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From listmasteranimalgenome.org  Tlistmaster Jan  3 15:25:01 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 (#1, 2019)
Date: Thu, 03 Jan 2019 15:25:02 -0600

What's new on the NAGRP animal genome web site (#1, 2019)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of
  the QTLdb (Release 37) and CorrDB (Release 5):

  QTLdb (Dec 23, 2018): 5,763 new QTL/associations have been added to the
  database.  (New additions less obsolete/retracted ones: Catfish: 0; Cattle:
  4,055; Chicken: 127; Horse: 628; Pig: 757; Sheep: 196; Rainbow trout: 0 --
  Net increase: 5,763). The current total number of QTL/associations in the
  database: 164,262 [Break down: Cattle: 120,122; Chicken: 10,944; Horse:
  2,023; Pig: 28,720; Sheep: 2,325; Rainbow trout: 128].

  URL: https://www.animalgenome.org/QTLdb

  CorrDB (Dec 27, 2018): 2,033 new correlations have been added to the
  database.  [Break down by species -- Pig: 1,076 (32 new traits); Cattle:
  819 (0 new traits); Chicken: 70 (5 new traits); Sheep: 68 (7 new traits)]
  and 72 new heritability estimates [Break down by species -- Pig: 69 (0
  new traits); Cattle: 154 (29 new traits); Chicken: 15 (3 new traits);
  Sheep: 12 (9 new traits)] have been curated into the CorrDB.

  URL: https://www.animalgenome.org/CorrDB

  Database developments:

  (1) A QTL/association data enrichment analysis tool has been implemented
  in the Animal QTLdb. The tool uses a set of selected traits to perform a
  genome-wide data distribution analysis with Chi-square test of a two-way
  contingency table (traits by chromosomes) to determine the locations where
  certain traits are most likely to be over-represented. The tool has been
  reported in our recent paper "Building a livestock genetic and genomic
  information knowledgebase through integrative developments of Animal QTLdb
  and CorrDB" published in the upcoming Nucleic Acids Research 2019 Database
  issue.

  URL: (browse "Search and Analysis" tools under each species for details)
   e.g. https://www.animalgenome.org/...-bin/QTLdb/BT/nscape (cattle)
        https://www.animalgenome.org/...-bin/QTLdb/SS/nscape (pig)
        https://www.animalgenome.org/...-bin/QTLdb/GG/nscape (chicken)
        etc.

  (2) An improved version of the QTL/association data enrichment analysis
  tool was made available recently to allow user-defined sizes of chromosome
  regions for enrichment testing. The new feature is to be presented at the
  upcoming Plant and Animal Genome meeting in San Diego, with a poster titled:
  "Implementation of a new data enrichment analysis tool in the Animal QTL
  Database" (Poster #35076).

  URL: https://www.animalgenome.org/QTLdb

  (3) Automated updates of Animal QTLdb user visits and data download
  activities have been added to the web site (on the main page, see light
  cyan text below the graph column on the right hand side). The text is
  hyper-linked to a world map showing locations of unique visitors to the
  database, which was also made available recently.

  URL: https://www.animalgenome.org/QTLdb

  (4) New Ensembl gene models for the new cattle genome build BovARS_1.2 have
  been added to JBrowse tracks that align with QTL/associations, Genbank
  annotations, and SNP liftover locations.

  URL: https://www.animalgenome.org/jbrowse/


o Data repository:

  The volume of supplementary files hosted by the NAGRP repository has
  increased four-fold in 2018 over the previous year. This resulted from the
  doubling of the number of publications that requested us to host their
  supplementary data.

  URL: https://www.animalgenome.org/repository/pub/

  A set of cattle genome variant mapping data (to ARS-UCD1.2 Cow Genome
  Assembly, by Robert Schnabel’s group from the University of Missouri) has
  been deposited to the NAGRP Community Data Repository.

  URL: https://www.animalgenome.org/repository/


o Ontology developments

  New data releases were made for Vertebrate Trait (VT) Ontology (three times;
  the latest version is v.8.8), Livestock Product Trait (LPT) Ontology (one
  time; the latest version is v.2.2), and Livestock Breed Ontology (LBO)
  (three times; the latest version is v.3.8).

   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 FAANG Web site:

  - An interactive world map showing the FAANG memberships has been added to
    the FAANG website.
  - The September newsletter of FAANG Europe COST Action is posted on the
    FAANG web site.
  - Congratulations to six recent grant recipient groups – Recent FAANG
    Funded Projects list is updated.

  URL: https://www.faang.org


o Misc.:

  - US Pig Genome Newsletter #126 is posted on ANGENMAP and its PDF and
    text versions are archived.
  URL: https://www.animalgenome.org/pig/newsletter

  - Aquaculture genomics newsletter #47 is deposited.
  URL: https://www.animalgenome.org/...s/activity

  - A world map showing the distribution of AnGenMap Members has been added
    to the web site.
  URL: https://www.animalgenome.org/community/angenmap


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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