(May 01, 2004): Announcing the launch of Pig QTLdb, a web-based database to harbors all published pig QTL results for easy look up and comparisons. The current release of the database is NCBI Implementation, that contains 466 curated pig QTL. This implementation is a collaboration with NCBI. The pig QTL data is available at the LocusLink of NCBI Entrez Databases.

(Dec 20, 2004): Announcing the creation of the Pig QTLdb NAGRP Implementation, with a total of 791 curated pig QTL from published resources. This release features a browseable QTL alignment tool to view QTL data on pig chromosome graphs (linkage map based).

(Jan 04, 2006): New data types from recent genomic works are aligned to pig QTL data on graphic chromosome views. These genomics features include pig FPC, RH, and human gene maps. The total number of curated pig QTL has increaed to 1,263.

(Aug 15, 2006): The QTLdb tools are extended to also include cattle and chicken QTL data, "Pig QTLdb" is renamed to "Animal QTLdb".

Current data after additions of newly curated data:
- Pig QTL: 1,287;
- Cattle QTL: 630;
- Chicken QTL: 657.

NEW
(1) Launch of Chicken QTLdb - goes online
(2) Launch of Cattle QTLdb - goes online
(3) Animal QTLdb curator/editor tools open to public for new curators / editors to sign up

(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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 [Breakdown by species -- 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 Asked 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 [Breakdown by species -- 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 [Breakdown by species -- 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).
( This is a joint release with the 1st CorrDB release) 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 [Breakdown by species -- 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) 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. (2) 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 [Breakdown by species -- 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) We have introduced the use of DOI (Digital Object Identifiers) on reference 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 [Breakdown by species -- 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.

(Dec 23, 2018): A sum of 5,763 new QTL have been added to the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 4,055; Chicken: 127; Horse: 628; Pig: 757; Sheep: 196; Rainbow trout: 0 -- Net increase: 5,763). The current total number of QTL in the database: 164,262 [Breakdown by species -- Cattle: 120,122; Chicken: 10,944; Horse: 2,023; Pig: 28,720; Sheep: 2,325; Rainbow trout: 128]
( This is a joint release with the 5th CorrDB release)

Database developments: (1) A QTL/association data enrichment test tool has been implemented in the Animal QTLdb. The tool takes a set of selected traits to perform a genome-wide data distribution analysis with Chi-square test of a two-way contingency table (traits by chromosomes) for the most plausible locations where certain traits may be over-represented. The tool has been reported in our recent paper "Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB" published on the upcoming Nucleic Acids Research 2019 Database issue. (2) An improved version of the QTL/association data enrichment test tool was made available recently to allow user defined sizes of chromosome regions for enrichment test. The new feature is to be presented on the upcoming Plant and Animal Genome meeting in San Diego, with a poster titled: "Implementation of a new data enrichment analysis tool in the Animal QTL Database". (3) Automated updates of the Animal QTLdb user visits and data download activities is added to the web site (on the main page, see light cyan text below the graph column on the right hand side). The text is hyper-linked to a world map showing locations of unique visitors to the database, which is also made available recently. (4) A new Ensembl gene models for the new cattle genome build BovARS_1.2 is added to its JBrowse tracks that align with QTL/associaitons, Genbank annotations, and SNP liftover locations.

(Apr 24, 2019): A sum of 3,881 new QTL have been added to the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 2,771; Chicken: 197; Horse: 7; Pig: 325; Sheep: 581; Rainbow trout: 0 -- Net increase: 3,881). The current total number of QTL in the database: 168,143 [Breakdown by species -- Cattle: 122,893; Chicken: 11,141; Horse: 2,030; Pig: 29,045; Sheep: 2,906; Rainbow trout: 128]
( This is a joint release with the 6th CorrDB release)

Database developments: (1) Extensive improvements of curator tools were made for better streamed workflows and more intuitive environments to follow curation steps. The development efforts were focused at reducing the chances for a curator to manually enter some critical info where automatic carry-over can be implemented. At-the-site user instructions were developed/revised to offer better helps to curators. (2) Continued debug of curator/editor tools that also helped with improved data-debugs (improvement of data quality control processes). (3) Continued development of QTL/association data enrichment tools in terms of allowing user defind genome (chromosomal) regions and selection of multiple traits for evaluations. The tool is still at developmental stage but an alpha-test version is available on the "Search and Analysis Tools" page for user inputs.

(Aug 22, 2019): A sum of 6,098 new QTL have been added to the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 4,298; Chicken: 199; Horse: 230; Pig: 820; Sheep: 95; Rainbow trout: 456 -- Net increase: 6,098). The current total number of QTL in the database: 174,241 [Breakdown by species -- Cattle: 127,191; Chicken: 11,340; Horse: 2,260; Pig: 29,865; Sheep: 3,001; Rainbow trout: 584]
( This is a joint release with the 7th CorrDB release)

Database developments: (1) "Shadow/Pseudo QTL" (serving as anchors) is introduced as a new data-control concept in the Animal QTLdb for curation of QTL/association locus that have been detected but its statistical tests have not reached a significant threshold. The purpose for recording such data is for the entry of significantly validated epistatic and pleiotropic data where these loci serve as anchor/target locations. (2) The epistatic and pleiotropic data was introduced for curation into the Animal QTLdb in 2009 and 2014 respectively. New implementations are made to allow them to be viewed in public portal (currently in the data summary per publications; e.g. epistatic data display; pleiotropic data display). More display options for epistatic and pleiotropic data will be developed. (3) A new batch upload tool is integrated into the Animal QTLdb curator/editor tools for general curators to upload pre-formatted data prepared according to the Minimum Required Information Guideline. An upload data processing pipeline is developed to allow proper data flow and jobs routing between general curators, QTLdb curators, QTLdb editors, and database administrators. (4) Some curated QTL/association reports in the Animal QTLdb can be related because they could be follow up studies, combined analysis of previous works, re-analysis, confirmation studies, or reports from the same experiments. Now these information are also curated in the QTLdb, and can be seen on publication information pages, for example, the abstract page (e.g. https://www.animalgenome.org/cgi-bin/QTLdb/BT/qabstract?PUBMED_ID=30644110), or curated data summary page (when viewing list of QTL/associations from a publication, e.g. https://www.animalgenome.org/cgi-bin/QTLdb/BT/pubtails?PUBMED_ID=30644110). (5) Dynamic data download options are added to the Animal QTLdb "Trait Centric" and "Gene Centric" views (accessible through "Search and Analysis" tools) which all data shown on a search results page can be downloaded. In this way users can relatively easily locate the data they look for by tunning their search terms, and download them for further data mining/analysis.

(Dec 29, 2019): A sum of 4,250 new QTL have been added to the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 3,216; Chicken: 478; Horse: 153; Pig: 305; Sheep: 98; Rainbow trout: 0 -- Net increase: 4,250). The current total number of QTL in the database: 178,491 [Breakdown by species -- Cattle: 130,407; Chicken: 11,818; Horse: 2,413; Pig: 30,170; Sheep: 3,099; Rainbow trout: 584]
( This is a joint release with the 8th CorrDB release)

Database developments: (1) A new version of the QTL/associations enrichment analysis tool is available in the Animal QTLdb (listed under "Search and Analysis" tools). This version of the tool allows users to select traits and chromosome regions of interests for analysis of QTL/associations representations in the region versus that of the whole genome. (2) The DOI (Digital Object Identifier) data in the Animal QTLdb is made visible on the abstract view and data summary view pages. Users can follow the DOI link to the full text of a publication when they are available. (3) First phase of curator/editor tools renovation as a result of data model and database structural changes due to the inclusion of eQTL data into the database.

(Apr 26, 2020): A sum of 12,931 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 11,854; Chicken: 428; Horse: 33; Pig: 410; Sheep: 206; Rainbow trout: 0 -- Net increase: 12,931). The current total number of QTL in the database: 191,422 [Breakdown by species -- Cattle: 142,261; Chicken: 12,246; Horse: 2,446; Pig: 30,580; Sheep: 3,305; Rainbow trout: 584]
( This is a joint release with the 9th CorrDB release)

Database developments: (1) Continued curator tools developments and enhancements to improve efficiency and improve needed information captures and recordings. An on-going work is how the pleiotropy data curation may be improved. (2) Continued works on the capability to support multiple genome builds. A preliminary QTL/association data lifeover tool is developed.

(Aug 27, 2020): A sum of 18,247 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 17,583; Chicken: 262; Horse: 5; Pig: 291; Sheep: 106; Rainbow trout: 0 -- Net increase: 18,247). The current total number of QTL in the database: 209,669 [Breakdown by species -- Cattle: 159,844; Chicken: 12,508; Horse: 2,451; Pig: 30,871; Sheep: 3,411; Rainbow trout: 584]
( This is a joint release with the 10th CorrDB release)

Database developments: (1) A newly developed batch SNP query tool is added to the Animal QTLdb web tools family (linked from "1. Search and Analysis tools" on a species main page). With this tool, up to 2,000 SNP IDs (dbSNP 'rs' numbers) can be posted for query. The returned results are aggregated surrounding each SNP, i.e. information are "SNP centric". The information include QTL/association genome locations, linked traits and trait ontology terms, related genes, publication references, etc on each SNP. Each of these information are further dynamicly linked to related data tools in the QTLdb. Comments are welcome to add more features and improvements for better utility. (The SNP query link is also added to "trait search", "gene search", "location search", and "general search" tools.) (2) Progress continued improving the Animal QTLdb in terms of supporting data mapping to multiple genomes. The latest outcomes included additions of several genome builds for JBrowse views of QTL/ association data. The support of multiple genomes in Animal QTLdb is based on QTL/association mapping data lifts between genomes with the aid of SNP location coordinates information on each build. (3) The Animal QTLdb FAQ is updated with new items to address common user questions as how QTL/association data can be downloaded with specific scope targeted at certain traits or trait classes.

(Dec 23, 2020): A sum of 2,123 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 815; Chicken: 275; Goat: 0; Horse: 21; Pig: 584; Sheep: 151; Rainbow trout: 277 -- Net increase: 2,123). The current total number of QTL in the database: 211,792 [Breakdown by species -- Cattle: 160,659; Chicken: 12,783; Goat: 0; Horse: 2,472; Pig: 31,455; Sheep: 3,562; Rainbow trout: 861]
( This is a joint release with the 11th CorrDB release)

Database developments: (1) Goat QTLdb: The groundwork has been laid by preparing the goat linkage maps, genome maps, SNP map data, trait management space, and other required information in order to include goat as a new species for curation of published QTL and associations data into the database. (2) New dbxref data link services were added to both Animal QTLdb to allow external URL links to specific QTL data across species. Such links are often used by web services, API tools, or database xref pointers. The syntax to use the service is URL like https://www.animalgenome.org/...TLdb/q?id=QTL_ID:[id] . (Replace "id" with respective actual id, which is the unique numerical identifier for a specific QTL. Refer to QTLdb API documentation or downloaded data about the ids). (3) Curated gene-eQTL data now can be delivered through web tools in the Animal QTLdb ("trait-eQTL" have already been delivered since 2009). The web links include lists by publication through permanent record locator, QTL/association data details, and a number of search results pages. It will be pushed to downloads soon. (4) A data curation helper tool has been developed to facilitate flanking SNPs lookup for given genome intervals. The tool picks the leftmost and the rightmost SNPs as flanking candidates for a searched span, along with their coordinates for curators to determine the use of the queried SNPs for data annotations. (5) Another data curation helper tool has been developed to look up SNP stable 'rs' numbers by their alternate names (usually from SNP discovery environment, original publications, and genotyping platforms). The tool allows copy/paste of a spreadsheet table for addition of a new column with the matched ‘rs’ numbers, thus greatly improving the efficiency and accuracy of data curation. (6) Frequently asked questions were updated with the addition of new items, updates to existing items, and corrections to several items. See "NEW" indicator on the page for details.

(Apr 26, 2021): A sum of 5,176 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Cattle: 1,116; Chicken: 1,173; Pig: 2,351; Sheep: 25; Rainbow trout: 509 -- Net increase: 5,176). In addition, 453 previously curated data were updated as part of our data quarantine routine. The current total number of QTL in the database: 216,194 [Breakdown by species -- Cattle: 161,756; Chicken: 14,049; Goat: 0; Horse: 2,470; Pig: 33,143; Sheep: 3,571; Rainbow trout: 1,205]
( This is a joint release with the 12th CorrDB release)

Database developments: (1) The Animal QTLdb is published on Figshare open access platform through the Iowa State University Library. Subsequently, now each database has an universal Digital Object Identifier (DOI), and all are covered by the Creative Commons licenses. As a result, there can be alternative ways how the users of the QTLdb or CorrDB can properly cite the use of the database resources and/or tools. Please check each database website to find more details (click on respective web page footages for copyright claims, and citation details; the same information is pre-pended to all download data files as well). (2) Continued improvements are being made to facilitate the curation of eQTL information into the database. For example, Cis/Trans eQTL information are curated to the Animal QTLdb and can be seen on QTL details and data summary (by publication) pages where such data is available. (3) We have been engaged in continued developmental works to transit the QTLdb from linkage map based database infrastructure to be genome map based, and to accommodate more structural genomics data types.

Thanks to Holly Neibergs from Washington State University and Gabrielle Becker from University of Idaho for contributing their data and curation efforts.

(Aug 23, 2021): A sum of 4,166 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 1,944; Chicken: 1,417; Goat: 64; Horse: 1; Pig: 397; Sheep: 180; Rainbow trout: 163 -- Net increase: 4,166). The current total number of QTL in the database: 220,401 [Breakdown by species -- Cattle: 163,725; Chicken: 15,475; Goat: 64; Horse: 2,473; Pig: 33,540; Sheep: 3,752; Rainbow trout: 1,372]
( This is a joint release with the 13th CorrDB release)

Highlights:
(1) The Goat QTLdb is alive! The first batch of goat QTL/association data was curated into it.
(2) A move to supporting genome coordinate-based map only on QTL/association data reports.

Database developments:
(1) As a result developing the QTLdb to support multiple genome builds, a major change in this release is a transition from using a mixed linkage distance (cM) / genome (bps) location system, to using genome (bps) locations only, for all QTL/association data depositions (for export). Linkage map based QTL reports will still be curated into the database and their cM map locations will be lifted to genome maps coordinates. ('cM' map locations maybe available upon requests only).
(2) A new hierarchy display tool has been developed to build front-ends of Animal QTLdb web portal for data access using traits from Vertebrate Trait (VT), Livestock Product Trait (LPT) Ontology, and Clinical Measurement Ontology (CMO). Built into the display tool also included a search capability, that helps users to quickly find relevant terms in large ontologies. The tool is implemented on all species QTLdb front pages, all VT/LPT/CMP home pages at AnimalGenome.ORG.
(3) Extensive re-organization of the web portal structure were made to improve user experience for easier data access by eliminating some intermediate pages for fewer browse/search steps to reach data.
(4) We have developed an in-house procedure to map known SNPs to a genome assembly with flanking sequences, which can be submitted OR be lifted from an older version of genome builds. This greatly accelerated our progress on supporting multiple/new genomes when they become available without extended waiting for official SNP identifiers ('rs' number) become available, which presented a bottleneck on timely QTLdb data release.
(5) Changes are made in the policy on Minimum information required for Animal QTLdb data entry. The change clarifies the minimum information on SNP-based data reports, and opens ways for new types of SNP information, such as those SNP without official 'rs' numbers but with flanking sequences.

(Dec 27, 2021): A sum of 15,569 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 13,474; Chicken: 796; Goat: 4; Horse: 132; Pig: 802; Sheep: 320; Rainbow trout: 41 -- Net increase: 15,569). The current total number of QTL in the database: 235,970 [Breakdown by species -- Cattle: 177,199; Chicken: 16,271; Goat: 68; Horse: 2,605; Pig: 34,342; Sheep: 4,072; Rainbow trout: 1,413]
( This is a joint release with the 14th CorrDB release.)

Database developments:
Recent new database developments have been highlighted in our recent paper published in the 2022 Database Issue of Nucleic Acids Research, "Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services", that include (1) A standardized protocol for adding new species to QTLdb/CorrDB; (2) Livestock SNP ID/name matching repository to assist SNP-based data curation; (3) A pipeline for mapping QTL/association data to a genome build, enabling support of QTLdb for multiple assemblies within a species; and (4) Extensive web portal revisions and web interface redevelopment in order to accommodate new tools while facilitate a straight forward user experiences using the web portal.

(Apr 25, 2022): A sum of 17,360 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 15,726; Chicken: 366; Goat: 60; Horse: 31; Pig: 1,042; Sheep: 135; Rainbow trout: 0 -- Net increase: 17,360). To date, the current total number of QTL in the database: 253,330 [Breakdown by species -- Cattle: 192,925 (on 701 traits); Chicken: 16,637 (on 443 traits); Goat: 128 (on 25 traits); Horse: 2,636 (on 65 traits); Pig: 35,384 (on 716 traits); Sheep: 4,207 (on 281 traits); Rainbow trout: 1,413 (on 41 traits)]
( This is a joint release with the 15th CorrDB release.)

Database developments:
(1) The curator tools have been extensively (involving 15 scripts serving 47 curator views/functions) re-developed in the way how "trait variants" (previously called "sibling traits") information is curated. This improvement is aimed not only to bring the erratic livestock traits curation to be practically doable, but also to gear the management of such data towards a better structure in terms of information disseminations and ontology developments. (2) As part of the efforts implementing trait variant management, more than 8 user view pages were modified to accommodate the changes.

(Aug 24, 2022): New data updates made to previously curated QTL/association data: 254,573 [Breakdown by species -- cattle: 195,041; chicken: 16,613; goat: 129; horse: 2,699; pig: 34,793; rainbow trout: 1,225; sheep: 4,202]. These changes related to previously curated traits: 2,111 [Breakdown by species -- cattle: 683; chicken: 369; horse: 65; pig: 691; sheep: 264; rainbow trout: 39].

In addition, a sum of 981 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 291; Chicken: 19; Goat: 0; Horse: 0; Pig: 462; Sheep: 209; Rainbow trout: 0 -- Net increase: 981). To date, the current total number of QTL in the database: 254,311 [Breakdown by species -- Cattle: 193,216 (on 684 traits); Chicken: 16,656 (on 370 traits); Goat: 128 (on 25 traits); Horse: 2,636 (on 65 traits); Pig: 35,846 (on 693 traits); Sheep: 4,416 (on 266 traits); Rainbow trout: 1,413 (on 43 traits)]
( This is a joint release with the 16th CorrDB release.)

Database developments summary:
(1) The data released above with regard to curation updates reflects our continued efforts toward implementing a new trait variant management system (reported in our 2022 WCGALP paper), as our work this summer has been focused on extensive data curation changes on all existing data in the QTLdb and CorrDB. The trait curation changes provide supporting evidence that the new data management structural change implemented in the spring works as designed (see our database release 47). A positive effect from the new trait data management in QTLdb/CorrDB is a significant reduction in the number of traits maintained in the database (for correlation data, from 902 to 786, -12.9%; for heritability data, from 1,061 to 928, -14.9%; for QTL/association data, from 2,272 to 2,146, -5.9%). Overall, this is an approximate 10% reduction in total base trait numbers. (2) Default genome: Since the Animal QTLdb has been supporting multiple genome builds since 2021 for a species, one genome assembly per species is now selected as default "reference" genome for the QTLdb web tools search and online map display. The selection of the default genome is in alignment with NCBI/Ensembl updates. The supported "default genome" information can be found on "Supported Genome Assemblies for Data Alignments" page on our website.

(Dec 28, 2022): A sum of 3,979 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 425; Chicken: 1,657; Goat: 1; Horse: 13; Pig: 879; Sheep: 88; Rainbow trout: 916 -- Net increase: 3,979). To date, the current total number of QTL in the database: 258,290 [Breakdown by species -- Cattle: 193,641 (on 686 traits); Chicken: 18,313 (on 370 traits); Goat: 129 (on 26 traits); Horse: 2,649 (on 65 traits); Pig: 36,725 (on 698 traits); Sheep: 4,504 (on 267 traits); Rainbow trout: 2,329 (on 47 traits)]. In addition, updates have been made to previously curated 395 QTL / associations as part of our efforts on data quality controls.
( This is a joint release with the 17th CorrDB release.)

Database developments summary:
(1) Genomic marker types as a curation parameter was added to Animal QTLdb curation pipelines in early 2016. We have retrospectively caught up marker type information for data curated prior to that time. Subsequently we have added this parameter for data downloads. The marker types data counts can be found on "data summary" pages of each species (choose "5. Number of QTL/associations by marker types" from the option list.) (2) Developmental works on data pipeline automations to streamline the processes bringing the QTL/association information across different genome builds and dbSNP releases.

(Apr 25, 2023): A sum of 12,595 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 257; Chicken: 98; Goat: 0; Horse: 0; Pig: 12,119; Sheep: 121; Rainbow trout: 0 -- Net increase: 12,595). To date, the current total number of QTL in the database: 270,885 [Breakdown by species -- Cattle: 193,898 (on 680 traits); Chicken: 18,411 (on 372 traits); Goat: 129 (on 26 traits); Horse: 2,649 (on 65 traits); Pig: 48,844 (on 673 traits); Sheep: 4,625 (on 272 traits); Rainbow trout: 2,329 (on 47 traits)].
In addition, as part of our efforts on data quality controls, updates have also been made to previously curated 4,387 QTL / associations, 165 base traits, and 1,113 trait variants.
( This is a joint release with the 18th CorrDB release.)

Database developments summary:
(1) Our works on devising new structures/curation pipelines introducing "trait variants" date type is published on recent issue of Oxford journal Database (Volume 2023, baad024), "A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants" (DOI: 10.1093/database/baad024). (2) As a result of implementing trait variant curation, several changes are visible on this data release: (a) There are new parameters to describe traits in GFF files (column 9) for data downloads, namely 'BaseTrait', 'TraitVariant', and 'TraitReprtNM', for "base trait", "trait variants", and "reported trait names," respectively (see the QTLdb FAQ "Terminology" section for details). (b) Data summaries on trait variants are visible (you may have noticed on our database releases since last year a reduction in the number of base traits and increase in the number of trait variants -- for those who are interested to know the reason, please read our paper for details). (c) Changes are coming on web pages describing traits; stay tuned. (3) We retrospectively fixed some non-current-standard characters stored in the database, which sometimes displayed as black diamonds or other types of "gibberish" in a web browser, introduced during historical data curations when these characters were copied/pasted into the database over the past 20 years. The "non-current-standard characters" include symbols representing "plus-minus sign" (± or +/-), "multiplication sign" (x or x), and may involve decodes from ASCII, UNICODE, HEX code, and/or HTML character coding methods. The solutions included character settings alignment in the backend storage engine and web interface programming environments, in compliance with current standards. Procedures have been implemented in the curation environment to automatically catch or convert non-standard characters or flag to make suggestions to curators.

(Aug 25, 2023): A sum of 12,478 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 1,113; Chicken: 235; Goat: 429; Horse: 0; Pig: 5,972; Sheep: 4,729; Rainbow trout: 0 -- Net increase: 12,478). To date, the current total number of QTL in the database: 278,738 [Breakdown by species -- Cattle: 195,011 (on 680 traits); Chicken: 18,646 (on 372 traits); Goat: 558 (on 26 traits); Horse: 2,649 (on 65 traits); Pig: 54,816 (on 673 traits); Sheep: 4,729 (on 272 traits); Rainbow trout: 2,329 (on 47 traits)].
( This is a joint release with the 19th CorrDB release.)

Database developments notes:
(1) We continued the transition from using "sibling traits" to "trait variants" (see our recent publication "A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants"; DOI: 10.1093/database/baad024). Since April 2023, 1,597 new trait variants have been created on QTLdb, linked to 3,128 previously curated QTL/association data, and 1,494 new trait variants created on CorrDB, linked to 7,037 previously curated correlation/heritability data. (2) Given the fact that the linkage-map–based QTL/association data being curated into the QTLdb has significantly diminished in the past 6 years (e.g. 2018: 115; 2019: 84; 2020: 1; 2021: 2; 2023: 0), and the fact that all current genome works have already shifted to using sequence maps, we plan to cease the curation of linkage-map–based QTL/association data in 2023, and place all previously curated linkage-map–based QTL/association data in separate downloads/archives by the next database release. Any comments regarding this move are welcome.

(Dec 27, 2023): A sum of 3,539 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 1,893; Chicken: 237; Goat: 643; Horse: 35; Pig: 350; Sheep: 381; Rainbow trout: 0 -- Net increase: 3,539). To date, the current total number of QTL in the database: 282,277 [Breakdown by species -- Cattle: 196,904 (on 680 traits); Chicken: 18,883 (on 372 traits); Goat: 1,201 (on 26 traits); Horse: 2,684 (on 65 traits); Pig: 55,166 (on 673 traits); Sheep: 5,110 (on 272 traits); Rainbow trout: 2,329 (on 47 traits)].
( This is a joint release with the 20th CorrDB release.)

In addition, we continued to commit our efforts on date updates on previously curated data. The data updates have been made on a total of 1,987 QTL/associations on 604 base traits in 5 species since last release.

Database developments notes:
(1) Multiple Genome Support: A number of updates were made using the new EVA dbSNP Release 5 data (Sept. 2023) on 19 genome builds in 7 livestock species. These updates included the addition of two genome builds (goat CHIR_1.0 and cattle ARS_UCD2.0). Support for goat CHIR_1.0 was made possible by the new dbSNP release, and the new cattle ARS_UCD2.0 (July 2023 release) support was made possible by our in-house SNP liftover procedures. Also included was the retirement of two chicken genome builds (chicken.GRCg6a and chicken.GRCg7w). (2) Legacy Data: As planned (see QTLdb release #51), a total of 13,309 linkage-map–based QTL/association data curated to the Animal QTLdb during 1999 through 2021 have been deposited to Github as of Dec. 17, 2023. This step represents the separation of the legacy data from the current QTLdb, as we move forward with the sequence-based genome maps and SNP-based analysis results. These legacy data were on 6 livestock species: cattle, chicken, horse, pigs, sheep, and rainbow trout. (3) "Ontologizing" Livestock Trait Terms: As part of our efforts to "ontologize" livestock trait terms during the process of data annotation into the QTLdb/CorrDB, two additional ontologies have been introduced for ontology term mappings: Uberon anatomy/tissue ontology, and RGD Disease Ontology. The outcomes from this work may be visible to the public in the near future. (4) Misc. Updates and Bug Fixes: (a) Continued efforts to stay current on QTLdb link-outs in agreement with usage in public citations for journal articles. (b) Fixes of missing or incorrect DOI brought in by erroneous extraction of outdated PubMed XML structure. (c) Debugging of data status control in the CorrDB curation pipeline. (5) Continued "Sibling Traits" to "Trait Variants" Transitions: As a result of our implementation of experiment-level curation of traits with modifiers (trait variants), continued reductions in the number of base traits and increase in trait variants are observed. This continues to have a positive impact on the QTLdb/CorrDB with regard to future developments. (6) New Data Summary Statistics: With the new developments (described above) and our continued efforts on data curations, several new statistics have been added to the data summary page for each species. These include 1) Counts of each trait appearance in experiments, 2) Counts of each trait variant appearance in experiments, and 3) Number of data in the curation pipelines.

(Apr 28, 2024): A sum of 2,676 new QTL/associations have been curated into the database (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 512; Chicken: 322; Goat: 300; Horse: 1; Pig: 1,193; Sheep: 348). To date, the current total number of QTL in the database: 266,160 (less all linkage map based QTL data that was put on archive since the last release). [Breakdown by species -- Cattle: 191,181 (on 680 traits); Chicken: 15,581 (on 372 traits); Goat: 1,501 (on 26 traits); Horse: 2,216 (on 65 traits); Pig: 48,875 (on 673 traits); Sheep: 4,605 (on 272 traits); Rainbow trout: 2,201 (on 47 traits)].
( This is a joint release with the 21st CorrDB release.)

In addition, as part of our data quality assurance efforts, updates were continually made to previously curated data.

This release is with the following updates:
(1) All linkage-map based data are excluded from data downloads since they have been separated and archived upon last QTLdb release (#52). As a result, you may expect to see a reduction in total data number in the current data summaries on the web. (2) In addition to mapped data deposition for downloads for supported genome assemblies, we have also included a copy of all curated data deposition (data reported on various genome assemblies, in .tsv file format). This data set has either SNP information OR genome locations on a particular genome which may be lifted to a target genome by users employing a method of their choice. In this way, we are not holding back any data just because of the inability to lift *some* data to some assemblies due to unavailability of mapped SNPs on that build. (3) In addition to JBrowse built for QTLdb, we are setting up the newer JBrowse2 as an experimental alternative to display chromosomal mappings for default reference genomes. In the meantime, we have retired the GBrowse display from the site (which was used for QTLdb data display since 2009). Currently, the JBrowse2 setup is in preliminary tests and you may expect to see improvements in the next few months. Our goal is to gradually phase out our in-house chromosomal data display tool. (4) The Frequently Asked Questions list has been updated with some newly added Q&A, such as "why the data counts on each build within a species are not the same", etc.

(Aug 25, 2024): A sum of 11,682 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Catfish: 0; Cattle: 1,066; Chicken: 3,021; Goat: 644; Horse: 0; Pig: 6,813; Sheep: 138; Rainbow trout: 0 -- Net increase: 11,682). To date, the current total number of QTL in the database: 277,842 [Breakdown by species -- Cattle: 192,247 (on 552 traits); Chicken: 18,602 (on 244 traits); Goat: 2,145 (on 81 traits); Horse: 2,216 (on 60 traits); Pig: 55,688 (on 407 traits); Sheep: 4,743 (on 167 traits); Rainbow trout: 2,201 (on 35 traits)].
( This is a joint release with the 22nd CorrDB release.)

In addition, as part of our data quality assurance efforts, updates works were performed on 2,020 SNP associations and 115 base traits data.

Database developments notes:
(1) Multiple Genome Support: Local SNP maps are updated with new EVA dbSNP release 6 (https://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/) for 19 genome assemblies. In addition, SNPs are lifted to 3 more genomes for cattle (ARS_UCD2), pig (MARC1), and sheep (Rambo1) using our in-house procedures. This facilitated QTL/association data support for 22 genome assemblies. We will consider depositing this in-house tool for free download if there is a community need. (2) Towards data curation automations: Thanks to Yuepei Li and Kang Zhou from Qi Li's group in computer science at the Iowa State University for their excellent collaborative works, an AI powered literature classification tool has been implemented in the QTLdb the data curation pipeline which has greatly accelerated the literature data processing. See their paper Distantly Supervised Named Entity Recognition via Confidence-Based Multi-Class Positive and Unlabeled Learning" for details. (3) FAQ: the "Frequently asked questions" list has been updated with a few newly added items. The most recent one is on the "QTL sizes" in downloaded data. Please check it out for more details.

(Dec 23, 2024): A sum of 11,506 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Cattle: 89; Chicken: 9,842; Goat: 324; Horse: 9; Pig: 927; Sheep: 315; Rainbow trout: 0 -- Net increase: 11,506). To date, the current total number of QTL in the database: 289,348 [Breakdown by species -- Cattle: 192,336 (on 553 traits); Chicken: 28,444 (on 245 traits); Goat: 2,469 (on 82 traits); Horse: 2,225 (on 60 traits); Pig: 56,615 (on 403 traits); Sheep: 5,058 (on 170 traits); Rainbow trout: 2,201 (on 35 traits)].
( This is a joint release with the 23rd CorrDB release.)

In addition, 13,830 updates were made to previously curated data in cattle, chicken, goat, pig, and sheep QTLdb.

Database developments notes:
(1) Miscellaneous updates to the QTLdb FAQ and website. (2) Numerous improvements were made to the curator tools.

(Apr 24, 2025): A sum of 3,390 new QTL/associations have been curated into the database. (New additions less obsolete/retracted ones: Cattle: 1,117; Chicken: 672; Goat: 244; Horse: 257; Pig: 426; Sheep: 674; Rainbow trout: 0 -- Net increase: 3,390). To date, the current total number of QTL in the database: 292,423 [Breakdown by species -- Cattle: 193,453 (on 558 traits); Chicken: 29,116 (on 246 traits); Goat: 2,713 (on 90 traits); Horse: 2,482 (on 71 traits); Pig: 57,041 (on 406 traits); Sheep: 5,417 (on 178 traits); Rainbow trout: 2,201 (on 35 traits)] curated from 2,964 publications.

In addition, updates have been made to 853 QTL/associations, 82 base traits and 3,771 trait variants on data curated prior to Release 55 (December 2024).

Database developments notes:
(1) Multiple Genome Support: All currently released data in all 7 species are lifted to 22 genome assemblies aided by SNP mappings from new (April 2, 2025) dbSNP Release 7 data (direct dbSNP mapping data for 19 genomes, and our in-house procedures extended the mappings for additoinal 3 genomes). (2) JBrowse2 was introduced a year ago (April 2024; QTLdb Release 53) and now has been made the default QTL/association map viewer on respective "default genomes" (one per species is supported). The older JBrowse (version 1) is completely retired from this site as of this release. Links to using JBrowse2 for QTL/associations are listed on each QTLdb species homepage.