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From  Tue Sep  1 10:28:06 2020
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From: "Hu, Zhiliang [AN S]" <>
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To: Members of AnGenMap <>
Subject: What's new on the NAGRP animal genome web site (#3,
Date: Tue, 01 Sep 2020 10:28:06 -0500
What's new on the NAGRP animal genome web site (#3, 2020)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the QTLdb
 (Release 42) and CorrDB (Release 10):

  QTLdb (Aug. 27, 2020): A sum of 18,247 new QTL/associations have been
  curated into the database. (New additions less obsolete/retracted ones:
  Catfish: 0; Cattle: 17,583; Chicken: 262; Horse: 5; Pig: 291; Sheep: 106;
  Rainbow trout: 0 -- Net increase: 18,247). The current total number of
  QTL in the database: 209,669 [Breakdown: Cattle: 159,844; Chicken: 12,508;
  Horse: 2,451; Pig: 30,871; Sheep: 3,411; Rainbow trout: 584]

  In addition, there were also 1,206 QTL/association data curated during this
  period that have been placed on hold due to the lack of some minimum
  required information. They will be updated once this information becomes
  available. In other words, we have curated 19,259 data points since the
  last data release in April.


  CorrDB (Aug. 27, 2020): A sum of 909 new correlations [Breakdown by species
  -- Pig: 12 (2 new traits); Cattle: 800 (14 new traits); Chicken: 6 (1 new
  trait); Sheep: 91 (8 new traits)] and a sum of 237 new heritability data
  [Breakdown by species -- Pig: 27 (5 new traits); Cattle: 193 (21 new traits);
  Chicken: 3 (0 new traits); Sheep: 14 (9 new traits)] have been curated into
  the CorrDB.  To date, the total number of correlation data in the database:
  20,391 [Breakdown by species -- Cattle: 10,976; Chicken: 1,247; Horse: 209;
  Pig: 6,428; Sheep: 1,531], and total heritability data: 3,831 [Breakdown by
  species -- Cattle: 1,734; Chicken: 287; Horse: 118; Pig: 1,530; Sheep: 162],
  curated from 344 publications.


  Database developments:

  (1) A newly developed batch SNP query tool has been added to the Animal
  QTLdb web tools family (linked from "1. Search and Analysis tools" on a
  species main page). With this tool, up to 2,000 SNP IDs (dbSNP 'rs' numbers)
  can be posted for query. The returned results are aggregated surrounding
  each SNP, i.e., information is "SNP centric".  The information includes QTL
  or SNP association genome locations, linked traits and trait ontology terms,
  related genes, publication references, etc. for each SNP. Each of these
  details are further dynamically linked to related data tools in the QTLdb.
  We welcome your comments and suggestions to help us add more features and
  improve database utility. (The SNP query link is added to "trait search",
  "gene search", "location search", and "general search" tools.

  (2) Improvements are ongoing in the Animal QTLdb with regard to supporting
  data mapping to multiple genomes. The latest outcomes include additions
  of several genome builds for JBrowse views of QTL/association data. The
  support of multiple genomes in Animal QTLdb is based on QTL/association
  mapping data liftover between genomes with the aid of SNP location
  coordinate information on each build.

  (3) The Animal QTLdb FAQ has been updated with new items to address common
  user questions regarding how QTL/association data can be downloaded with
  specified scope targeting certain traits or trait classes.

  (4) Numerous bug fixes have been made on CorrDB public browse/query tools.

o Ontology developments:

  Three (3) data updates were made to the Vertebrate Trait (VT) Ontology
  (versions 10.4, 10.5, and 10.6).  Refer to QTLdb/CorrDB release information
  above for the number of new traits added in each species.


  One (1) data update was made to the Livestock Breed Ontology (LBO) (version


  A local workflow and pipeline have been added to the current ontology data
  update and public release pipeline for the development of the Vertebrate
  Trait (VT) Ontology, Livestock Product Trait (LPT) Ontology, and Livestock
  Breed Ontology (LBO). This data release process includes new data
  synchronizations among BioPortal, GitHub (which pipes data to OntoBee, EBI,
  OBO Foundry, uPheno, AgroPortal, etc.) and databases
  (feeding data to QTLdb trait mappers, project websites for data query and
  browse, etc).

Check out the daily "what's new" ( 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 (,
James Koltes (, Fiona McCarthy (
Or talk to us using our Helpdesk (

NAGRP Bioinfo Team



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