The Animal QTLdb Releases

    (May 01, 2004): Pig QTLdb, NCBI Implementation, with 466 pig QTL. This release features the links of QTL to Locus Link of NCBI Entrez Databases.

    (Dec 20, 2004): Pig QTL db, NAGRP Implementation, with a total of 791 pig QTL. This release features browseable QTL alignments as viewed in chromosomal graphs.

    (Jan 04, 2006): Pig FPC, RH, and human maps are aligned; 1,263 pig QTL

    (Aug 15, 2006): The QTLdb tools are extended to also include cattle and chicken QTL data, "Pig QTLdb" is renamed to "Animal QTLdb", Pig QTL: 1,287; Cattle QTL: 630; Chicken QTL: 657.

    (Jan 05, 2007): SNPs and New microsatellite markers are aligned (Pig QTLdb); Linked to genome tracks (Cattle QTLdb); Pig QTL: 1,675; Cattle QTL: 846; Chicken QTL: 657.

    (Jan 08, 2008): More SNPs and microarray elements are aligned (Pig QTLdb, Cattle QTLdb); Tools were built to port SNP minor allele frequency data from dbSNP (Cattle QTLdb); Oligo array expression data are incorporated (Pig QTLdb). Pig QTL: 1,675; Cattle QTL: 1125; Chicken QTL: 657; Sheep: 51.4

    (Jan 09, 2009): Two new functions are introduced: (1) GBrowse is introduced to display alignments of QTL against other genome features. (2) QTL data is now freely downloadable in several ways (download all QTL for a species or download a snapshot from a customized chromosomal view).

    (Apr 21, 2009): (1) 955 new QTL data are added to the database (Pig: 569; Cattle: 252; Chiken: 134). (2) Data download also includes QTL genome locations ("bp") now. (3) Pig QTL are ported to view in GBrowse for chromosomes that have genome assemblies available. Cattle QTL: 1,377; Chicken QTL: 791; Pig QTL: 2,102; Sheep QTL: 84.
    New functions added: (1) QTL data can now be downloaded in GFF format for use in external analysis such as uploading to UCSC site or to a GBrowse for genome feature alignments. (2) Bovine 50K SNP chip elements are aligned in GBrowse.

    (Sep 15, 2009): Cattle QTL: 2,344; Chicken QTL: 1,290; Pig QTL: 4,928; Sheep QTL: 84 (The number of new QTL added to the database: 4,079 -- Cattle: 983; Chicken: 502; Pig: 2,594, including 897 eQTL).

    (Dec 30, 2009): The QTLdb CGI codes are restructured and modified to accommodate housing of multiple species. The restructure has helped for an easy code/process management. Cattle QTL: 2,359; Chicken QTL: 1,863; Pig QTL: 5,621; Sheep QTL: 84 (New QTL added to the database: 1,281 -- Cattle: 15; Chicken: 573; Pig: 693).
    New functions added: QTLdb data are ported to and synchronized with NCBI Entrez Gene Database.

    (Apr 23, 2010): Cattle QTL: 3,891; Chicken QTL: 1,863; Pig QTL: 5,732; Sheep QTL: 84 (New QTL added to the database: 1,643 -- Cattle: 1532; Pig: 111).
    New functions added: SAM data format is now available for QTL data download.

    (Sep 13, 2010): Total QTL in the database: 12,635 [Break down: Cattle QTL: 4,281; Chicken QTL: 2,284; Pig QTL: 5,986; Sheep QTL: 84 ] (New QTL added to the database: 1,065 -- Cattle: 390; Chicken: 421; Pig: 254; Sheep: 0).

    (Dec 31, 2010): Total QTL in the database: 13,825 [Break down: Cattle QTL: 4,682; Chicken QTL: 2,451; Pig QTL: 6,344; Sheep QTL: 348 ] (New QTL added to the database: 1,190 -- Cattle: 401; Chicken: 167; Pig: 358; Sheep: 264).
    New functions added: (1) The Sheep QTLdb has been migrated from its Australia to its Iowa State University site. (2) Pig QTLs are aligned to the pig genome preliminary assembly 9.2. (3) A QTL meta-plot analysis tool is added to the QTLdb. (4) Cytogenetic G-banded chromosome ideograms have been added to QTL maps within the QTLdb for cattle, sheep, pigs and chicken.

    (Apr 20, 2011): Total QTL in the database: 13,931 [Break down: Cattle QTL: 4,682; Chicken QTL: 2,451; Pig QTL: 6,344; Sheep QTL: 454 ] (New QTL added to the database: Sheep: 106; Efforts in this period were mainly on improving data qualities and quality control procedures).

    (Sep 22, 2011): Total QTL in the database: 14,239 [Break down: Cattle QTL: 4,802; Chicken QTL: 2,451; Pig QTL: 6,347; Sheep QTL: 639 ] (New QTL added to the database: 308 -- Cattle: 120; Chicken: 0; Pig: 3; Sheep: 185).

    (Jan 02, 2011): Total QTL in the database: 15,014 [Break down: Cattle QTL: 5,207; Chicken QTL: 2,736; Pig QTL: 6,432; Sheep QTL: 639; Rainbow trout: 27] (New QTL added to the database: 802 -- Cattle: 405; Chicken: 285; Pig: 85; Sheep: 0; Rainbow trout: 27).
    New functions added: (1) ATO/QTL traits are mapped to VT, PT and CMO traits; (2) QTLdb is revamped to accommodate QTL/assiciation data on genome maps (map unit: bp); (3) Animal breed information can now be seen on the QTL detail page; (4) Rainbow trout was added as a new member of species in the Animal QTLdb; (5) lists of references are available for all QTL seen within any chromosomal view window.

    (Apr 20, 2012): Total QTL in the database: 16,584 [Break down: Cattle QTL: 5,920; Chicken QTL: 3,162; Pig QTL: 6,818; Sheep QTL: 684; Rainbow trout: 73] (New QTL added to the database: 1,616 -- Cattle: 713; Chicken: 426; Pig: 386; Sheep: 45; Rainbow trout: 73).
    New functions added: (1) Updated map location conversion (cM to bp) algorithms; (2) Multiple QTL can be searched for customized QTL alignments and meta-plots; (3) QTL overview within a super-trait is made possible; (4) New query for QTL publication summary by super-trait (trait-type); (5) Structured literature search can better target search scopes; (6) An extensive overhaul of the QTLdb curator tools.

    (Aug 21, 2012): A sum of 1,006 new QTL added to the database. The current total number of QTL in the database: 17,566 [Break down: Cattle: 5,920; Chicken: 3,442; Pig: 7,451; Sheep: 753; Rainbow trout: 88] (New additions less obsolete ones: Cattle: 0; Chicken: 280; Pig: 633; Sheep: 69; Rainbow trout: 15 -- Net increase: 997).
    Functions: A number of behind-the-sence improvement were made to the QTLdb, which include semi-automated checks and updates the temporary publication IDs used in initial data curation against updated PubMed IDs, to avoid accidental re-entry of the same data; Also, when a QTL becomes obsolete, the same entry at the NCBI will not be deleted but becomes unavailable, with a message: "DISCONTINUED: This record was withdrawn by the AnimalQTLdb".

    (Dec 27, 2012): A sum of 1,249 new QTL added to the database. The current total number of QTL in the database: 18,815 [Break down: Cattle: 6,305; Chicken: 3,442; Pig: 8,315; Sheep: 753; Rainbow trout: 88] (New additions less obsolete ones: Cattle: 385; Chicken: 0; Pig: 864; Sheep: 0; Rainbow trout: 0 -- Net increase: 1,249). ( This is a joint release with the first CorrDB release)

    Functions: More data fields are added to the Animal QTLdb data download files (e.g. "test models", "significant levels", and "map types") so that users can sort them out on their own.

    (Apr 20, 2013): The total number of QTL/association data in the database has reached 20,217. The current total number of QTL in the database: 20,090 [Break down: Cattle: 7,091; Chicken: 3,808; Pig: 8,402; Sheep: 789; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 7091; Chicken: 3808; Pig: 8402; Sheep: 789; Rainbow trout: 127 -- Net increase: 20,217).
    Functions: Fixed bugs where chromosomes were not properly displayed when a default chromosome length ratio was not met in odd situations. Improved QTLdb Curator tools: (1) Added options to allow manual search and import of PubMed references for data curation; (2) Added data review functions for curator/editor to update QTL data status; (3) Improved reference based QTL data status counts and list summary for review/retract actions; (4) Improved QTL data flow route to eliminate ambiguous data status route.

    (Aug 26, 2013): A sum of 1,563 new QTL added to the database. The current total number of QTL in the database: 21,558 [Break down: Cattle: 7,931; Chicken: 3,919; Pig: 8,919; Sheep: 789; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 915; Chicken: 115; Pig: 533; Sheep: 0; Rainbow trout: 0 -- Net increase: 1,563).
    Functions: (1) A China mirror site is set up at the Huazhong Agriculture Univeristy, in Wuhan, China, thanks to the generous offer by Dr. Shu-hong Zhao and hard works by her colleagous. (2) Database expanded to include gene network analysis results. More additions on the functionality is going to happen in the coming months. (2) Search for candidate genes in QTLdb is made easier - Candidate genes is displayed where applicable when users search for traits or for partial gene names/symbols. (3) Fixed a couple dozen minor bugs in both public data portal and in the curator tools.

    (Dec 28, 2013): A sum of 1,317 new QTL/association data has been added to the database. The current QTL/association number in the database: 23,002 [Cattle: 8,305; Chicken: 3,919; Pig: 9,862; Sheep: 789; Rainbow trout: 127].
    Functions: (1) Horse QTLdb: Many THANKS to Cecilia Penedo of UC-Davis, Andy Law of Roslin Institute, Samantha Brooks of Cornell University, and Ernest Bailey of University of Kentucky; now the Animal QTLdb has the structure set up for collecting horse QTL/association data. Please note it will take a while for the new horse data to pass curation and release pipelines before they show up on the Horse QTLdb portal. (2) New members to Animal QTLdb data alliances: - Ensembl: Thanks to Fiona Cunningham, Animal QTLdb data is now synchronized to Ensembl. To use, go to http://www.ensembl.org and choose a species to search for a trait name; among the output results, all QTL/association data are flagged by "Phenotype" in parentheses. You can utilize all Ensembl tools to explore further on your traits of interest. The genome features are linked back to Animal QTLdb for curated details. Please note that data at Ensembl or UCSC is for species that has a genome assembly available (e.g., cattle, chicken, sheep, or pig). (3) Animal QTLdb Search Tools are being reformatted for users to easily locate information for exploration, or to easily find data access points for analysis. - NEW: QTL genome distribution query tool: New search tools have been added to allow users to view genome location distributions of targeted traits. Go to "Search" -> "Data Analysis Tools" -> "Find QTL genome distributions on a particular trait" to try it out. - NEW: User-defined download tool by genome locations: Users now can search and download QTL data by user-defined genome locations (in terms of "bp"). Go to "Search" -> "Data Analysis Tools" -> "Find QTL by their genome locations", for species that have a genome build (currently cattle, chicken, and pig). (4) New data types in the Animal QTLdb: In parallel to the classical "QTL" data, we have modified the database and tools to allow curation of eQTL and GWAS (association) data; now we are modifying the database and tools to allow curation of copy number variation (CNV) data into the database. It is our goal to be inclusive on all types of trait mapping features linking phenotypes to genotypes. (5) Welcome new curators to the Animal QTLdb; we now have 65 active curator accounts. As always, we encourage all interested persons to register for a curator account to actively enter new data.

    (Apr 21, 2014): A sum of 1,873 new QTL added to the database. The current total number of QTL in the database: 24,748 [Break down: Cattle: 9,180; Chicken: 4,282; Pig: 10,497; Sheep: 789; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 875; Chicken: 363; Pig: 635; Sheep: 0; Rainbow trout: 0 -- Net increase: 1,873).
    Functions: (1) Pleiotropic QTL/association data are now included for curation. (2) Sheep QTL/association data are mapped to the sheep genome. (3) The Animal QTLdb has been improved to allow users to analyze QTL by their trait types. See QTLdb FAQ items for details. (4) A "grand search" tool is made available to simplify the database-wide search. (5) The map viewer has been improved to allow user defined QTL to be viewed. (6) Search for Vertebrate Trait (VT) Ontology, Product Trait (PT) Ontology, and Clinical Measurement Ontology (CMO) terms within the Animal QTLdb is made possible.

    (Aug 25, 2014): A sum of 3,876 new QTL added to the database. The current total number of QTL in the database: 28,624 [Break down: Cattle: 11,543; Chicken: 4,337; Horse: 345; Pig: 11,610; Sheep: 789; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 2363; Chicken: 55; Horse: 345; Pig: 1113; Sheep: 0; Rainbow trout: 0 -- Net increase: 3,876).
    Functions: (1) UCSC: The complete implementation of livestock animal QTL tracks at the UCSC site took extended time and they are finally made available in the recent new release of UCSC Genome browser. Thanks to Pauline Fujita and Robert Kuhn for their deligent works to facilitate this. (2) A new QTLdb curator tool is added to help users batch deposit their QTL/association data. As a matter of fact among 3876 newly curated QTL/association data, two thirds of them (2,550) were curated using this tool. (3) A new search tool is added to the Animal QTLdb to allow query of neighboring QTL/associations by a user-defined view window. Its utility comes with a sliding window, also defined by user on viewing size and slide distance. The tool also included a graphical representation of the two window positions relative to their chromosome locations. Hyper links enable users to bring the QTL/associations to visualize for their alignments in GBrowse. (4) We have begun to create video tutorials to introduce new tools developed for Animal QTLdb users to easily access and analyse the QTL data curated into the database. More tutorials are to be added in the coming weeks. We welcome vedio tutorial contribution from users to share your experiences as how you discovered the QTLdb utilities.

    (Dec 29, 2014): A sum of 3,314 new QTL added to the database. The current total number of QTL in the database: 32,065 [Break down: Cattle: 13,145; Chicken: 4,379; Horse: 1,005; Pig: 12,618; Sheep: 791; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 1,602; Chicken: 42; Horse: 660; Pig: 1,008; Sheep: 2; Rainbow trout: 0 -- Net increase: 3,314).
    Functions: (1) The state of art online alignment tool - Jbrowse - has been setup for QTL/association data alignment with annotated genes among other genome features. The advantage of Jbrowse is that it allows easy user quantitative data - XYPlot, Density, in BAM or VCF format - to be loaded for comparisons directly to users browser in users local environment. The links to JBrowse can be found on both the front page of AnimalGenome.ORG, and on the Animal QTLdb front page. (2) A preliminary application programming interface (API) has been added to the Animal QTLdb. This implementation used REST web service architecture and XML markup lanuage for data transportations. The added scritable access to the QTLdb is aimed to facilitate end users for a more dynamic access of QTLdb data. (3) Horse QTL data is now streamed to UCSC Genome Browser, Ensembl database for alignment display and data mining using the tools available at UCSC/Ensembl. QTL data stream to NCBI is on the way. (4) A Wordle representation of QTL/ Association discovery trends is made as a fun project.

    (Apr 27, 2015): A sum of 5,344 new QTL added to the database. The current total number of QTL in the database: 37,409 [Break down: Cattle: 17,908; Chicken: 4,525; Horse: 1,018; Pig: 13,030; Sheep: 801; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 4,763; Chicken: 146; Horse: 13; Pig: 412; Sheep: 10; Rainbow trout: 0 -- Net increase: 5,344).
    Functions: We devoted to debug the processes with which QTL/association map location data are converted to allow dispaly in GBrowse/JBrowse. Should there be any odd situations, please feel free to contact us.

    (Aug 28, 2015): A sum of 20,005 new QTL added to the database. The current total number of QTL in the database: 57,414 [Break down: Cattle: 36,693; Chicken: 4,676; Horse: 1,124; Pig: 13,958; Sheep: 836; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 18,785; Chicken: 151; Horse: 106; Pig: 928; Sheep: 35; Rainbow trout: 0 -- Net increase: 20,005).
    Functions: The QTLdb curator tools have been improved (1) There is now a better review environment for private data, including an overall view of data from a report, and a special URL link and channels for external reviews of data (e.g., by journal editors/reviewers) prior to the public data release. (2) A companion tool has been created for curators to search officially published SNPs based on reported genome location. This allows curation of QTL/association data that was previously excluded from data entry due to lack of minimum required information for curation. Using official dbSNP IDs helps consistently anchor the map locations of reported QTL/association data. (3) It's now possible to enter QTL/association data using genome map coordinates if stable dbSNP identifiers are not available. Previously, the genome coordinates were imported based on official dbSNP information. We have now developed a method to record genome coordinates with build versions represented by chromosome RefSeq IDs. (4) Although all QTL/association data must be assigned to an existing trait ontology entry (VT/PT/CMO), curators can now include the reported trait names in the QTL record to allow retrospective review and improve future ontology development.

    (Dec 29, 2015): A sum of 6,622 new QTL added to the database. The current total number of QTL in the database: 64,036 [Break down: Cattle: 42,019; Chicken: 5,196; Horse: 1,125; Pig: 14,479; Sheep: 1,090; Rainbow trout: 127] (New additions less obsolete ones: Cattle: 5,326; Chicken: 520; Horse: 1; Pig: 521; Sheep: 254; Rainbow trout: 0 -- Net increase: 6,622).
    Functions: (1) New information pages were set up to describe the steps needed to upload a large quantity of new QTL/association data. An important part of this information is a set of guidelines regarding the minimum Information required for preparation of new QTL/association data. Actual working examples will be added in the coming months. (2) A new plot tool for whole genome view of QTL/association data was created. This is to overcome the space limitations of the old plot tool where all chromosomes are arranged in a panel with a fixed dimension (as such the old whole genome plot only gives a brief overview of QTL/associations with limited number of data allowed by the space). Currently the new plot tool is linked from the old tool as an alternative. It will be made as default, and more query/plot options will be implemented for wider applications in the coming months. (3) An user input portal is added to the QTL/association view page. The purpose of this function is for users to add annotations, comments, and report problems. Additional annotation data will aid future meta analysis; problem report will help with our data quality control efforts. (4) A new function is added that it is not possible to review QTL/association data by traits, and enter the same comments for multiple QTL/association data for the same trait. This relives curators from laborious repeats and helps for a better data review. (5) A number of debugs in the curator/editor tools were found and fixed. This continued effort helps to ensure an improved data curation process.

    (Apr 29, 2016): A sum of 30,421 new QTL added to the database. The current total number of QTL in the database: 94,457 [Break down: Cattle: 71,448; Chicken: 5,462; Horse: 1,139; Pig: 15,108; Sheep: 1,173; Rainbow trout: 127] (New additions less obsolete/retracted ones: Cattle: 29,429; Chicken: 266; Horse: 14; Pig: 629; Sheep: 83; Rainbow trout: 0 -- Net increase: 30,421).
    Functions: (1) A new structure is being developed for the QTLdb to allow supplementary data from a publication to be uploaded "as is". These data include original genotypes, phenotypes, near-significant or other association/QTL data from the same experiment, supplementary to the curated data. We are still in the process of developing schemes where the use of these data by the public or third parties can best be managed. (2) The QTLdb was developed to allow two sets of genome maps for cattle. As the genome assemblies of multiple species are being improved, we are working to revamp the structure to allow alternative genome maps to show association/QTL data. Stay tuned for further details to come. (3) We continue to improve processes and tools for post-curation data debugging and data release procedures to ensure good data quality. (4) Now the QTLdb can "retract" data once the paper is retracted by the journal. (5) Five new curators have signed up for a curator account, adding the total number of QTLdb curators to 91.

    (Aug 29, 2016): A sum of 11,571 new QTL added to the database. The current total number of QTL in the database: 106,028 [Break down: Cattle: 81,652; Catfish: 0; Chicken: 5,683; Horse: 1,197; Pig: 16,033; Sheep: 1,336; Rainbow trout: 127] (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 10,204; Chicken: 221; Horse: 58; Pig: 925; Sheep: 163; Rainbow trout: 0 -- Net increase: 11,571).
    New developments: (1) Introducing the new chicken genome build (GG_5.0) to the QTLdb. We have completed the first trial of lifting the QTL/association coordinates to the new build. Continued efforts will be made to verify the transferred data in the upcoming weeks. Please note the availability of chicken QTL/association data for download and for graphic visualization online may be affected. (2) New file format examples are being added to the "Minimum information required for Animal QTLdb data entry" page in the form of Excel work sheets. Click the icon on the right hand side to see an example, and scroll to the bottom of the page to download all Excel templates. More such templates are still being added to provide a convenient way for users to prepare their data for upload into the QTLdb.

    (Dec 30, 2016): A sum of 15,237 new QTL have been added to the database. The current total number of QTL in the database: 121,265 [Break down: Cattle: 95,332; Catfish: 0; Chicken: 6,633; Horse: 1,245; Pig: 16,516; Sheep: 1,412; Rainbow trout: 127] (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 13,680; Chicken: 950; Horse: 48; Pig: 483; Sheep: 76; Rainbow trout: 0 -- Net QTL number increase: 15,237).
    New developments: (1) The curation tools are improved to allow automatic verification and streamlined curation of SNP information into the database. The improvements involved data quality control processes in which multiple genome builds are maintained for cattle, chicken, and sheep. (2) curation protocols are modified that preliminary SNPs (with 'ss' numbers only) are allowed to be entered to anchor QTL/association mapping locations. The QTL/association mapping data represented by the 'ss' SNPs are not subject to normal data release procedure unless the manually entered map coordinates are also available. The 'ss' SNP information will eventually be replaced with their 'rs' SNP information once they are assigned by dbSNP. (3) The QTLdb Frequently Aked Questions are updated.

    (Apr 27, 2017): A sum of 21,004 new QTL added to the database. The current total number of QTL in the database: 125,753 [Break down: Cattle: 98,090; Chicken: 6,791; Horse: 1,275; Pig: 17,955; Sheep: 1,515; Rainbow trout: 127] (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 2,758; Chicken: 158; Horse: 30; Pig: 17,955; Sheep: 103; Rainbow trout: 0 -- Net increase: 21,004).
    Other developments: (1) Access to the Wordle representation of QTL/association-mapped traits by year, across all species, can now be found in the data summary area of each species on the Animal QTLdb. (2) Efforts have continued to improve QTLdb curator/editor/release tools and procedures in terms of debugs, adding new parameters, and optimize the procedures for various data updates, especially to meet the challenges accommodating multiple genomes, aligning map coordinates between linkage maps, SNP represented coordinates, manually entered coordinates, and conversions between where needed.

    (Aug 26, 2017): A sum of 10,384 new QTL added to the database. The current total number of QTL in the database: 136,137 [Break down: Cattle: 99,652; Chicken: 7,812; Horse: 1,278; Pig: 25,610; Sheep: 1,658; Rainbow trout: 127] (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 1,562; Chicken: 1,021; Horse: 3; Pig: 7,655; Sheep: 143; Rainbow trout: 0 -- Net increase: 10,384).
    Database developments: (1) A "permanent record locator" has been implemented in the AnimalQTLdb to provide unique and stable links to all curated QTL/association data for a publication. The new "permanent record locator" is a replacement of a "URL Link" function introduced two years ago and overcomes some of its shortcomings. It can be used by the authors to refer to their published data, to provide proof of evidence of data entry at the Animal QTLdb to journal editors/manuscript reviewers, and to serve other purposes. All QTLdb curators/editors have access to this tool for their curated data. (2) The backend database structure and processes to handle curation of QTL traits paralleled with VT/LPT/CMO ontology developments have been undergoing further improvements in terms of facilitating curation of trait terms modified by a diversified list of entities such as time, anatomical locations, measurement methods, etc. This is in conjunction with Animal Correlation Database (CorrDB) development. Stay tuned for further news. (3) We have registered 5 users for new curator accounts this year. We encourage users to apply for an Animal QTLdb curator account to learn how it may help their research, and to possibly be more involved in database development. We love to work with you and appreciate your useful ideas, suggestions, and/or requests, which all help to make the database/tools more useful to the community. (4) Periodic data checks on "on-hold", "conditionally released" (such as QTL/associations marked with 'ss' SNPs), and "suspended" data have been automated. This helps to make sure no sub-optimal data goes unnoticed.

    (Dec 21, 2017): A sum of 9,705 new QTL added to the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 8,388; Chicken: 551; Horse: 26; Pig: 466; Sheep: 274; Rainbow trout: 0 -- Net increase: 9,705). The current total number of QTL in the database: 145,842 [Break down: Cattle: 108,040; Chicken: 8,363; Horse: 1,304; Pig: 26,076; Sheep: 1,932; Rainbow trout: 127]
    ( This is a joint release with the 2nd CorrDB release)

    Database developments: (1) The development of the initial sets of curator tools has completed for the Animal Correlation Database (CorrDB). With this release, we open the CorrDB curation for free registration for anyone who wish to be a curator to enter own or public correlation and heritability data. (2) As part of the Animal QTLdb/CorrDB co-development efforts, functions are developed to link QTL data with trait correlation data through common trait terms where such data exist. For example, within the CorrDB, under the Table View of correlation data, a hyper-linked red "QTL" label is added when QTL data exists on the trait; Like-wise, within the QTLdb on the trait search results, an hyper-linked tag is added on traits where correlation data are found. (3) New web portals are developed for display of "gene centric view" and "trait centric view" of QTL/association data where underlining gene information is available. This tool helps users to relatively quickly to interrogate and understand genotype-to-phenotype information in a synopsis. A quick way to use the tool to view information is to try a search by genes or by traits (e.g. try "grand search", then go to "genes" or "traits"), or go from a "Trait Details" view to following links on "List all QTL/association data where a gene may exist". The returned query results are displayed in one of the two ways - "gene centric" or "trait centric" view - at user's choice.

    (Apr 29, 2018): A sum of 7,308 new QTL added to the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 5,216; Chicken: 615; Horse: 45; Pig: 1,389; Sheep: 43; Rainbow trout: 0 -- Net increase: 7,308). The current total number of QTL in the database: 153,150 [Break down: Cattle: 113,256; Chicken: 8,978; Horse: 1,349; Pig: 27,465; Sheep: 1,975; Rainbow trout: 127]
    ( This is a joint release with the 3rd CorrDB release)

    Database developments: (1) The Animal QTLdb has introduced the use of DOI (Digital Object Identifiers) on data that have a DOI record. This is to facilitate the link-out service useful for unification of identified records and database federation. Where applicable, DOI will become part of the required data for submission to the Animal QTLdb. (2) Active curator/editor tool improvements have continued. The most recent improvements include managing the trait list with modifiers (for traits that are the "same" by nature but slightly different in terms of attached information, such as time, location, and other conditions as "modifiers"), which helps the curators better manage the curation environment. Another improvement is to wrap the critical database internal identifiers in the backend process to avoid situations where errors might be introduced.

    (Aug 22, 2018): A sum of 5,349 new QTL have been added to the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 2,811; Chicken: 1,839; Horse: 46; Pig: 498; Sheep: 154; Rainbow trout: 1 -- Net increase: 5,349). The current total number of QTL in the database: 158,499 [Break down: Cattle: 116,067; Chicken: 10,817; Horse: 1,395; Pig: 27,963; Sheep: 2,129; Rainbow trout: 128]
    ( This is a joint release with the 4th CorrDB release)

    Database developments: (1) Thanks to Robert Schnabel from the University of Missouri, for his efforts mapping the cattle SNPs to the new genome build ARS_UCD1.2, we were able to start lifting the cattle QTL/association data to the new genome build. A preliminary set of cattle QTL/association data based on the new build is now available for download on Animal QTLdb. Please check it out and let us know if you identify any problems or needs for improvements. (NOTE: Due to the limitations of the number of genomes we can handle within the current Animal QTLdb, we are experimenting with ways to handle the additional genome build without having to remove the older ones. Currently, the cattle QTL/association data for the new build is available for download but not for web tools, such as built-in QTLdb web browsing.) (2) A new feature has been added to the JBrowse tool - dynamic hyperlinks are now available for each alignment to link to Animal QTLdb for details, which provide further links to related information, such as trait ontologies, as well as other types of annotated data.

For most recent updates, please refer to "major updates" or "permanent additions" section in "What's New" on the AnimalGenome.ORG site.
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