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From listmasteranimalgenome.org  Mon Jan  4 13:48:20 2021
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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, 2021)
Date: Mon, 04 Jan 2021 13:48:20 -0600

What's new on the NAGRP animal genome web site (#1, 2021)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
  QTLdb (Release 43) and CorrDB (Release 11):

  QTLdb (Dec 23, 2020): A sum of 2,123 new QTL/associations have been curated
  into the database. (New additions less obsolete/retracted ones: Catfish: 0;
  Cattle: 815; Chicken: 275; Goat: 0; Horse: 21; Pig: 584; Sheep: 151;
  Rainbow trout: 277 -- Net increase: 2,123). The current total number of QTL
  in the database: 211,792 [Breakdown: Cattle: 160,659; Chicken: 12,783;
  Goat: 0; Horse: 2,472; Pig: 31,455; Sheep: 3,562; Rainbow trout: 861]

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

  CorrDB (Dec 26, 2020): A sum of 645 new correlations [Breakdown by species
  -- Pig: 307 (5 new traits); Cattle: 301 (11 new traits); Sheep: 37 (9 new
  traits)] and a sum of 488 new heritability data [Breakdown by species --
  Pig: 315 (27 new traits); Cattle: 147 (19 new traits); Sheep: 26 (15 new
  traits)] have been curated into the CorrDB. To date, the total number of
  correlation data in the database: 21,036 [Breakdown by species -- Cattle:
  11,277; Chicken: 1,247; Horse: 209; Pig: 6,735; Sheep: 1,568], and total
  heritability data: 4,319 [Breakdown by species -- Cattle: 1,881; Chicken:
  287; Horse: 118; Pig: 1,845; Sheep: 188], curated from 344 publications.

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

  Database developments:

  (1) Goat QTLdb and Goat CorrDB: The groundwork has been laid by preparing
  the goat linkage maps, genome maps, SNP map data, trait management space,
  and other required information in order for both the Animal QTLdb and the
  CorrDB to expand to include goat as a new species for curation of published
  QTL, associations, correlations, and heritability data into respective
  databases.

  (2) New dbxref data link services were added to both Animal QTLdb and
  Animal CorrDB to allow external URL links to specific QTL or correlation
  data across species. Such links are often used by web services, API tools,
  or database xref pointers. The syntax to use the service is a URL like
  https://www.animalgenome.org/...TLdb/q?id=QTL_ID:[id] for QTLdb and
  https://www.animalgenome.org/...rrDB/q?id=CorrID:[id] for CorrDB,
  respectively (Replace "id" with respective actual id, which is the
  unique numerical identifier for a specific QTL or correlation record. Refer
  to QTLdb API documentation or downloaded data about the ids).

  (3) Curated gene-eQTL data now can be delivered through web tools in the
  Animal QTLdb ("trait-eQTL" have already been delibvered since 2009). The web
  links include lists by publication through permanent record locator,
  QTL/association data details, and a number of search results pages. It will
  be pushed to downloads soon.

  (4) A data curation helper tool has been developed to facilitate flanking
  SNPs lookup for given genome intervals. The tool picks the leftmost and the
  rightmost SNPs as flanking candidates for a searched span, along with their
  coordinates for curators to determine the use of the queried SNPs for data
  annotations.

  (5) Another data curation helper tool has been developed to look up SNP
  stable 'rs' numbers by their alternate names (usually from SNP discovery
  environment, original publications, and genotyping platforms). The tool
  allows copy/paste of a spreadsheet table for addition of a new column with
  the matched ‘rs’ numbers, thus greatly improving the efficiency and
  accuracy of data curation.

  (6) Frequently asked questions for both Animal QTLdb and CorrDB were
  updated with the addition of new items, updates to existing items, and
  corrections to several items. See "NEW" indicator on the page for
  details.

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


o Ontology developments:

  (1) One update was made to the Vertebrate Trait (VT) Ontology data (version
  10.7). Refer to QTLdb/CorrDB release information above for the number of
  new traits added in each species.

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

  (2) Webpages for the Vertebrate Trait (VT) Ontology, Livestock Product
  Trait (LPT) Ontology, Clinical Measurement Ontology (CMO), and Livestock
  Breed Ontology (LBO) projects are updated with new utility searches added
  for livestock trait correlations and heritability data in the Animal CorrDB
  and QTL/SNP association data in the Animal QTLdb.

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

o Miscellaneous items:

  (1) The community event web bulletin board has been continually updated
  with new and updated meeting information. Currently the list includes
  events for the next 18 months. Please feel free to add your items to the
  list as a way to keep the community informed of what’s going on.

  URL: https://www.animalgenome.org/community/meetings

  (2) The community data sharing platform has been updated to include
  voluntary contributions of public SNP identification information. The
  "SNP identification information" mainly refers to custom SNP
  identifications generated from SNP discovery processes, custom genotyping
  platforms, and other SNP works that involve SNP identifications in
  addition to their official ‘rs’ numbers. This effort is geared towards a
  potential public platform to facilitate proper SNP matches needed in data
  curation, information annotation data merge/combined analysis, and other
  related efforts.

  URL: https://www.animalgenome.org/...i-bin/util/fileshare

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


 
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