From listmasteranimalgenome.org Wed Apr 29 16:02:47 2020
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#2, 2020)
Date: Wed, 29 Apr 2020 16:02:47 -0500
What's new on the NAGRP animal genome web site (#2, 2020)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 41) and CorrDB (Release 9):
QTLdb (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: Cattle: 142,261; Chicken:
12,246; Horse: 2,446; Pig: 30,580; Sheep: 3,305; Rainbow trout: 584]
Thanks to Holly Neibergs from Washington State University for curating his
data into the database.
CorrDB (Apr. 27, 2020): A sum of 844 new correlations [Breakdown by species:
Pig: 434 (31 new traits); Cattle: 100 (9 new traits); Chicken: 20 (4 new
traits); Sheep: 290 (19 new traits)] and a sum of 330 new heritability
data [Breakdown by species - Pig: 125 (24 new traits); Cattle: 137 (43 new
traits); Chicken: 12 (9 new traits); Sheep: 56 (21 new traits)] have been
curated into the CorrDB. To date, the total number of correlation data in
the database: 19,482 (breakdown by species - Cattle: 10,176; Chicken: 1,241;
Horse: 209; Pig: 6,416; Sheep: 1,440), and total heritability data: 3,594
(breakdown by species - Cattle: 1,541; Chicken: 284; Horse: 118; Pig: 1,503;
Sheep: 148), curated from 344 publications.
(1) Improvements on the Animal CorrDB have continued. The latest changes are
rephrased data categories and reformatted web page layouts for better eye
catch. Internally, centralized configurations have been expanded to include
the use of names and parameters for uniform web page formatting and
information passage to query engines.
(2) In QTLdb, we have continued curator tool developments and enhancements
to improve efficiency and information capture and recording. Ongoing work
focuses on improvement of the tools for pleiotropy data curation.
(3) Work continues to expand the capability to support multiple genome builds.
A preliminary QTL/association data liftover tool has been developed.
o Ontology developments:
Three (3) data updates were made to the Vertebrate Trait (VT) ontology
(versions 10.1, 10.2, and 10.3).
Four (4) data updates were made to the Livestock Breed Ontology (LBO),
(versions 5.1, 5.2, 5.3, and 5.4).
A data loader is being developed to streamline the ontology data in OBO
format to load to MySQL database tables serving the online ontology queries
and data viewers like AmiGO. This fills a gap where the support for AmiGO
and related tools were no longer available. This effort is being made in
order to facilitate VT, LPT, LBO, and CMO ontology development and as a
peripheral tool for Animal QTLdb/CorrDB.
(1) The NRSP8/NAGRP 2020 leadership list has been updated following the 2020
PAG meeting in San Diego, CA.
(2) The website is updated for the upcoming VISIONS III conference: Star
Gazing into the Galaxy of Animal Genetics and Genomics, with new
information on the date change, updated speakers and sponsors, and a
new room-share bulletin board.
(3) FAANG data has been processed and archived through the FAANG Data
Portal. An FAQ item has been developed to describe how these data can
be easily accessed.
Check out the daily "what's new" (https://www.animalgenome.org/news/) items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links/errors, or suggesting corrections on our site.
Your input is always appreciated. Feel free to contact us at any time with
your needs, requests, and/or suggestions: Jim Reecy (jreecyiastate.edu)
James Koltes (jekoltesiastate.edu), Fiona McCarthy (fionamccarizona.edu).
Or talk to us using our Helpdesk (https://www.animalgenome.org/helpdesk).
NAGRP Bioinfo Team