceed, for manual data entry or for batch data upload. You can keep your data in private status until a time when you wish to making it public.
    Batch Data Submission: A useful alternative to curate large amounts of data is to upload them in batches for our team to help you out a streamlined process. Please prepare your data in required formats described in the Minimum Required Information Guideline, in three simple steps.
    Video Tutorials: Video tutorials to show how to use newly developed database tools to access and analyze information stored in the Animal QTLdb.
    Frequently Asked Questions: Questions and answers designed to serve as a general user's guide to the Animal QTLdb, addressing common questions such as functions, data scopes, database usages, applications, new developments, etc.
    Related resources:  ·  ·  VT / LPT / CMO  ·  ·  MIQAS  ·  ·  MIBBI  ·  ·  MI  ·  ·  Animal CorrDB  ·  · 
    REFERENCES:
    Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2022). Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. Nucleic Acids Research, Volume 50, Issue D1, Pages D956–D961. DOI: 10.1093/nar/gkab1116

    Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2019). Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. Nucleic Acids Research, Volume 47, Issue D1, 8 January 2019, Pages D701–D710. DOI: 10.1093/nar/gky1084

    Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2018). Development of Animal QTLdb and CorrDB: Resynthesizing Big Data to Improve Meta-analysis of Genetic and Genomic Information. The 11th World Congress on Genetics Applied to Livestock Production (WCGALP). New Zealand, February 11-16, 2018.

    Zhi-Liang Hu, Carissa A. Park and James M. Reecy (2016). Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research, 44 (D1): D827-D833. DOI: 10.1093/nar/gkv1233

    Zhi-Liang Hu, Carissa A. Park, Xiao-Lin Wu and James M. Reecy (2013). Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Research, 41 (D1): D871-D879; DOI: 10.1093/nar/gks1150

    Zhi-Liang Hu, Carissa A. Park, Eric R. Fritz and James M. Reecy (2010). QTLdb: A Comprehensive Database Tool Building Bridges between Genotypes and Phenotypes. Invited Lecture with full paper published electronically on The 9th World Congress on Genetics Applied to Livestock Production. Leipzig, Germany August 1-6, 2010.

    Zhi-Liang Hu and James M. Reecy (2007). Animal QTLdb: Beyond a Repository - A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information. Mammalian Genome, Volume 18(1), 1-4 (2007). DOI: 10.1007/s00335-006-0105-8

    Zhi-Liang Hu, Eric Ryan Fritz and James M. Reecy (2007). AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research, 2007, 35 (Database issue):D604-D609.

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