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From listmasteranimalgenome.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 1,623 new correlations [Break down by
  species -- Pig: 1,199 (53 new traits); Cattle: 320 (0 new traits);
  Chicken: 102 (3 new traits); Sheep: 2 (1 new traits)] and a sum of 422
  new heritability data [Break down by species -- Pig: 347 (0 new traits);
  Cattle: 57 (20 new traits); Chicken: 16 (5 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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