Release 36
(Aug 22, 2018)
 

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:
2,040
7
1,992
158,499

This graph is partly adopted from
the RGD with kind permission
Last 4 weeks visitor activities
  • 827 visitors, who made
  • 95,885 web hits, and
  • 262.94 MB data downloads
  • Cattle QTL

    There are 116,067 QTLs from 869 publications curated into the database. Those QTLs represent 602 different traits (see data summary for details).

    Chicken QTL

    There are 10,817 QTLs from 293 publications curated into the database. Those QTLs represent 402 different traits (see data summary for details).

    Horse QTL

    There are 1,395 QTLs from 80 publications curated into the database. Those QTLs represent 54 different traits (see data summary for details).

    Pig QTL

    There are 27,963 QTLs from 635 publications curated into the database. Those QTLs represent 670 different traits (see data summary for details).

    Rainbow Trout QTL

    There are 128 QTLs from 11 publications curated into the database. Those QTLs represent 15 different traits (see data summary for most recent updates).

    Sheep QTL

    There are 2,129 QTLs from 152 publications curated into the database. Those QTLs represent 249 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: Scriptable access to the Animal QTLdb.
    Curator / Editor Tools: You can register for a curator account (free) to directly curate your data into the database. Once your curator's account is granted, you can follow a step-by-stel guide in the Curator's Manual to get a jump start. A bonus benefit for direct data curation is that you can keep your data in private status while utilizing internal tools for comparisons against existing data. You will have controls over your data and options to release them at a time of your choice.
    Batch Data Submission: If you have large amounts of data to curate, a useful alternative is to upload them in batches for a streamlined process. To use this data route, you need to prepare your data in well-defined formats following our Minimum Required Information Guideline, in these 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 Links:  ·  ·  VT / LPT / CMO  ·  ·  MIQAS  ·  ·  MIBBI  ·  ·  MI  ·  ·  Animal CorrDB
    REFERENCES:
    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, gky1084 (Published early online, Nov., 8 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.

    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

    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..

    Zhi-Liang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). A QTL Resource and Comparison Tool for Pigs: PigQTLDB. Mammalian Genome. (2005) Volume 16(10):792-800.


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