From listmaster animalgenome.org Tlistmaster Aug 29 14:07:09 2019
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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,
2019)
Date: Thu, 29 Aug 2019 14:07:09 -0500
What's new on the NAGRP animal genome web site (#3, 2019)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
QTLdb (Release 39) and CorrDB (Release 7):
QTLdb (Aug 22, 2019): A sum of 6,098 new QTL have been added to the
database. (New additions less obsolete/retracted ones: Cattle: 4,298;
Chicken: 199; Horse: 230; Pig: 820; Sheep: 95; Rainbow trout: 456 -- Net
increase: 6,098). The current total number of QTL in the database: 174,241
[Break down: Cattle: 127,191; Chicken: 11,340; Horse: 2,260; Pig: 29,865;
Sheep: 3,001; Rainbow trout: 584]
URL: https://www.animalgenome.org/QTLdb
CorrDB (Aug 22, 2019): A sum of 1,631 new correlations [Break down by
species -- Cattle: 320 (0 new traits); Chicken: 102 (3 new traits);
Pig: 1,199 (53 new traits); Horse: 8 (1 new trait); Sheep: 2 (1 new traits)]
and a sum of 426 new heritability data [Break down by species -- Cattle: 57
(20 new traits); Chicken: 16 (5 new traits); Horse: 4 (1 new trait); Pig: 347
(0 new traits); Sheep: 2 (2 new traits)] have been curated into the CorrDB.
URL: https://www.animalgenome.org/CorrDB
Database developments:
(1) Epistatic and pleiotropic data were introduced for curation into the
Animal QTLdb in 2009 and 2014, respectively. Now these data can be viewed
in public web portals. Epistatic data and pleiotropic data display can be
found from the data summary by publication (see example URL below), or
from the QTL details view.
URL: e.g. https://www.animalgenome.org/...b/supp/?t=IuBr2D1HiG
URL: e.g. https://www.animalgenome.org/...b/supp/?t=OrFt0Y4MaX
(2) A new batch upload tool has been integrated into the Animal QTLdb
curator/ editor tools for community curators to upload pre-formatted data
prepared according to the Minimum Required Information Guidelines. An
uploaded data processing pipeline has been developed to allow proper data
flow and curation task routing between community curators, QTLdb curators,
QTLdb editors, and database administrators.
URL: https://www.animalgenome.org/QTLdb/doc/minfo/
(3) Some curated QTL/association reports in the Animal QTLdb may be related
to each other, in terms of follow-up studies, combined analysis of previous
works, re-analysis, confirmation studies, or additional reports from the
same experiments. Now these records are linked within the QTLdb, and their
relationships can be seen on publication information pages, for example,
the abstract page (e.g.
https://www.animalgenome.org/...D=30644110),
or curated data summary page (when viewing list of QTL/associations from a
publication, e.g. https://www.animalgenome.org/...RbEq9K9LtC).
(4) Dynamic data download options have been added to the Animal QTLdb
"Trait-Centric" and "Gene-Centric" views (accessible through "Search and
Analysis" tools) where all data shown on a search results page can be
downloaded. In this way, users can relatively easily locate the data by
adjusting the key words, and download what they need for further data
mining/analysis.
URL:
https://www.animalgenome.org/...dwnlod.png
o FAANG website:
The FAANG website has a new face. The new web face comes with a
restructured information mapping that puts emphasis on easy access to
certain areas for people who wish to get involved in various FAANG
activities. Thanks to Peter Harrison from EBI for useful discussions and
inputs. While we continue to improve the web structure for easier access
to information, any inputs/requests will be appreciated.
URL: https://www.faang.org
o Ontology developments
- New data updates were released twice for the Livestock Breed Ontology
(LBO, versions 4.4 and 4.5), and once for the Vertebrate Trait (VT)
ontology (version 9.1).
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/
URL: https://www.animalgenome.org/...bioinfo/projects/vt/
o Data repository:
The NAGRP Data Repository has been scaled down in terms of its acceptance
of certain types of files for deposition. In particular, we have ceased to
accept supplementary data for publications. Users are advised to use Open
Science Framework (OFS, https://osf.io/) instead.
o Misc. updates:
Some minor updates were made to Frequently Asked Questions (FAQ) of both
AnGenMap and Animal QTLdb.
URL: https://www.animalgenome.org/...mmunity/angenmap/faq (version 8).
URL: https://www.animalgenome.org/QTLdb/faq (version 13).
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 simply use our online Helpdesk to make a request
(https://www.animalgenome.org/helpdesk).
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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