From listmaster animalgenome.org Fri Aug 24 22:51:24 2018
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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,
2018)
Date: Fri, 24 Aug 2018 22:51:24 -0500
What's new on the NAGRP animal genome web site (#3, 2018)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of
the QTLdb (Release 36) and CorrDB (Release 4).
QTLdb: (Aug 22, 2018): A sum of 5,349 new QTL/association data were
curated to the database. (New additions less obsolete/retracted ones:
Catfish: 0; Cattle: 2,811; Chicken: 1,839; Horse: 46; Pig: 498; Sheep:
154; Rainbow trout: 1 -- Net increase: 5,349). The current total number
of QTL in the database: 158,499 [Breakdown: Cattle: 116,067; Chicken:
10,817; Horse: 1,395; Pig: 27,963; Sheep: 2,129; Rainbow trout: 128]
We thank Mohamed Salem from Alexandria University in Egypt and Holly
Neibergs from Washington State University, who contributed 29 and 390
QTL/association data respectively.
URL: https://www.animalgenome.org/QTLdb
CorrDB: (Aug 23,2018): A sum of 2,099 new correlations [Breakdown by
species -- Pig: 188 (on 9 traits); Cattle: 1283 (on 71 traits); Chicken:
628 (on 40 traits)] and a sum of 424 new heritability data [Breakdown by
species -- Pig: 55 (on 23 traits); Cattle: 172 (on 95 traits); Chicken:
157 (on 67 traits); Sheep: 40 (on 38 traits)] have been curated into the
database.
URL: https://www.animalgenome.org/CorrDB
Database developments:
(1) Thanks to Robert Schnabel from the University of Missouri, for his
efforts mapping the cattle SNPs to the new genome build ARS_UCD1.2, we
were able to start lifting the cattle QTL/association data to the new
genome build. A preliminary set of cattle QTL/association data based on
the new build is now available for download on Animal QTLdb. Please
check it out and let us know if you identify any problems or needs for
improvements. (NOTE: Due to the limitations of the number of genomes
we can handle within the current Animal QTLdb, we are experimenting with
ways to handle the additional genome build without having to remove the
older ones. Currently, the cattle QTL/association data for the new build
is available for download but not for web tools, such as built-in QTLdb
web browsing.)
URL: https://www.animalgenome.org/jbrowse/
(2) A new feature has been added to the JBrowse tool - dynamic hyperlinks
are now available for each alignment to link to Animal QTLdb for details,
which provide further links to related information, such as trait
ontologies, as well as other types of annotated data.
URL: https://www.animalgenome.org/...wse/q?data=db/bovARS
(3) A Frequently Asked Questions section has been added to the CorrDB.
This is to address common questions raised with regard to design, usage,
application, utilities, new developments, and other related issues in the
use and development of the CorrDB.
URL: https://www.animalgenome.org/CorrDB/faq/
(4) A set of data release tools has been created to assist with
consistent, flawless data review and release processes for CorrDB. This
included some essential data constringe checks and complex queries to
gather data status statistics for release processes.
o Data repository:
(1) An improvement has been made to the NAGRP Community Data Repository
to allow restricted access to data (available upon request, and approval
by the data owner only). With this controlled access to data, we aim to
provide more flexibility for data owners in terms of how, when, and to
whom certain data can be made available while meeting the requirements
for publication.
(2) Annotations for the new cattle genome assembly ARS_UCD1.2 have been
loaded to the NAGRP JBrowse alignment tool. The alignment tool is ready
to accept any new alignment information for display when they become
available. Cattle QTL/association tracks will be added once we get the new
SNP mapping information.
(3) The NAGRP Data Repository for Supplementary Data to Publications has
been more actively used. The hosted data have been increasing in magnitude
by 2-3 folds compared to a couple years ago, and they are still increasing.
Partly as a result we have revised our File Sharing Platform interface to
better serve this purpose.
URL: https://www.animalgenome.org/repository/pub/
URL: https://www.animalgenome.org/...i-bin/util/fileshare
o Ontology developments
Several new ontology data updates have been made with new data versions of
Vertebrate Trait (VT) Ontology, Livestock Product Trait (LPT) Ontology,
and Livestock Breed Ontology (LBO). In 2018, there have been 5 new VT data
releases, 1 LPT data release, and 3 LBO data releases. This is to ensure
that the most updated versions of these ontologies are made publicly
available for search, browse, and download by the research community.
URL: https://www.animalgenome.org/...bioinfo/projects/vt/ (VT)
URL: https://www.animalgenome.org/...ioinfo/projects/lpt/ (LPT)
URL: https://www.animalgenome.org/...ioinfo/projects/lbo/ (LBO)
o Other developments:
Information updates on the site:
- Aquaculture Genomics Newsletter #46
(URL: https://www.animalgenome.org/aquaculture/)
- NAGRP-8 community information updates
(URL: https://www.animalgenome.org/community/NRSP-8/)
- New memberships for the Functional Annotation of ANimal Genomes (FAANG)
initiative continue to increase (https://www.faang.org/). A new addition
to the site is a Frequently Asked Questions (FAQ) page. In addition, we
have worked closely with Peter Harrison at the European Bioinformatics
Institute (EMBL-EBI) to ensure the two FAANG-related websites,
http://data.faang.org/...faang.org/, function seamlessly
in terms of information consistency, references, and dynamic links.
New funding opportunities within the scope of FAANG have been updated
(https://www.faang.org/).
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 any time with
your needs, requests, and/or suggestions. You can reach us in multiple
ways: contact Jim Reecy (+1-515-294-9269) for new projects/priorities,
email the team at the email address below, or use our online Helpdesk site
to make requests (https://www.animalgenome.org/...s/helpdesk).
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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