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: | 2,725 |
| Species: | 7 |
| Genome builds: | 19 |
| Linkage maps: | 11 |
| Measured traits: | 2,135 |
| QTL/associations: | 278,738 |
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Cattle QTLThere are 195,011 QTL (including eQTL/SNP associations) from 1,141 publications curated into the database. Those QTL represent 680 different base traits and 292 trait variants. (see cattle data summary for more details). |
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Chicken QTLThere are 18,646 QTL (including eQTL/SNP associations) from 389 publications curated into the database. Those QTL represent 372 different traits and 152 trait variants. (see chicken data summary for more details). |
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Goat QTLThere are 558 QTL (including eQTL/SNP associations) from 8 publications curated into the database. Those QTL represent 26 different base traits and 15 trait variants. (see goat data summary for more details). |
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Horse QTLThere are 2,649 QTL (including eQTL/SNP associations) from 107 publications curated into the database. Those QTL represent 65 different base traits and 1 trait variants. (see horse data summary for more details). |
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Pig QTLThere are 54,816 QTL (including eQTL/SNP associations) from 809 publications curated into the database. Those QTL represent 673 different base traits and 523 trait variants. (see pig data summary for more details). |
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Rainbow Trout QTLThere are 2,329 QTL (including eQTL/SNP associations) from 23 publications curated into the database. Those QTL represent 47 different base traits and 6 trait variants. (see rainbow trout data summary for more details). |
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Sheep QTLThere are 4,729 QTL (including eQTL/SNP associations) from 248 publications curated into the database. Those QTL represent 272 different base traits and 127 trait variants. (see sheep data summary for more details). |
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 reference builds.
Supported genomes/maps: Multiple genome sequence builds and linkage maps are used for data curations and mappings in the QTLdb. Up to date the QTLdb is supporting 11 linkage maps and 19 genome builds. One per map type per species are used as default references).
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:
Data is available for download at each species main page or each chromosome page,
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:
Scriptable access to the Animal QTLdb using a REpresentational State Transfer
(REST) protocol, and dbxref links into the database for extended 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 make 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: A general user's guide in forms of questions
and answers addressing common questions such as how to access data, often related with
various web tools, functions, access points and/or routes to get to certain data, etc.
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 (WCGALP). 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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