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.
