Notes on the Animal QTL Database Development

The Animal QTL Database development is a project driven by a team at the Iowa State University, initially under the NAGRP Pig Genome Program (1999-2003) led by Max F. Rothschild and currently under the NAGRP Bioinformatics Coordination Program (2003-2008, 2008-2013, 2013-2018, 2018-2023) led by James M. Reecy.

Initial proposals, plans, and design scratches on developing a (pig) QTL database was made within the NAGRP Pig Genome Coordination Program in the fall of 1998. During the early days of the initial developments, much of the informal discussions about visions, designs and implementations were among scientists from Roslin Institute (UK) and within Iowa State University. Part of the missions of my 2-week working visit to the Roslin in the summer of 1999 was on this. Those who were involved in the discussions include Drs. Alan Archibald, Jian Hu, Andy Law, Lizhen Wang, Jack Dekkers, et al. Discussions with John Bastiaansen on trait data organizations was also useful while I served as an consultant to PIC in late 2001. The database layout, design, initial data curation and preliminary exploration on the approaches implementing user portals were actually tried out in 2002/2003 when I returned to Iowa State University where I stayed as an Associate Scientist until now.

Working with NCBI team was a boost to the QTLdb development in terms of implementation of a data structure using their mouse QTL data template. Under an agreement between the NAGRP Bioinformatics Coordinator and the NCBI, a copy of the database is implemented at the NCBI. Thanks for the works of Drs. Donna Maglott, Svetlana Dracheva, and Wonhee Jang, a preliminary release with partial data was made on NCBI portals in June 2004 (Release 1). Subsequently the NAGRP made a second release (Release 2) with many customized user interface tools in December, 2004 as the data collection and new tools development came to a completion. As initially planned, the pig QTL data is synchronized between the NCBI and NAGRP databases. During the re-development of Locus Link into its successor Gene DB, the QTL data synchronization was at a pause during 2006-2009 and was resumed in 2009, with continued efforts in making the data stream smooth.

The pig QTL data visualization tools were developed in 2004, which resulted in our first paper on PigQTLdb published by Mammalian Genome in 2005 (Volume 16(10):792-800). subsequently, the QTLdb was expanded for new functionalities and utilities. The first of which was the addition of the set of curator/editor tools. The second of which was the expansion of the QTLdb to include cattle/chicken QTL data in 2005/2006. The third of which was additions of structural alignment of the QTL maps with RH maps, human maps, FPC maps etc., with includsion of SNPs, Microarray elements, and new microsatellites for alignments in 2006/7 (see FAQ #11 for details). As a result, two more papers were published ( Nucleic Acids Research, 2007, 35 [Database issue]: D604-D609; Mammalian Genome, 18: 1-4, 2007 on a new database name, Animal QTLdb).

During the course of the project development, many attempts were made to utilize existing tools. Initially, we contacted a number of research groups and attempted several existing tools, which include: Roslin Institute for Anubis1 tool, Cold Spring Harbor Lab for cMAP, University of Tennessee Bioinformatics group for their Mouse/Human Bone Density QTL Database2, Sweden RatMap3 Group for its QTL tools, Texas A&M University for a Bovine QTL Viewer, among others. For various reasons none of these tools was worked out with the available facilities, against our list of goals in terms of both wanted functions and utilities. As the last resort we explored a Perl/GD and MySQL approach to program out the needed tools for integrating, displaying and analyzing the stored QTL data. All current peripheral tools and utilities as they stand now are built on this basis.

Releases of the QTLdb with new data and functions were made at lease once per year in the earlier years (2004-2008), and was made 3-4 times a year (since 2009) as we took more aggressive approaches by implementing multiple channels for new data curation, and dedicated curator for routine data curation activities. New additions of functions and tools became as part of the routine as well (See Animal QTLdb Releases).

The database and its peripheral tools at the NAGRP implementation was designed mainly for users to compare, confirm and locate the most plausible locations on a chromosomes for QTL. This is aimed at providing a tool for structural genomic information mining for genes responsible for quantitative traits important to animal production; The NCBI implementation has all marker information matched to marker records in NCBI's UniSTS database. This allows automatic matching of markers to public sequence data by e-PCR. Data on the NCBI and the NAGRP Animal Genome servers are cross-referenced to each other. This function allows all of the unique information on each site to appear to be integrated on the same database server via worldwide web.

A noticible extended feature developed into the QTLdb is that diverse types of structural genome features, such as microsatellites, SNPs, microarray elements, tiled FPC BACs, can be aligned with QTL map locations to aid the data mining. Further more, different map types, such as RH maps, genome sequence maps, human maps, can also be align where available data is available to establish links. This functionality is further enhanced with the use of GBrowse tool for alignment of essentially any structural genomic features, such as transcripts, mRNA and gene structures mapped to the genome.

As part of our efforts to benefit the research community, we offered the QTLdb software tools to Jill Maddox of The University of Melbourne to set up a Sheep QTLdb in Australia in March, 2007. The Sheep QTL data were curated, and the QTLdb maintain, by Jill Maddox until 2010 when the site was migrated back to Iowa State University in October, 2010.

In order to cope with increasing demands on daily database queries, a new development was to establish mirror sites to distribute the server and network loads. The first Animal QTLdb mirror site was set up in the summer of 2013 in Wuhan, China with a courtesy by Dr. Shu-hong Zhao's group at Huazhong Agriculture University, Hubei, China. Network traffic from 18 Asia countries are currently redirected to this site: http://cn.animalgenome.org/QTLdb (The mirror site ceased operation after 2014)

Further developments of the database in the 2010s were geared towards extentions of QTLdb under a federated database model. A good example is the successful integrated development of the Animal Trait Genetic Correlation Database (CorrDB) by sharing common resources and tools in the backend, such as trait management with integrated trait ontology developments (see Vertebrate Trait (VT) Ontology, Livestock Product Trait (LPT) Ontology, Clinical Trait Ontology, and Livestock Breed Ontology). Other featured developments include additions of new species (rainbow trout, catfish, sheep, horse, etc) and new data types (GWAS, CNV, Haplotypes, epistatics, pleitropics, gene networks, polygenic data links, etc), new data curation/edit tools (automations of new data imports and managements from Pubmed, batch curation tools, permanent data locator to facilitate publication reviews, new trait data types with modifiers, etc.), new users tools such as genome alignment tools with GBrowse and JBrowse, gene and trait centric views of data, and establishing external data alliances with Ensembl, UCSC, Reuters Data Citation Index, Monarch Project, etc (previously we already established data flows with NCBI GeneDB). etc.

The success of our efforts developing the QTLdb is marked with a series of publications throughout the course of this work:

2003: Zhi-Liang Hu and Max Rothschild (2003). A Frame-Work for Developing the Pig QTL Database. [The 13th North American Colloquium on Animal Cytogenetics & Gene Mapping. Louisville, Kentucky, July 13-17, 2003.] Cytogenet Genome Res 102:357.

2005: Zhi-Liang Hu, James Reecy and Max Rothschild (2005). A Quantitative Trait Loci Resource and Comparison Tool for Pigs: PigQTLDB. Iowa State "Animal Industry 2005 Report". (Cited by 7 publications)

2005: Zhi-Liang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). PigQTLdb: A Pig QTL Database. Plant & Animal Genome XIII Conference, San Diego, CA, January 15-19, 2005. (Cited by 2 publications)

2005: 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. DOI: 10/fcrzqv (Cited by 183 publications)

2006: Zhi-Liang Hu, Sean Humphray, Carol Scott, Stacey N. Meyers, Jane Rogers, Max F. Rothschild and James M. Reecy (2006). Extension of PigQTLdb: Genome-wide Alignment of BAC FPC Maps and RH Maps for QTL Positional Gene Mining. Plant & Animal Genome XIV Conference, San Diego, CA, January 14-18, 2006. (Cited by 1 publication)

2007: 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. (Cited by 245 publications)

2007: Zhi-Liang Hu, Eric Ryan Fritz and James M. Reecy (2007). Computer Demo: A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information. Plant & Animal Genome XV Conference, San Diego, CA, January 13-17, 2007.

2007: 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 (Cited by 115 publications)

2008: Zhi-Liang Hu and James M. Reecy (2008). Extension Of Animal QTLdb (II): Alignment Of New Microsatellite Markers, SNPs And Microarray Elements To Cattle, Chicken And Pig QTL Maps And Comparative Mapping Tools For Positional Genome Information Mining. January 12-16, 2008, Town & Country Convention Center, San Diego, CA.

2008: Zhi-Liang Hu, Eric Ryan Fritz, Svetlana Dracheva, Behnam Abasht, Stacey N. Meyers, Denis M. Larkin John Bastiaansen, Carol Scott, Xiao-Ping Li, Wonhee Jang, Kwan-Suk Kim, Donna Maglott, Sean Humphray, Jonathan E. Beever, Susan J. Lamont, Harris A. Lewin, Shu-hong Zhao, Jane Rogers, Jill Maddox, Max F. Rothschild and James M. Reecy (2008). Animal QTLdb: A Tool Set to Warehouse and Compare Cattle, Pigs, Chicken and Sheep QTL Within and Between Species. International Society for Animal Genetics (ISAG), RAI Conference Centre, Amsterdam,The Netherlands. July 20-24, 2008.

2009: Zhi-Liang Hu, Cari Park, Eric Fritz, Mindy Dwindell, Mary Shimoyama, James M. Reecy (2009). Expanding the Utility of Animal QTLdb. Plant & Animal Genomes XVII Conference, January 10-14, 2009, Town & Country Convention Center, San Diego, CA. (Cited by 1 publication)

2010: 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. (Cited by 41 publications)

2011: Zhi-Liang Hu, Xiao-lin Wu, Cari Park and James M. Reecy (2011). Extension of Animal QTLdb (IV): QTL Meta-Analysis on the Fly. Plant & Animal Genomes XIX Conference, January 14-19, 2011. Town & Country Convention Center, San Diego, CA. (Cited by 1 publication)

2011: Zhi-Liang Hu, Xiao-Lin Wu and James M. Reecy (2011). Extension of Animal QTLdb: QTL Meta-analysis on the Fly. Poster paper published on ACM-BCB '11, August 1-3, 2011, Chicago, IL, USA. (Cited by 4 publications)

2012: Zhi-Liang Hu, Cari Park and James M. Reecy (2012). Animal QTLdb Extension (V): Addition of New Data Types and Functions. Plant & Animal Genomes XX Conference, January 14-19, 2012. Town & Country Convention Center, San Diego, CA. (Cited by 1 publication)

2013: 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 (Cited by 387 publications)

2015: Zhi-Liang Hu, Carissa A. Park, James E. Koltes, Eric Fritz-Waters and James M. Reecy (2015). An Application Programming Interface (API) for Programmable Access to Animal QTLdb. Plant & Animal Genomes XXIII Conference, January 10-15, 2015. Town & Country Convention Center, San Diego, CA. (Cited by 2 publications)

2016: Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2016). Animal QTLdb: towards a comprehensive database and tool set for livestock genome research. Plant & Animal Genomes XXIV Conference, January 10-15, 2016. Town & Country Convention Center, San Diego, CA.

2016: 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 (Cited by 237 publications)

2018: Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2018). Animal QTLdb and CorrDB updates: integrative development of genetics/genomics databases and tools to meet new challenges. Plant & Animal Genomes XXVI Conference, January 13-17, 2018. Town & Country Convention Center, San Diego, CA.

2018: 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. (Cited by 2 publications)

2019: 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 (Cited by 231 publications)

2022: 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

It is worth to note that our publications on the development of Animal QTLdb have been cited 1460 times5 as of May 24, 2022. In addition, the use of Animal QTLdb has been mentioned (including both literature citation and referencing the use of the QTLdb).

First draft: January 3, 2005
Modified : January 4, 2006
Modified : January 11, 2007
Modified : January 08, 2008
Modified : September 25, 2009
Modified : July, 24, 2010
Last updated: August 30, 2019
By Zhiliang Hu
Associate Scientist
Dept of Animal Science
Iowa State University

Footnotes:
  1. Anubis: A graphic tool made in Java that draws (comparative) linkage maps. It was developed by Chris Mungal at the Roslin Institute and served the Arkdb during 1995-2003. Now it's no longer supported.
  2. Mouse/Human Bone Density QTL Database: URL: http://132.192.64.52/qtl/ by Weikuan Gu's group at the University of Tennessee. It is no longer publicly available.
  3. RatMap QTL Tools: URL: http://ratmap.gen.gu.se/ by Sweden RatMap Group. No longer publicly available.
  4. Sheep QTLdb: The Sheep QTL data was curated and maintained at the The University of Melbourne (Australia) between March 2007 and November 2010 by Jill Madox using the QTLdb software suite. The Sheep QTLdb was migrated from its Australia to its Iowa State University site in October 2010.
  5. This number may be inflated because a publication may cite more than one of our papers on the QTLdb.
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