Notes on the Development and Release History
of the Animal QTL Database

The 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. The vision layout, complete database design, initial data curation and preliminary exploration on the approaches was not made until 2002/2003 when I returned to Iowa State. The pig QTL data visualization tools were developed in 2004, which result in our first paper on PigQTLdb published (Mammalian Genome 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 Anubis tool, Cold Spring Harbor Lab for cMAP, University of Tennessee Bioinformatics group for their Mouse/Human Bone Density QTL Database, Sweden RatMap Group for its QTL tools, Texas A&M University for a Bovine QTL Viewer, among others. For various reasons none of these tools could be worked out with the available facilities, satisfection of our check list of goals in terms of 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.

Under an agreement between the NAGRP Bioinformatics Coordinator and the NCBI, a copy of the database is implemented at the NCBI. As the development work went, the NCBI made a preliminary release with partial data in June 2004 (Release 1); and the NAGRP made a second release (Release 2) 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. Due to the NCBI database structural change and re-development (e.g. Case of Locus Link database and the creation of Gene database), the QTL synchronization was at a pause during 2006-2009. The data synchronization was resumed in 2009, with continued efforts in making the data stream smooth.

The QTLdb release was made at lease once per year in the first few years. We currently try to do more frequent releases, e.g. about 3-4 time a year, as new data added to the database (See Box 1).

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.

Related publications throughout the course of this work (in reverse chronical order):

• 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.
• # 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 XVIII Conference, January 14-19, 2011. Town & Country Convention Center, San Diego, CA.
• 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, 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.
• 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.
• 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.
• 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, 1-4 (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.
• 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; doi:10.1093/nar/gkl946.
• 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.
• 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.
• 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 XIV Conference, San Diego, CA, January 15-19, 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".
• 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.

• 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.
• 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.
• RatMap QTL Tools: URL: http://ratmap.gen.gu.se/ by Sweden RatMap Group. No longer publicly available.
• 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.