Release 52
(Dec 27, 2023):
A sum of 3,539 new QTL/associations have been curated into the
database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 1,893; Chicken: 237; Goat: 643; Horse: 35; Pig: 350;
Sheep: 381; Rainbow trout: 0 -- Net increase: 3,539).
To date, the current total number of QTL in the database: 282,277
[Breakdown by species -- Cattle: 196,904 (on 680 traits);
Chicken: 18,883 (on 372 traits); Goat: 1,201 (on 26 traits); Horse:
2,684 (on 65 traits); Pig: 55,166 (on 673 traits); Sheep: 5,110
(on 272 traits); Rainbow trout: 2,329 (on 47 traits)].
(
This is a joint release with the 20th CorrDB
release.)
In addition, we continued to commit our efforts on date updates on previously
curated data. The data updates have been made on a total of 1,987
QTL/associations on 604 base traits in 5 species since last release.
Database developments notes:
(1)
Multiple Genome Support: A number of updates were made using the new
EVA dbSNP Release 5 data (Sept. 2023) on 19 genome builds in 7 livestock
species. These updates included the addition of two genome builds (goat
CHIR_1.0 and cattle ARS_UCD2.0). Support for goat CHIR_1.0 was made possible
by the new dbSNP release, and the new cattle ARS_UCD2.0 (July 2023 release)
support was made possible by our in-house SNP liftover procedures. Also
included was the retirement of two chicken genome builds (chicken.GRCg6a and
chicken.GRCg7w).
(2)
Legacy Data: As planned (see QTLdb release #51), a total of 13,309
linkage-map–based QTL/association data curated to the Animal QTLdb during
1999 through 2021 have been deposited to Github as of Dec. 17, 2023. This
step represents the separation of the legacy data from the current QTLdb, as
we move forward with the sequence-based genome maps and SNP-based analysis
results. These legacy data were on 6 livestock species: cattle, chicken,
horse, pigs, sheep, and rainbow trout.
(3)
"Ontologizing" Livestock Trait Terms: As part of our efforts to
"ontologize" livestock trait terms during the process of data annotation into
the QTLdb/CorrDB, two additional ontologies have been introduced for ontology
term mappings: Uberon anatomy/tissue ontology, and RGD Disease Ontology. The
outcomes from this work may be visible to the public in the near future.
(4)
Misc. Updates and Bug Fixes: (a) Continued efforts to stay current on
QTLdb link-outs in agreement with usage in public citations for journal
articles. (b) Fixes of missing or incorrect DOI brought in by erroneous
extraction of outdated PubMed XML structure. (c) Debugging of data status
control in the CorrDB curation pipeline.
(5)
Continued "Sibling Traits" to "Trait Variants" Transitions: As a result
of our implementation of experiment-level curation of traits with modifiers
(trait variants), continued reductions in the number of base traits and
increase in trait variants are observed. This continues to have a positive
impact on the QTLdb/CorrDB with regard to future developments.
(6)
New Data Summary Statistics: With the new developments (described
above) and our continued efforts on data curations, several new statistics
have been added to the data summary page for each species. These include
1) Counts of each trait appearance in experiments, 2) Counts of each trait
variant appearance in experiments, and 3) Number of data in the curation
pipelines.
