AnGenMap

Archived Post

From listmasteranimalgenome.org  Mon Aug 30 22:27:44 2021
Return-Path: <listmasteranimalgenome.org>
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, 2021)
Date: Mon, 30 Aug 2021 22:27:44 -0500

What's new on the NAGRP animal genome web site (#3, 2021)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
  QTLdb (Release 45) and CorrDB (Release 13):

  This database release is highlighted by two major events: (1) The Goat
  QTLdb/CorrDB is live! The first batch of goat QTL/association data has
  been curated into the Goat QTLdb and CorrDB, and (2) Progress toward
  supporting only genome coordinate-based maps for QTL/association data
  reports (more details below), with revised procedures and structures to
  support multiple genome assemblies in terms of QTL/association mappings.

  (Aug 23, 2021): A sum of 4,166 new QTL/associations have been curated into
  the database. (New additions less obsolete/retracted ones: Catfish: 0;
  Cattle: 1,944; Chicken: 1,417; Goat: 64; Horse: 1; Pig: 397; Sheep: 180;
  Rainbow trout: 163 -- Net increase: 4,166). The current total number of
  QTL in the database: 220,401 [Breakdown: Cattle: 163,725; Chicken: 15,475;
  Goat: 64; Horse: 2,473; Pig: 33,540; Sheep: 3,752; Rainbow trout: 1,372]

  Thanks are due to Dr. Holly Neibergs from Washington State University, and
  Gabrielle Becker from University of Idaho for their commitment curating
  their data into the QTLdb.

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

  (Aug 23, 2021): A sum of 1,148 new correlations [Breakdown by species --
  Pig: 193 (7 new traits); Cattle: 579 (26 new traits); Chicken: 18 (1 new
  traits); Sheep: 47 (4 new traits); Goat: 311 (32 new traits)] and a sum of
  194 new heritability data [Breakdown by species -- Pig: 48 (6 new traits);
  Cattle: 115 (25 new traits); Chicken: 7 (2 new traits); Sheep: 22 (5 new
  traits); Goat: 2 (1 new traits)] have been curated into the CorrDB. To
  date, the total number of correlation data in the database: 23,552
  [Breakdown by species -- Cattle: 12,801; Chicken: 1,455; Goat: 311; Horse:
  209; Pig: 7,161; Sheep: 1,615], and total heritability data: 4,273
  [Breakdown by species -- Cattle: 2,173; Chicken: 318; Goat: 2; Horse: 118;
  Pig: 1,444; Sheep: 218]

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

  Database developments:

  (1) Multiple genome support: The current Animal QTLdb currently supports
  20 genome builds for 7 species. This is a result of progress in database
  restructuring and new data pipeline developments, along with several tools
  for data lift-over between assemblies (more below).

  (2) We have developed an in-house procedure to map known SNPs to a genome
  assembly using flanking sequences, which can be lifted over from older
  genome builds. This has greatly accelerated our progress on supporting
  multiple/new genomes when they become available without extended waiting
  periods for official SNP identifiers ('rs' numbers) to become available,
  which presented a bottleneck for timely QTLdb data release. The
  procedures developed also can help to match SNPs when 'rs' numbers are
  missing from a data set.

  (3) As a result of changes made in (2), modifications have been made to
  the policy on minimum information required for Animal QTLdb data entry.
  The change clarifies the minimum information for SNP-based data reports,
  and opens avenues for new types of SNP information, such as those SNPs
  without official 'rs' numbers must provide flanking sequences.

  (4) A new hierarchy display tool has been developed for the Animal QTLdb
  web portal for data access using traits from the Vertebrate Trait (VT)
  Ontology, Livestock Product Trait (LPT) Ontology, and Clinical Measurement
  Ontology (CMO). The display tool also includes search capability, which
  helps users to quickly find relevant terms in large ontologies. The tool
  has been implemented on all species QTLdb front pages, as well as on the
  VT/LPT/CMO home pages at AnimalGenome.ORG.

  (5) As a result of the changes made in (4), the Animal QTLdb web portal
  structure has been reorganized to improve data access by requiring fewer
  browse/search steps before reaching the level of pages for data.

  (6) Animal CorrDB: A Data Summary text table has been added on several
  pages to provide extended information on the current data window. A
  featured function is a display of median and interquartile ranges of
  heritability data when multiple measurement results exist for the same
  trait.

  (7) Animal CorrDB: The web portal on the Animal CorrDB website has been
  extensively reformed. A number of new data filters along with search/
  browse functions help to provide the scope of data so users have an
  idea of what to expect rather than needing to guess what to search for.
  Added links and flags on web pages can effectively enable users to
  traverse from one data type to another (e.g., from traits to
  QTL/association data; from heritability data to correlation data; from a
  table view to graphic view). Linking traits to VT/LPT/CMO ontologies
  facilitates data links with external databases where such ontologies are
  also used.


o FAANG website updates

  New updates are continually made to the FAANG website to cope with changes
  on the advancement of the consortium for the next decade of FAANG research
  (FAANG to Fork strategy) to link G2P in diverse populations of animals and
  apply innovative new technologies to model G2P at the cell, tissue, and
  whole-animal levels. The FAANG website updates serve an important role to
  inform our peers and the public what we do and how we are doing better.

  URL: https://www.faang.org/


o Tool developments

  Thanks to the individuals and groups (see data source acknowledgement on
  the web page cited below) who shared their SNP names, custom SNP ID data
  from their SNP discovery works that helped us to be able to upgrade the
  previous tool for matching SNP names/'ss'/'rs' numbers into a livestock
  SNP ID/name match repository with a new collection of over 7.8 million
  non-redundant matches between various types of SNP names, identifiers, and
  their final dbSNP 'rs' IDs. This dataset and tools are part of the NAGRP
  Tool Box and useful for SNP-related data annotations and integrations. We
  will continue to seek and accept new data contributions.

  URL: https://www.animalgenome.org/tools/SNPnmids/


o Ontology developments:

  (1) Five updates were made to the Vertebrate Trait (VT) Ontology data
      (versions 11.6, 11.7, 11.8, 11.9, and 11.10).
  (2) Three updates were made to the Livestock Breed Ontology (LBO, versions
      6.3, 6.4, and 6.6).

  URL: https://www.animalgenome.org/...bioinfo/projects/vt/
       https://www.animalgenome.org/...ioinfo/projects/lbo/


o Misc.

  (1) Data repository:
      SNP liftover (an in-house procedure, see above) from chicken assembly
      Gallus_gallus-5.0) to more recent builds Chicken GRCg7b and GRCg7w are
      deposited at the NAGRP data repository as requested by users.  More
      data deposits can be made upon user requests.

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

  (2) The website has been updated for the upcoming VISIONS III conference:
      Star Gazing into the Galaxy of Animal Genetics and Genomics, with new
      information on the date change, updated speakers and sponsors.

  URL: https://www.animalgenome.org/share/visions


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 talk to us using our Helpdesk (https://www.animalgenome.org/helpdesk).

--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org


 
© 2003-2022 USA · USDA · NAGRP · Bioinformatics Coordination Program.
Contact: NAGRP Bioinformatics Team
Helpdesk