Release 1 (May 01, 2004): Pig QTLdb,
NCBI Implementation, with 466 pig QTL. This release features the
links of QTL to Locus Link of NCBI Entrez Databases.
Release 2 (Dec 20, 2004): Pig QTL db,
NAGRP Implementation, with a total of 791 pig QTL.
This release features browseable QTL alignments as viewed in chromosomal graphs.
Release 3 (Jan 04, 2006):
Pig FPC, RH, and human maps are aligned; 1,263 pig QTL
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",
Pig QTL: 1,287; Cattle QTL: 630; Chicken QTL: 657.
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 (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 (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 (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.
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 (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.
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).
New functions added: SAM data format is now available for QTL data
Release 12 (Sep 13, 2010):
Total QTL in the database: 12,635
[Break down: Cattle QTL: 4,281; Chicken QTL: 2,284;
Pig QTL: 5,986; Sheep QTL: 84 ] (New QTL added to the database:
1,065 -- Cattle: 390; Chicken: 421; Pig: 254; Sheep: 0).
Release 13 (Dec 31, 2010): Total QTL in the database:
13,825 [Break down: Cattle QTL: 4,682; Chicken QTL: 2,451; Pig QTL: 6,344;
Sheep QTL: 348 ] (New QTL added to the database: 1,190 --
Cattle: 401; Chicken: 167; Pig: 358; Sheep: 264).
New functions added: (1) The Sheep QTLdb has been migrated from its
Australia to its Iowa State University site. (2) Pig QTLs are aligned to
the pig genome preliminary assembly 9.2. (3) A QTL meta-plot analysis tool
is added to the QTLdb. (4) Cytogenetic G-banded chromosome ideograms have
been added to QTL maps within the QTLdb for cattle, sheep, pigs and chicken.
Release 14 (Apr 20, 2011): Total QTL in the database:
13,931 [Break down: Cattle QTL: 4,682; Chicken QTL: 2,451; Pig QTL: 6,344;
Sheep QTL: 454 ] (New QTL added to the database: Sheep: 106; Efforts in this
period were mainly on improving data qualities and quality control procedures).
Release 15 (Sep 22, 2011): Total QTL in the database:
14,239 [Break down: Cattle QTL: 4,802; Chicken QTL: 2,451; Pig QTL: 6,347;
Sheep QTL: 639 ] (New QTL added to the database: 308 --
Cattle: 120; Chicken: 0; Pig: 3; Sheep: 185).
Release 16 (Jan 02, 2011): Total QTL in the database:
15,014 [Break down: Cattle QTL: 5,207; Chicken QTL: 2,736; Pig QTL: 6,432;
Sheep QTL: 639; Rainbow trout: 27] (New QTL added to the database: 802 --
Cattle: 405; Chicken: 285; Pig: 85; Sheep: 0; Rainbow trout: 27).
New functions added: (1) ATO/QTL traits are mapped to VT, PT and CMO traits;
(2) QTLdb is revamped to accommodate QTL/assiciation data on genome maps (map unit:
bp); (3) Animal breed information can now be seen on the QTL detail page; (4) Rainbow
trout was added as a new member of species in the Animal QTLdb; (5) lists of
references are available for all QTL seen within any chromosomal view window.
Release 17 (Apr 20, 2012): Total QTL in the database:
16,584 [Break down: Cattle QTL: 5,920; Chicken QTL: 3,162; Pig QTL: 6,818;
Sheep QTL: 684; Rainbow trout: 73] (New QTL added to the database: 1,616 --
Cattle: 713; Chicken: 426; Pig: 386; Sheep: 45; Rainbow trout: 73).
New functions added: (1) Updated map location conversion (cM to bp)
algorithms; (2) Multiple QTL can be searched for customized QTL alignments and
meta-plots; (3) QTL overview within a super-trait is made possible; (4) New
query for QTL publication summary by super-trait (trait-type); (5) Structured
literature search can better target search scopes; (6) An extensive overhaul
of the QTLdb curator tools.
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
[Break down: Cattle: 5,920; Chicken: 3,442; Pig: 7,451;
Sheep: 753; Rainbow trout: 88] (New additions less obsolete ones:
Cattle: 0; Chicken: 280; Pig: 633; Sheep: 69; Rainbow trout: 15 -- Net
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".
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
[Break down: Cattle: 6,305; Chicken: 3,442; Pig: 8,315;
Sheep: 753; Rainbow trout: 88] (New additions less obsolete ones:
Cattle: 385; Chicken: 0; Pig: 864; Sheep: 0; Rainbow trout: 0 -- Net
( 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 (Apr 20, 2013): The total number of
QTL/association data in the database has reached 20,217. The current total
number of QTL in the database: 20,090 [Break down: Cattle:
7,091; Chicken: 3,808; Pig: 8,402; Sheep: 789; Rainbow trout: 127]
(New additions less obsolete ones: Cattle: 7091; Chicken: 3808; Pig: 8402;
Sheep: 789; Rainbow trout: 127 -- Net increase: 20,217).
Functions: Fixed bugs where chromosomes were not properly displayed when
a default chromosome length ratio was not met in odd situations. Improved QTLdb
Curator tools: (1) Added options to allow manual search and import of PubMed
references for data curation; (2) Added data review functions for curator/editor
to update QTL data status; (3) Improved reference based QTL data status counts
and list summary for review/retract actions; (4) Improved QTL data flow route to
eliminate ambiguous data status route.
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
[Break down: Cattle: 7,931; Chicken: 3,919; Pig: 8,919;
Sheep: 789; Rainbow trout: 127] (New additions less obsolete ones:
Cattle: 915; Chicken: 115; Pig: 533; Sheep: 0; Rainbow trout: 0 --
Net increase: 1,563).
(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
(3) Fixed a couple dozen minor bugs in both public data portal and in the
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].
(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
- 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.
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
[Break down: Cattle: 9,180; Chicken: 4,282; Pig: 10,497;
Sheep: 789; Rainbow trout: 127] (New additions less obsolete ones:
Cattle: 875; Chicken: 363; Pig: 635; Sheep: 0; Rainbow trout: 0 --
Net increase: 1,873).
(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
(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
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
[Break down: Cattle: 11,543; Chicken: 4,337; Horse: 345;
Pig: 11,610; Sheep: 789; Rainbow trout: 127] (New additions less
obsolete ones: Cattle: 2363; Chicken: 55; Horse: 345; Pig: 1113; Sheep: 0;
Rainbow trout: 0 -- Net increase: 3,876).
(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.
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
[Break down: Cattle: 13,145; Chicken: 4,379; Horse: 1,005;
Pig: 12,618; Sheep: 791; Rainbow trout: 127] (New additions less
obsolete ones: Cattle: 1,602; Chicken: 42; Horse: 660; Pig: 1,008; Sheep: 2;
Rainbow trout: 0 -- Net increase: 3,314).
(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.
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
[Break down: Cattle: 17,908; Chicken: 4,525; Horse: 1,018;
Pig: 13,030; Sheep: 801; Rainbow trout: 127] (New additions less
obsolete ones: Cattle: 4,763; Chicken: 146; Horse: 13; Pig: 412; Sheep: 10;
Rainbow trout: 0 -- Net increase: 5,344).
Functions: We devoted to debug the processes with which QTL/association
map location data are converted to allow dispaly in GBrowse/JBrowse. Should
there be any odd situations, please feel free to contact us.
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
[Break down: Cattle: 36,693; Chicken: 4,676; Horse: 1,124;
Pig: 13,958; Sheep: 836; Rainbow trout: 127] (New additions less
obsolete ones: Cattle: 18,785; Chicken: 151; Horse: 106; Pig: 928; Sheep: 35;
Rainbow trout: 0 -- Net increase: 20,005).
Functions: The QTLdb curator tools have been improved
(1) There is now a better review environment for private data, including
an overall view of data from a report, and a special URL link and channels
for external reviews of data (e.g., by journal editors/reviewers) prior to
the public data release.
(2) A companion tool has been created for curators to search officially
published SNPs based on reported genome location. This allows curation of
QTL/association data that was previously excluded from data entry due to
lack of minimum required information for curation. Using official dbSNP
IDs helps consistently anchor the map locations of reported QTL/association
(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
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
[Break down: Cattle: 42,019; Chicken: 5,196; Horse: 1,125;
Pig: 14,479; Sheep: 1,090; Rainbow trout: 127] (New additions less
obsolete ones: Cattle: 5,326; Chicken: 520; Horse: 1; Pig: 521; Sheep: 254;
Rainbow trout: 0 -- Net increase: 6,622).
Functions: (1) New information pages were set up to describe the steps
needed to upload a large quantity of new QTL/association data. An important
part of this information is a set of guidelines regarding the minimum
Information required for preparation of new QTL/association data. Actual
working examples will be added in the coming months. (2) A new plot tool for
whole genome view of QTL/association data was created. This is to overcome the
space limitations of the old plot tool where all chromosomes are arranged in a
panel with a fixed dimension (as such the old whole genome plot only gives a
brief overview of QTL/associations with limited number of data allowed by the
space). Currently the new plot tool is linked from the old tool as an
alternative. It will be made as default, and more query/plot options will be
implemented for wider applications in the coming months. (3) An user input
portal is added to the QTL/association view page. The purpose of this function
is for users to add annotations, comments, and report problems. Additional
annotation data will aid future meta analysis; problem report will help with
our data quality control efforts. (4) A new function is added that it is not
possible to review QTL/association data by traits, and enter the same comments
for multiple QTL/association data for the same trait. This relives curators
from laborious repeats and helps for a better data review. (5) A number of
debugs in the curator/editor tools were found and fixed. This continued effort
helps to ensure an improved data curation process.
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
[Break down: Cattle: 71,448; Chicken: 5,462; Horse: 1,139;
Pig: 15,108; Sheep: 1,173; Rainbow trout: 127] (New additions less
Cattle: 29,429; Chicken: 266; Horse: 14; Pig: 629; Sheep: 83; Rainbow trout: 0
-- Net increase: 30,421).
(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.
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
[Break down: Cattle: 81,652; Catfish: 0; Chicken: 5,683; Horse: 1,197;
Pig: 16,033; Sheep: 1,336; Rainbow trout: 127] (New additions less
Catfish: 0; Cattle: 10,204; Chicken: 221; Horse: 58; Pig: 925; Sheep: 163;
Rainbow trout: 0 -- Net increase: 11,571).
(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.
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 [Break down: Cattle: 95,332; Catfish: 0; Chicken:
6,633; Horse: 1,245; Pig: 16,516; Sheep: 1,412; Rainbow trout: 127]
(New additions less obsolete/retracted ones: Catfish: 0; Cattle: 13,680;
Chicken: 950; Horse: 48; Pig: 483; Sheep: 76; Rainbow trout: 0 -- Net
QTL number increase: 15,237).
(1) The curation tools are improved to allow automatic verification and streamlined
curation of SNP information into the database. The improvements involved data
quality control processes in which multiple genome builds are maintained for
cattle, chicken, and sheep.
(2) curation protocols are modified that preliminary SNPs (with 'ss' numbers only)
are allowed to be entered to anchor QTL/association mapping locations. The
QTL/association mapping data represented by the 'ss' SNPs are not subject to normal
data release procedure unless the manually entered map coordinates are also available.
The 'ss' SNP information will eventually be replaced with their 'rs' SNP information
once they are assigned by dbSNP. (3) The QTLdb Frequently Aked Questions are updated.
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
[Break down: Cattle: 98,090; Chicken: 6,791; Horse: 1,275;
Pig: 17,955; Sheep: 1,515; Rainbow trout: 127] (New additions less
Catfish: 0; Cattle: 2,758; Chicken: 158; Horse: 30; Pig: 17,955; Sheep: 103;
Rainbow trout: 0 -- Net increase: 21,004).
(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.
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
[Break down: Cattle: 99,652; Chicken: 7,812; Horse: 1,278;
Pig: 25,610; Sheep: 1,658; Rainbow trout: 127] (New additions less
obsolete/retracted ones: Catfish: 0; Cattle: 1,562; Chicken: 1,021;
Horse: 3; Pig: 7,655; Sheep: 143; Rainbow trout: 0 -- Net increase: 10,384).
(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
(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.
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
[Break down: Cattle: 108,040; Chicken: 8,363; Horse: 1,304; Pig: 26,076;
Sheep: 1,932; Rainbow trout: 127]
This is a joint release with the 2nd CorrDB release)
(1) The development of the initial sets of curator tools
has completed for the Animal Correlation Database (CorrDB). With this release,
we open the CorrDB curation for free registration for anyone who wish to be a
curator to enter own or public correlation and heritability data.
(2) As part of the Animal QTLdb/CorrDB co-development efforts, functions are
developed to link QTL data with trait correlation data through common trait terms
where such data exist. For example, within the CorrDB, under the Table View of
correlation data, a hyper-linked red "QTL" label is added when QTL data exists
on the trait; Like-wise, within the QTLdb on the trait search results, an hyper-linked
tag is added on traits where correlation data are found.
(3) New web portals are developed for display of "gene centric view" and
"trait centric view" of QTL/association data where underlining gene information
is available. This tool helps users to relatively quickly to interrogate and
understand genotype-to-phenotype information in a synopsis. A quick way to use
the tool to view information is to try a search by genes or by traits (e.g. try
"grand search", then go to "genes" or "traits"), or go from a "Trait
Details" view to following links on "List all QTL/association data where a gene
may exist". The returned query results are displayed in one of the two ways -
"gene centric" or "trait centric" view - at user's choice.
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
[Break down: Cattle: 113,256; Chicken: 8,978; Horse: 1,349; Pig: 27,465;
Sheep: 1,975; Rainbow trout: 127]
This is a joint release with the 3rd CorrDB release)
(1) The Animal QTLdb has introduced the use of DOI (Digital Object Identifiers)
on data that have a DOI record. This is to facilitate the link-out service useful
for unification of identified records and database federation. Where applicable,
DOI will become part of the required data for submission to the Animal QTLdb.
(2) Active curator/editor tool improvements have continued. The most recent
improvements include managing the trait list with modifiers (for traits that are
the "same" by nature but slightly different in terms of attached information,
such as time, location, and other conditions as "modifiers"), which helps the
curators better manage the curation environment. Another improvement is to wrap
the critical database internal identifiers in the backend process to avoid
situations where errors might be introduced.
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
[Break down: Cattle: 116,067; Chicken: 10,817; Horse: 1,395; Pig: 27,963; Sheep:
2,129; Rainbow trout: 128]
This is a joint release with the 4th CorrDB release)
(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
(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 (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
[Break down: 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)
(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.