From listmasteranimalgenome.org Wed Jan 11 13:18:09 2017
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 (#1, 2017)
Date: Wed, 11 Jan 2017 13:18:09 -0600
What's new on the NAGRP animal genome web site (#1, 2017)
o NRSP-8 Bioinformatic Coordination Activity Updates
The annual updates from NRSP-8 Bioinformatic Coordinators are available
online. It covered related works in and supports to a number of areas
including ontology development, minimal standards development, expanding
Animal QTLdb functionality, software development, facilitating research,
multi-species support, community support, user services and reaching out.
o Animal QTLdb updates:
Announcing Release 31 of the Animal QTLdb. A sum of 15,237 new QTL
have been added to the database. The current total number of QTL in
the database: 121,265 [Break down: Cattle: 95,332; Catfish: 0; Chicken:
6,633; Horse: 1,245; Pig: 16,516; Sheep: 1,412; Rainbow trout: 127]
(New additions less obsolete/retracted ones: Catfish: 0; Cattle: 13,680;
Chicken: 950; Horse: 48; Pig: 483; Sheep: 76; Rainbow trout: 0 -- Net
QTL number increase: 15,237). URL: http://www.animalgenome.org/QTLdb/
(1) The curation tools have been improved to allow automatic verification
and streamlined curation of SNP information into the database. The
improvements involve data quality control processes in which multiple
genome builds are maintained for cattle, chicken, and sheep.
(2) Curation protocols have been modified so that preliminary SNPs (with
'ss' numbers only) are allowed to be entered to anchor QTL/association
mapping locations. The QTL/association mapping data represented by the
'ss' SNPs are not subject to normal data release procedures unless the
manually entered genome map coordinates are also available. The SNP 'ss'
numbers will eventually be replaced with the corresponding SNP 'rs'
numbers once they are assigned by dbSNP.
(3) The Frequently Asked Questions have also been updated to include a
couple new small items.
(4) Five people applied to become new Animal QTLdb curators since the last
update in August. Training processes are underway to bring them up to
speed on data curation protocols.
o Ontology developments:
Three ontologies have been under active development at Iowa State
University. New versions of the ontologies have been released:
Vertebrate Trait (VT) Ontology, version 6.9; Livestock Product Trait
(LPT) Ontology, version 1.3; and Livestock Breed Ontology (LBO),
version 1.7. In addition, the VT has been made available for direct
download at the Github site.
o NAGRP Data Repository:
The hosted publication supplementary data has now been merged with the
NAGRP Shared Data Repository. Its contents can be found by searching the
Thanks to Ben Rosen from the USDA/ARS and his colleagues for their efforts
putting together a new goat genome assembly. The new goat assembly is now
loaded to JBrowse for map alignment views. Currently available tracks
include NCBI gene model annotations and Gnomon, the NCBI gene prediction
(1) US Pig Genome Coordinator's annual report for 2016 was posted. The
2016 NRSP-8 pig genome station reports also start to be online.
(2) Room sharing bulletin boards for PAG, PAG-Asia, and other meetings
have been improved by adding several administrator tools and a security
layer to prevent robot-like hackers.
(3) The AnGenMap listserv moderator's switchbox has been improved to
include functions to facilitate the list moderator's reviewing and posting
tasks. Improvements include functions/tools to clean mail text mixed with
quoted-printables, and to decode MIME-coded text.
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/...fo/services/helpdesk) for any routine
NAGRP Bioinfo Team