From listmaster animalgenome.org Tue Sep 1 10:28:06 2020
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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 (#3,
2020)
Date: Tue, 01 Sep 2020 10:28:06 -0500
What's new on the NAGRP animal genome web site (#3, 2020)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the QTLdb
(Release 42) and CorrDB (Release 10):
QTLdb (Aug. 27, 2020): A sum of 18,247 new QTL/associations have been
curated into the database. (New additions less obsolete/retracted ones:
Catfish: 0; Cattle: 17,583; Chicken: 262; Horse: 5; Pig: 291; Sheep: 106;
Rainbow trout: 0 -- Net increase: 18,247). The current total number of
QTL in the database: 209,669 [Breakdown: Cattle: 159,844; Chicken: 12,508;
Horse: 2,451; Pig: 30,871; Sheep: 3,411; Rainbow trout: 584]
In addition, there were also 1,206 QTL/association data curated during this
period that have been placed on hold due to the lack of some minimum
required information. They will be updated once this information becomes
available. In other words, we have curated 19,259 data points since the
last data release in April.
URL: https://www.animalgenome.org/QTLdb
CorrDB (Aug. 27, 2020): A sum of 909 new correlations [Breakdown by species
-- Pig: 12 (2 new traits); Cattle: 800 (14 new traits); Chicken: 6 (1 new
trait); Sheep: 91 (8 new traits)] and a sum of 237 new heritability data
[Breakdown by species -- Pig: 27 (5 new traits); Cattle: 193 (21 new traits);
Chicken: 3 (0 new traits); Sheep: 14 (9 new traits)] have been curated into
the CorrDB. To date, the total number of correlation data in the database:
20,391 [Breakdown by species -- Cattle: 10,976; Chicken: 1,247; Horse: 209;
Pig: 6,428; Sheep: 1,531], and total heritability data: 3,831 [Breakdown by
species -- Cattle: 1,734; Chicken: 287; Horse: 118; Pig: 1,530; Sheep: 162],
curated from 344 publications.
URL: https://www.animalgenome.org/CorrDB
Database developments:
(1) A newly developed batch SNP query tool has been added to the Animal
QTLdb web tools family (linked from "1. Search and Analysis tools" on a
species main page). With this tool, up to 2,000 SNP IDs (dbSNP 'rs' numbers)
can be posted for query. The returned results are aggregated surrounding
each SNP, i.e., information is "SNP centric". The information includes QTL
or SNP association genome locations, linked traits and trait ontology terms,
related genes, publication references, etc. for each SNP. Each of these
details are further dynamically linked to related data tools in the QTLdb.
We welcome your comments and suggestions to help us add more features and
improve database utility. (The SNP query link is added to "trait search",
"gene search", "location search", and "general search" tools.
(2) Improvements are ongoing in the Animal QTLdb with regard to supporting
data mapping to multiple genomes. The latest outcomes include additions
of several genome builds for JBrowse views of QTL/association data. The
support of multiple genomes in Animal QTLdb is based on QTL/association
mapping data liftover between genomes with the aid of SNP location
coordinate information on each build.
(3) The Animal QTLdb FAQ has been updated with new items to address common
user questions regarding how QTL/association data can be downloaded with
specified scope targeting certain traits or trait classes.
(4) Numerous bug fixes have been made on CorrDB public browse/query tools.
o Ontology developments:
Three (3) data updates were made to the Vertebrate Trait (VT) Ontology
(versions 10.4, 10.5, and 10.6). Refer to QTLdb/CorrDB release information
above for the number of new traits added in each species.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
One (1) data update was made to the Livestock Breed Ontology (LBO) (version
5.5).
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/
A local workflow and pipeline have been added to the current ontology data
update and public release pipeline for the development of the Vertebrate
Trait (VT) Ontology, Livestock Product Trait (LPT) Ontology, and Livestock
Breed Ontology (LBO). This data release process includes new data
synchronizations among BioPortal, GitHub (which pipes data to OntoBee, EBI,
OBO Foundry, uPheno, AgroPortal, etc.) and AnimalGenome.org databases
(feeding data to QTLdb trait mappers, project websites for data query and
browse, etc).
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
bioinfo-teamanimalgenome.org
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