From zhu iastate.edu Mon Aug 31 20:18:32 2015
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#3,
2015)
Date: Mon, 31 Aug 2015 20:18:32 -0500
What's new on the NAGRP animal genome web site (#3, 2015)
o Animal QTLdb updates:
Announcing Release 27 of the Animal QTLdb. Thanks to the diligent efforts
of our curator Cari Park and others, an unprecedented number of 20,005
new QTL/association data have been curated into the database since the
last database release in April. The current total number of QTL in the
database: 57,414 [Breakdown: Cattle: 36,693; Chicken: 4,676; Horse: 1,124;
Pig: 13,958; Sheep: 836; Rainbow trout: 127] (New additions less obsolete
ones: Cattle: 18,785; Chicken: 151; Horse: 106; Pig: 928; Sheep: 35;
Rainbow trout: 0 -- Net QTL number increase: 20,005).
We also wish to thank a number of volunteer curators for their input. They
are Fernando Ariza from National University of Colombia-Bogota, Dorota
Lewczuk from Institute of Genetics and Animal Breeding of the Polish Academy
of Sciences, and Andre Hidalgo from the Wageningen University. It's worth
mentioning that six (6) new curators have signed up to enter data over the
past 4 months. We look forward to their contributions.
Since the last QTLdb release, the QTLdb curator tools have also undergone a
number of improvements:
(1) There is now a better review environment for private data, including
an overall view of data from a report, and a special URL link and channels
for external reviews of data (e.g., by journal editors/reviewers) prior to
the public data release.
(2) A companion tool has been created for curators to search officially
published SNPs based on reported genome location. This allows curation of
QTL/association data that was previously excluded from data entry due to
lack of minimum required information for curation. Using official dbSNP
IDs helps consistently anchor the map locations of reported QTL/association
data.
(3) It's now possible to enter QTL/association data using genome map
coordinates if stable dbSNP identifiers are not available. Previously,
the genome coordinates were imported based on official dbSNP information.
We have now developed a method to record genome coordinates with build
versions represented by chromosome RefSeq IDs.
(4) Although all QTL/association data must be assigned to an existing trait
ontology entry (VT/PT/CMO), curators can now include the reported trait
names in the QTL record to allow retrospective review and improve future
ontology development.
URL: http://www.animalgenome.org/QTLdb/
o The NAGRP Data/Tools Repository updates:
(1) New VCF files are added to the CVF file repository, which included
- files from Mohammed Al Abri (Cornell University) and Samantha Brooks
(University of Florida).
- files from Jessica Petersen from the University of Nebraska-Lincoln
and Mohammed Al Abri from Cornell University . This data set is part of
their recent publication "The American Quarter Horse: Population
structure and relationship to the Thoroughbred" in Journal of Heredity.
(2014)105:148-162.
URL: http://www.animalgenome.org/...i-bin/util/vcf/index
(2) A new pre-compiled CRI-MAP (version 2.5.07) for MacOSX-10.10.4 has been
made available by Jill Maddox from Australia.
URL: http://www.animalgenome.org/tools/share/
(3) Minor improvements have eliminated some bugs in the VCF Data Repository
user tools.
URL: http://www.animalgenome.org/...i-bin/util/vcf/index
(4) The user interface for the NAGRP File Sharing Platform has received a
face lift to simplify user input.
URL: http://www.animalgenome.org/...i-bin/util/fileshare
o Miscellaneous:
- The web site for Functional Annotation of ANimal Genomes (FAANG)
consortium is continually improved/developed to maintain communication
channels and working group structure and to facilitate collaborative
interactions between members.
URL: http://www.faang.org
- New items have been added to the AnGenMap FAQ: Who can post recruitment
advertisements and why? Now the FAQ has 32 items.
URL: http://www.animalgenome.org/...mmunity/angenmap/faq
Check out the daily "what's new" (http://www.animalgenome.org/news/) items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links or web errors on AnimalGenome.ORG.
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
(http://www.animalgenome.org:bioinfo/services/helpdesk) for any routine
requests.
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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