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From listmasteranimalgenome.org  Tlistmaster Apr 27 14:33:35 2023
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From: "Hu, Zhiliang [ANS]" <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 (#2, 2023)
Date: Thu, 27 Apr 2023 14:33:35 -0500

What's new on the NAGRP animal genome web site (#2, 2023)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the QTLdb
  (Release 50) and CorrDB (Release 18):

  (Apr 25, 2023): A sum of 12,595 new QTL/associations have been curated into
  the QTLdb. (New additions less obsolete/retracted ones: Catfish: 0; Cattle:
  257; Chicken: 98; Goat: 0; Horse: 0; Pig: 12,119; Sheep: 121; Rainbow
  trout: 0 -- Net increase: 12,595). To date, the current total number of QTL
  in the database: 270,885 [Breakdown by species: Cattle: 193,898 (on 680
  traits); Chicken: 18,411 (on 372 traits); Goat: 129 (on 26 traits); Horse:
  2,649 (on 65 traits); Pig: 48,844 (on 673 traits); Sheep: 4,625 (on 272
  traits); Rainbow trout: 2,329 (on 47 traits)].

  In addition, as part of our efforts on data quality controls, updates have
  also been made to previously curated data for 4,387 QTL/associations, 165
  base traits, and 1,113 trait variants.

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

  (Apr 26, 2023): A sum of 1,131 new correlations [Breakdown by species --
  Pig: 198; Cattle: 597; Chicken: 202; Sheep: 134] and a sum of 371 new
  heritability data [Breakdown by species -- Pig: 108; Cattle: 202; Chicken:
  20; Horse: 8; Sheep: 33] have been curated into the CorrDB. To date, the
  total number of correlation data in the database: 27,970 [Breakdown by
  species -- Cattle: 14,068 (on 357 traits, 162 trait variants); Chicken:
  2,037 (on 81 traits, 47 trait variants); Horse: 209 (on 27 traits, 0 trait
  variants); Pig: 9,100 (on 238 traits, 107 trait variants); Sheep: 2,245 (on
  77 traits, 90 trait variants); Goat: 311 (on 32 traits, 0 trait variants)],
  and total heritability data: 5,149 [Breakdown by species -- Cattle: 2,532
  (on 410 traits, 179 trait variants); Chicken: 397 (on 108 traits, 39 trait
  variants); Horse: 131 (on 54 traits, 1 trait variant); Pig: 1,715 (on 286
  traits, 83 trait variants); Sheep: 369 (on 114 traits, 90 trait variants);
  Goat: 5 (on 2 traits, 3 trait variants)] curated from 520 publications.

  In addition, as part of our efforts on data quality controls, updates have
  been made to previously curated data that involved 8,165 correlations, 194
  base traits, and 1,044 trait variants.

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

  Database developments:

  (1) Our works on devising new structures/curation pipelines and introducing
  a "trait variant" data type have been published recently in the Oxford
  journal Database (Volume 2023, baad024): "A combinatorial approach
  implementing new database structures to facilitate practical data curation
  management of QTL, association, correlation and heritability data on trait
  variants" (DOI: 10.1093/database/baad024).

  (2) As a result of implementing trait variant curation, several changes are
  visible on this data release: (a) There are new parameters to describe
  traits in GFF files (column 9) for data downloads, namely 'BaseTrait',
  'TraitVariant', and 'TraitReprtNM', for "base trait", "trait variants", and
  "reported trait names," respectively (see the QTLdb FAQ "Terminology"
  section for details). (b) Data summaries on trait variants are visible (you
  may have noticed on our database releases since last year a reduction in
  the number of base traits and increase in the number of trait variants --
  for those who are interested to know the reason, please read our paper for
  details). (c) Changes are coming on web pages describing traits; stay tuned.

  (3) We retrospectively fixed some non-current-standard characters stored in
  the database, which sometimes displayed as black diamonds or other types of
  "gibberish" in a web browser, introduced during historical data curations
  when these characters were copied/pasted into the database over the past 20
  years. The "non-current-standard characters" include symbols representing
  "plus-minus sign" (± or +/-), "multiplication sign" (x or x), and may
  involve decodes from ASCII, UNICODE, HEX code, and/or HTML character coding
  methods. The solutions included character settings alignment in the backend
  storage engine and web interface programming environments, in compliance
  with current standards. Procedures have been implemented in the curation
  environment to automatically catch or convert non-standard characters or
  flag to make suggestions to curators.

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


o Ontology developments:

  The following data releases were made since our last "what's new" updates:

  (1) One Vertebrate Trait (VT) Ontology data release (version 13.1) with
  3,692 terms.
  (2) One Livestock Breed Ontology (LBO) data release (version 8.1) with
  1,116 terms.
  (3) Version 2.181 of Clinical Measurement Ontology (CMO) data from
  Bioportal with 3,863 terms was updated to the local QTLdb/CorrDB curation
  environment and for ontology hierarchy browsers and viewers on the site.

  As VT/LPT/CMO ontologies are under active development, the mapping of a
  trait term used in Animal QTLdb or CorrDB to one or more ontology terms may
  be out-of-date. We have implemented procedures to identify these potential
  problems for updates upon each ontology release or QTLdb/CorrDB release.

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


o Data repository:

  Following our success last year transferring 796 publication supplementary
  data files to Open Science Framework (OSF; https://osf.io), we are in the
  process of coordinating with data owners to organize the rest of the data
  files and tools in the NAGRP Repository for deposition to OSF, Github, or
  Ag Data Commons, among others.

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


o Support Community Activities:

  (1) The NRSP8 General Reports from the 2023 PAG meeting in San Diego are
  posted. Group reports from Aquaculture and Bioinformatics are also posted.
  URL: https://www.animalgenome.org/...mmunity/NRSP-8/2023/

  (2) Presentation slides from the 2023 FAANG Workshop are available on the
  FAANG website.
  URL: https://www.faang.org/...?s=2023workshop..txt
       aka https://www.animalgenome.org/community/FAANG/

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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