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.
