Release 1
(May 01, 2004): Pig QTLdb,
NCBI Implementation, with 466 pig QTL. The QTL in this release are
represented as an entry in the LocusLink 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
download.
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
(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.
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
(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
(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.
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).
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
[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".
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
(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.
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).
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.
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].
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.
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).
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.
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).
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.
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).
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.
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).
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
[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.
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).
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
[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.
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).
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.
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).
New developments:
(1) The curation tools are improved to allow automatic verification and streamlined
curation of SNP information into the database. The improvements involved data
quality control processes in which multiple genome builds are maintained for
cattle, chicken, and sheep.
(2) curation protocols are modified that preliminary SNPs (with 'ss' numbers only)
are allowed to be entered to anchor QTL/association mapping locations. The
QTL/association mapping data represented by the 'ss' SNPs are not subject to normal
data release procedure unless the manually entered map coordinates are also
available. The 'ss' SNP information will eventually be replaced with their 'rs'
SNP information once they are assigned by dbSNP. (3) The QTLdb Frequently Aked
Questions are updated.
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:
(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
[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).
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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]
(
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.
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)]
(
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.
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)]
(
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.
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.
(
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.
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)].
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.
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)].
(
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; 2021, 2; 2023, 1), 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.
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Live Notes
- (2023-09-01) Supported genome assemblies updates
Retired:
- chicken.GRCg7b
- chicken.GRCg7w
Additions:
- goat.CHIR_1.0
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