From listmaster animalgenome.org Mon Jan 4 13:48:20 2021
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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 (#1,
2021)
Date: Mon, 04 Jan 2021 13:48:20 -0600
What's new on the NAGRP animal genome web site (#1, 2021)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 43) and CorrDB (Release 11):
QTLdb (Dec 23, 2020): A sum of 2,123 new QTL/associations have been curated
into the database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 815; Chicken: 275; Goat: 0; Horse: 21; Pig: 584; Sheep: 151;
Rainbow trout: 277 -- Net increase: 2,123). The current total number of QTL
in the database: 211,792 [Breakdown: Cattle: 160,659; Chicken: 12,783;
Goat: 0; Horse: 2,472; Pig: 31,455; Sheep: 3,562; Rainbow trout: 861]
URL: https://www.animalgenome.org/QTLdb
CorrDB (Dec 26, 2020): A sum of 645 new correlations [Breakdown by species
-- Pig: 307 (5 new traits); Cattle: 301 (11 new traits); Sheep: 37 (9 new
traits)] and a sum of 488 new heritability data [Breakdown by species --
Pig: 315 (27 new traits); Cattle: 147 (19 new traits); Sheep: 26 (15 new
traits)] have been curated into the CorrDB. To date, the total number of
correlation data in the database: 21,036 [Breakdown by species -- Cattle:
11,277; Chicken: 1,247; Horse: 209; Pig: 6,735; Sheep: 1,568], and total
heritability data: 4,319 [Breakdown by species -- Cattle: 1,881; Chicken:
287; Horse: 118; Pig: 1,845; Sheep: 188], curated from 344 publications.
URL: https://www.animalgenome.org/CorrDB
Database developments:
(1) Goat QTLdb and Goat CorrDB: The groundwork has been laid by preparing
the goat linkage maps, genome maps, SNP map data, trait management space,
and other required information in order for both the Animal QTLdb and the
CorrDB to expand to include goat as a new species for curation of published
QTL, associations, correlations, and heritability data into respective
databases.
(2) New dbxref data link services were added to both Animal QTLdb and
Animal CorrDB to allow external URL links to specific QTL or correlation
data across species. Such links are often used by web services, API tools,
or database xref pointers. The syntax to use the service is a URL like
https://www.animalgenome.org/...TLdb/q?id=QTL_ID:[id] for QTLdb and
https://www.animalgenome.org/...rrDB/q?id=CorrID:[id] for CorrDB,
respectively (Replace "id" with respective actual id, which is the
unique numerical identifier for a specific QTL or correlation record. Refer
to QTLdb API documentation or downloaded data about the ids).
(3) Curated gene-eQTL data now can be delivered through web tools in the
Animal QTLdb ("trait-eQTL" have already been delibvered since 2009). The web
links include lists by publication through permanent record locator,
QTL/association data details, and a number of search results pages. It will
be pushed to downloads soon.
(4) A data curation helper tool has been developed to facilitate flanking
SNPs lookup for given genome intervals. The tool picks the leftmost and the
rightmost SNPs as flanking candidates for a searched span, along with their
coordinates for curators to determine the use of the queried SNPs for data
annotations.
(5) Another data curation helper tool has been developed to look up SNP
stable 'rs' numbers by their alternate names (usually from SNP discovery
environment, original publications, and genotyping platforms). The tool
allows copy/paste of a spreadsheet table for addition of a new column with
the matched ‘rs’ numbers, thus greatly improving the efficiency and
accuracy of data curation.
(6) Frequently asked questions for both Animal QTLdb and CorrDB were
updated with the addition of new items, updates to existing items, and
corrections to several items. See "NEW" indicator on the page for
details.
URL: https://www.animalgenome.org/QTLdb/faq/
https://www.animalgenome.org/CorrDB/faq/
o Ontology developments:
(1) One update was made to the Vertebrate Trait (VT) Ontology data (version
10.7). 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/
(2) Webpages for the Vertebrate Trait (VT) Ontology, Livestock Product
Trait (LPT) Ontology, Clinical Measurement Ontology (CMO), and Livestock
Breed Ontology (LBO) projects are updated with new utility searches added
for livestock trait correlations and heritability data in the Animal CorrDB
and QTL/SNP association data in the Animal QTLdb.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
https://www.animalgenome.org/...ioinfo/projects/lpt/
https://www.animalgenome.org/...ioinfo/projects/cmo/
https://www.animalgenome.org/...ioinfo/projects/lbo/
o Miscellaneous items:
(1) The community event web bulletin board has been continually updated
with new and updated meeting information. Currently the list includes
events for the next 18 months. Please feel free to add your items to the
list as a way to keep the community informed of what’s going on.
URL: https://www.animalgenome.org/community/meetings
(2) The community data sharing platform has been updated to include
voluntary contributions of public SNP identification information. The
"SNP identification information" mainly refers to custom SNP
identifications generated from SNP discovery processes, custom genotyping
platforms, and other SNP works that involve SNP identifications in
addition to their official ‘rs’ numbers. This effort is geared towards a
potential public platform to facilitate proper SNP matches needed in data
curation, information annotation data merge/combined analysis, and other
related efforts.
URL: https://www.animalgenome.org/...i-bin/util/fileshare
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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