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From listmasteranimalgenome.org  Tlistmaster Apr 28 11:12:08 2022
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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, 2022)
Date: Thu, 28 Apr 2022 11:12:08 -0500

What's new on the NAGRP animal genome web site (#2, 2022)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
  QTLdb (Release 47) and CorrDB (Release 15):

  (Apr 25, 2022): A sum of 17,360 new QTL/associations have been curated into
  the database. (New additions less obsolete/retracted ones: Catfish: 0;
  Cattle: 15,726; Chicken: 366; Goat: 60; Horse: 31; Pig: 1,042; Sheep: 135;
  Rainbow trout: 0 -- Net increase: 17,360). To date, the current total
  number of QTL in the database: 253,330 [Breakdown: Cattle: 192,925 (on 701
  traits); Chicken: 16,637 (on 443 traits); Goat: 128 (on 25 traits); Horse:
  2,636 (on 65 traits); Pig: 35,384 (on 716 traits); Sheep: 4,207 (on 281
  traits); Rainbow trout: 1,413 (on 41 traits)]

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

  (Apr 26, 2022): A sum of 752 new correlations [Break down by species --
  Pig: 156; Cattle: 172; Chicken: 170; Sheep: 254; ] and a sum of 155 new
  heritability data [Break down by species -- Pig: 44; Cattle: 47; Chicken:
  24; Horse: 1; Sheep: 36; Goat: 3; ] have been curated into the CorrDB.
  To date, the total number of correlation data in the database: 24,856
  [Breakdown by species -- Cattle: 13,003 (on 393 traits); Chicken: 1,625
  (on 90 traits); Horse: 209 (on 27 traits); Pig: 7,737 (on 267 traits);
  Sheep: 1,971 (on 93 traits) Goat: 311 (on 32 traits)], and total
  heritability data: 4,474 [Breakdown by species -- Cattle: 2,243 (on 426
  traits); Chicken: 343 (on 120 traits); Horse: 123 (on 53 traits); Pig:
  1,491 (on 306 traits); Sheep: 269 (on 124 traits) Goat: 5 (on 2 traits)],
  curated from 441 publications.

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

  Database developments:

  (1) The curator tools in both QTLdb and CorrDB have been extensively
  re-developed (involving 15 scripts serving 47 curator views/functions)
  in order to facilitate curation of "trait variants" (called "sibling
  traits" previously). This improvement is intended not only to improve
  consistency of livestock trait curation, but also to provide a better data
  management structure to facilitate information dissemination and trait
  ontology developments.  We have submitted a paper for the upcoming WCGALP
  to describe the new data structure and tools.

  (2) Batch data download from the CorrDB is now possible. A new section has
  been added to the CorrDB home page listing livestock animal trait
  correlation and heritability data. The data for download will be synced
  with the current database release.


o Ontology developments:

  (1) Six updates were made to the Vertebrate Trait (VT) Ontology data
      (versions 12.1, 12.2, 13.3, 12.4, 12.5, and 12.6).
  (2) Nine updates were made to the Livestock Breed Ontology (LBO, versions
      7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, and 7.9).

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


o Data repository:

  As of April 5, 2022, all NAGRP Data Repository–hosted supplementary data to
  publications (total of 796 data files, 84.25 GB in size, for 92 manuscripts
  published in 27 scientific journals) has been transferred to Open Science
  Framework (OSF; https://osf.io). Automatic web forwarding links for each of
  the publications have been set up. The URL forwarding will stay functioning
  as long as the AnimalGenome.org website is live.

  We have sent notifications to the data owners to sign up on OSF in order to
  take ownership of their data.  Currently, the transferred data are owned by
  one of our representatives (Zhiliang Hu). As soon as the proper ownership
  is established at OSF, we will withdraw from our role.

  The entire transition process took about four years to finish. (1) In
  Spring 2019, we announced our plan and started to scale down the service;
  (2) During 2020 and 2021, we provided a time window to update the journal
  information for those papers that were in the process of being accepted for
  publication. (3) In early 2022, we completed the data transfer. It is worth
  mentioning that by the end of this period, there remained 49 data files
  (3.6 GB in total size) on 17 manuscripts that were not transferred, since
  there is no indication that these manuscripts will ever get published.

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

  The above changes were only intended to improve long-term data stability.
  The data repository service is still available for short-term data sharing.

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


o Misc.

  (1) NRSP8 annual reports for 2020 are being made available on the
      website as they became available from each species coordinator.

  URL: https://www.animalgenome.org/...mmunity/NRSP-8/2022/

  (2) The website supporting the FAANG 2022 Workshop held in February has
      video recordings and slides available online.

  URL: https://www.faang.org/...?s=2022workshop..txt

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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