The Animal QTLdb Release
Dec 27, 2023

 

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.

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