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The Animal QTLdb Releases
2004 - 2024
Release 1
Release 1
(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. Release 2
Release 2
(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). Release 3
Release 3
(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. Release 4
Release 4
(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:
NEW Release 5
Release 5
(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. Release 6
Release 6
(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 Release 7
Release 7
(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). Release 8
Release 8
(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. Release 9
Release 9
(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). Release 10
Release 10
(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). Release 11
Release 11
(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). Release 12
Release 12
(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). Release 13
Release 13
(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). Release 14
Release 14
(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). Release 15
Release 15
(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). Release 16
Release 16
(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). Release 17
Release 17
(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).
Release 18
Release 18
(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). Release 19
Release 19
(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. Release 20
Release 20
(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). Release 21
Release 21
(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). Release 22
Release 22
(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]. Release 23
Release 23
(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). Release 24
Release 24
(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). Release 25
Release 25
(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). Release 26
Release 26
(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). Release 27
Release 27
(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). Release 28
Release 28
(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). Release 29
Release 29
(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). Release 30
Release 30
(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). Release 31
Release 31
(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). Release 32
Release 32
(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: Release 33
Release 33
(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). Release 34
Release 34
(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] 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. Release 35
Release 35
(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] 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. Release 36
Release 36
(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] 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. Release 37
Release 37
(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] 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. Release 38
Release 38
(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] 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. Release 39
Release 39
(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] 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. Release 40
Release 40
(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]
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. Release 41
Release 41
(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]
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. Release 42
Release 42
(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] 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. Release 43
Release 43
(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] 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. Release 44
Release 44
(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] 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. Release 45
Release 45
(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]
Highlights:
Database developments: Release 46
Release 46
(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]
Database developments: Release 47
Release 47
(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)]
Database developments: Release 48
Release 48
(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)]
Database developments summary: Release 49
Release 49
(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.
Database developments summary: Release 50
Release 50
(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)].
Database developments summary: Release 51
Release 51
(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)].
Database developments notes: Release 52
Release 52
(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)].
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: Release 53
Release 53
(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)].
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: Release 54
Release 54
Celebrating 20 years of Animal QTLdb
(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)].
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: Release 55
Release 55
Celebrating 20 years of Animal QTLdb
(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)].
In addition, 13,830 updates were made to previously curated data in cattle, chicken, goat, pig, and sheep QTLdb.
Database developments notes:
( The next database release will be in late April, 2025 )
For most recent updates, please refer to What's New
page on this site for related items.
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© 2003-2024:
USA · USDA · NRPSP8 · Program to Accelerate Animal Genomics Applications.
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