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ARCHIVE
What's New on the NAGRP Animal Genome Web Site ( 2018 - 2023 )
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| Major updates / new additions: |
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New database releases have been made: Animal QTLdb Release #52, and Animal CorrDB Release #20.
| | New, Dec 27, 2023 | |
| As we have planned (see QTLdb release #51), a total of 13,309 linkage-map–based QTL/association data curated to the Animal QTLdb during 1999 and 2021 have been deposited to Github as of Dec. 17, 2023. This step represents the separation of the legacy data from the current QTLdb, as we move forward with the sequence-based genome maps and SNP-based analysis results. These legact data were on 6 livestock species: cattle, chicken, horse, pigs, sheep, and rainbow trout. |
| New, Dec 18, 2023 |
| New cattle genome assembly ARS-UCD2.0 was released on July 1, 2023. As the SNP mappings on this build version is not available on the current dbSNP release (August 2023) we have performed a liftover of 96,180,721 SNPs from ARS-UCD1.0 build with our in-house procedures to accommodate the upcoming QTLdb data releases to include ARS-UCD2.0 build. |
| Update, Dec 12, 2023 |
| Version 13.14 of the Vertebrate Trait (VT) ontology data with 3,741 terms and several structural changes and updates. |
| Update, Nov 20, 2023 |
| Version 8.10 of Livestock Breed Ontology (LBO) data with 1,121 terms is released. |
| Update, Nov 20, 2023 |
| Version 13.13 of the Vertebrate Trait (VT) ontology data with 3,739 terms and several structural changes and updates. |
| Update, Nov 16, 2023 |
| Version 8.9 of Livestock Breed Ontology (LBO) data with 1,120 terms is released. |
| Update, Oct 26, 2023 |
| Version 13.12 of the Vertebrate Trait (VT) ontology data with 3,733 terms and several structural changes and updates. |
| Update, Oct 25, 2023 |
| An update (version 2.195) of Clinical Measurement Ontology (CMO) data with 3,897 terms from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Oct 23, 2023 |
| Started a process to retire inactive web pages, services, and materials.
https://www.animalgenome.org/aquaculture
https://www.animalgenome.org/pig
https://www.animalgenome.org/cattle
https://www.animalgenome.org/horse
https://www.animalgenome.org/poultry
https://www.animalgenome.org/sheep
https://www.animalgenome.org/bioinfo/service
https://www.animalgenome.org/bioinfo/service/computer
https://www.animalgenome.org/other/
https://www.animalgenome.org/other/Joomla
https://www.animalgenome.org/share/
https://www.animalgenome.org/share/critt
https://www.animalgenome.org/share/visions
https://www.animalgenome.org/share/survey
https://www.animalgenome.org/share/letter
https://www.animalgenome.org/blast
Reorganized:
https://www.animalgenome.org/repository/ https://www.animalgenome.org/tools/repository
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| Update, Oct 7, 2023 |
| As part of our effords to "ontologize" livestock trait terms in the process of data annotation into the QTLdb/CorrDB, two additional ontologies have been introduced for ontology term mappings: Uberon anatomy/tissue ontology, and rat disease ontology. The outcomes from this work may be visible to the public in the near future. |
| Update, Oct 3, 2023 |
| Obsoleted websites for NRSP8 cattle, chicken, horse, pig, and sheep coordination programs, and placed the website materials on archive. |
| Update, Oct 2, 2023 |
| An update (version 2.192) of Clinical Measurement Ontology (CMO) data with 3,889 terms from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Sep 25, 2023 |
| Version 13.11 of the Vertebrate Trait (VT) ontology data with 3,731 terms and several structural changes and updates. |
| Update, Sep 26, 2023 |
| Version 8.8 of Livestock Breed Ontology (LBO) data with 1,119 terms is released. |
| Update, Sep 12, 2023 |
| An update (version 2.191) of Clinical Measurement Ontology (CMO) data with 3,889 terms from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Sep 11, 2023 |
| Version 8.7 of Livestock Breed Ontology (LBO) data with 1,118 terms is released. |
| Update, Sep 11, 2023 |
| An update (version 2.189) of Clinical Measurement Ontology (CMO) data with 3,881 terms from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Sep 6, 2023 |
| Version 13.10 of the Vertebrate Trait (VT) ontology data with 3,733 terms and several structural changes and updates. |
| Update, Sep 6, 2023 |
| Several new data summary statistics are added to each species of QTLdb data summary page. These include "Experiments by Traits", "Data by Trait Variants", and "Experiments by Trait Variants". For example cattle QTLdb data summary. |
| Update, Sep 10, 2023 |
| The Animal QTLdb is updated with the new EVA dbSNP Release 5 data on 19 genome builds in 7 livestock species. This update also included the retirements of two chicken genome builds (chicken.GRCg7b and chicken.GRCg7w) and addition of one goat genome build (goat.CHIR_1.0). See QTLdb Supported Genome Assemblies for Data Alignments page for details. All currently released QTL/association data map lifts have also been updated accordingly (reflected in data download sections of each QTLdb species page). |
| Update, Sep 05, 2023 |
| What's new on the NAGRP animal genome web site (#3, 2023) |
| New, Apr 27, 2023 |
| Version 13.9 of the Vertebrate Trait (VT) ontology data with 3,732 terms and several structural changes and updates. |
| Update, Aug 22, 2023 |
| Version 13.8 of the Vertebrate Trait (VT) ontology data with 3,732 terms and a number of structural changes and updates. |
| Update, Aug 10, 2023 |
| An update (version 2.188) of Clinical Measurement Ontology (CMO) data with 2,188 terms from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Aug 7, 2023 |
| Version 8.6 of Livestock Breed Ontology (LBO) data with 1,122 terms is released. |
| Update, Aug 3, 2023 |
| Version 13.7 of the Vertebrate Trait (VT) ontology data with 3,732 terms is released to the public portal. |
| Update, Aug 3, 2023 |
| An update (version 2.187) of Clinical Measurement Ontology (CMO) data from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Aug 3, 2023 |
| Version 13.6 of the Vertebrate Trait (VT) ontology data with 3,729 terms is released to the public portal. |
| Update, Jul 12, 2023 |
| An update (version 2.185) of Clinical Measurement Ontology (CMO) data from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Jul 10, 2023 |
| Version 13.5 of the Vertebrate Trait (VT) ontology data with 3,711 terms is released to the public portal. |
| Update, Jun 30, 2023 |
| Version 13.4 of the Vertebrate Trait (VT) ontology data with 3,703 terms is released to the public portal. |
| Update, Jun 27, 2023 |
| An update (version 2.184) of Clinical Measurement Ontology (CMO) data from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Jun 26, 2023 |
| Version 8.5 of Livestock Breed Ontology (LBO) data with 1,121 terms is released. |
| Update, Jun 7, 2023 |
| Version 8.4 of Livestock Breed Ontology (LBO) data with 1,119 terms is released. |
| Update, Jun 5, 2023 |
| An update (version 2.182) of Clinical Measurement Ontology (CMO) data from Bioportal is ported to QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Jun 5, 2023 |
| Version 13.2 of the Vertebrate Trait (VT) ontology data with 3,703 terms is released to the public portal. |
| Update, May 24, 2023 |
| Version 8.2 of Livestock Breed Ontology (LBO) data with 1,117 terms is released. |
| Update, May 16, 2023 |
| Room-share bulletin board service is open for the upcoming 39th International Conference on Animal Genetics (ISAG). |
| Update, May 10, 2023 |
| Room-share bulletin board service is open for the upcoming Plant and Animal Genome (PAG) Australia conference. |
| Update, May 10, 2023 |
| What's new on the NAGRP animal genome web site (#2, 2023) |
| New, Apr 27, 2023 |
| New terminologies on trait variants, complex traits, and trait concept dissections are added to the Animal QTLdb FAQ. |
| New, Apr 25, 2023 |
| Version 2.181 of Clinical Measurement Ontology (CMO) data from Bioportal with 3,863 terms is ported to local QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Apr 11, 2023 |
| Version 13.1 of the Vertebrate Trait (VT) ontology data with 3,692 terms is released to the public portal. |
| Update, Apr 11, 2023 |
| The NRSP8 General Reports from 2023 PAG meeting at San Diego are posted. Group reports from Aquaculture, and Bioinformativcs are also posted. |
| New, Mar 14, 2023 |
| Presentation slides from 2023 FAANG Workshop are available on FAANG website. |
| New, Mar 05, 2023 |
| Version 8.1 of Livestock Breed Ontology (LBO) data with 1,116 terms is released. |
| Update, Feb 9, 2023 |
| Since all VT/LPT/CMO ontologies are under active developments, the mapping of a trait term used in Animal QTLdb or CorrDB to one or multiple of these ontologies may be found out-of-dated. We have implemented procedures to identify these potential problems for updates upon an ontology release and/or after each QTLdb/CorrDB release. |
| New, Jan 8, 2023 |
| What's new on the NAGRP animal genome web site (#1, 2023) |
| New, Jan 3, 2023 |
| Version 4.2 of the Livestock Product Trait (LPT) ontology data with 483 terms is updated to the public portal. |
| Update, Dec 20, 2022 |
| Experimental setting up separate JBrowse2 instances for multiple species was successful. A new JBrowse2 instance for PigGTEx gene expression pattern (permutated p-values) visualization is now available. The data is from Lingzhao Fang's group (private communications). |
| Update, Dec 1, 2022 |
| Version 12.10 of the Vertebrate Trait (VT) ontology data with 3,689 terms is released to the public portal. |
| Update, Oct 25, 2022 |
| Version 4.1 of the Livestock Product Trait (LPT) ontology data with 483 terms is updated to the public portal. |
| Update, Oct 24, 2022 |
| The Animal CorrDB web portal has been updated with addition/modification of its correlation netowrk visulization options. Now there are two ways to visulize a correlation netowrk: Graphviz dot graph and Cytoscape Web tools. These tools are available in sub-pages on various data summary or searched results page views. |
| New, Oct 23, 2022 |
| JBrowse2 (https://jbrowse.org/jb2/) is utilized to visualize data profilings from the genotype-tissue expression (GTEx) analysis. Our initial success was to use CattleGTEx data from Lingzhao Fang's study (https://www.nature.com/articles/s41588-022-01155-3; https://cgtex.roslin.ed.ac.uk/downloads/) to show gene expression patterns cross tissues with linear Manhattan plots https://www.animalgenome.org/gtex/cattle. |
| New, Oct 6, 2022 |
| A cytoscape web tool for visualizing complex networks has been successfully implemented at AnimalGenome.org to facilitate presentations of entity relationships for research projects and as database tools. Examples of such works include "An interactive cytoscape tool for query/visulization of phenotypically related cattle traits by their underlining gene interactions discovered via functional genomics through integration of multi-omics data". |
| New, Oct 1, 2022 |
| Version 12.9 of the Vertebrate Trait (VT) ontology data with 3,679 terms is released to the public portal. |
| Update, Sep 28, 2022 |
| Version 7.14 of Livestock Breed Ontology (LBO) data with 1,114 terms is released. |
| Update, Sep 28, 2022 |
| Version 2.171 of Clinical Measurement Ontology (CMO) data from Bioportal with 3,847 terms is ported to local QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Sep 28, 2022 |
| Genomic marker types as a curation parameter was added to Animal QTLdb curation pipelines in early 2016. We have retrospectively caught up marker type information for data curated prior to that time. Subsequently we have added this parameter for data downloads. The marker types data counts can be found on "data summary" pages of each species (choose "5. Number of QTL/associations by marker types" from the option list.) |
| New, Sep 21, 2022 |
| What's new on the NAGRP animal genome web site (#3, 2022) |
| New, Aug 26, 2022 |
| Since the Animal QTLdb has been supporting multiple genome builds since 2021 for a species, one genome assembly per species is now selected as default "reference" genome for the QTLdb web tools search and online map display. The selection of the default genome is in alignment with NCBI/Ensembl updates. The supported "default genome" information can be found on "Supported Genome Assemblies for Data Alignments" page on our website. |
| New, Aug 4, 2022 |
| The FAANG website is recently reformed to accommodate its new working structure - new task forces (TF) that replaced earlier working committees/groups. Web functions to facilitate the new working structure included TF membership management (self-elect or admits by organizers), organizer's ability to add new members, systematic mechanism to periodically check TF memberships, new working mailing listserv, and introductory web content for each TF. The web contents for the old working groups are placed on an archive, accessible by members only. |
| Update, Jul 29, 2022 |
| Version 2.169 of Clinical Measurement Ontology (CMO) data from Bioportal is ported to local QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Jul 28, 2022 |
| Version 7.12 of Livestock Breed Ontology (LBO) data is released. |
| Update, Jul 28, 2022 |
| Version 2.168 of Clinical Measurement Ontology (CMO) data from Bioportal is ported to local QTLdb/CorrDB curation environment and ontology browsers and viewers. |
| Update, Jul 21, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.11) data is released. |
| Update, Jul 21, 2022 |
| Version 12.8 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jul 21, 2022 |
| The AnGenMap and 17 other mailing lists are transitioned to using user profiles via web tools for users to manage their list subscriptions/unsubscriptions and other list options. The AnGenMap operates on Smartlist which depends auto-responsive email service to handle list subscription/unsubscription commands. Expanded web functions from the community directory coupled with the listserv was developed as an alternative to this operation and was in service since 2007. This complete shift to web functions helps to avoid multiple problems from maintaining some of the vulnerable listserv operations. |
| Update, Jul 07, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.10) data is released. |
| Update, Jun 20, 2022 |
| Version 12.7 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jun 09, 2022 |
| What's new on the NAGRP animal genome web site (#2, 2022) |
| New, Apr 28, 2022 |
| Version 12.6 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Apr 22, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.9) data is released. |
| Update, Apr 20, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.8) data is released. |
| Update, Apr 11, 2022 |
| As of April 5, 2022, all NAGRP Data Repository hosted supplementary data to publications has been transferred to Open Science Framework (OSF; https://osf.io). Automatic web forward links for each of the publications have been set up. The URL forward will stay functioning as long as the AnimalGenome.org website is alive. |
| New, Apr 05, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.7) data is released. |
| Update, Mar 22, 2022 |
| A new section is added to the CorrDB home page for batch download of livestock animal traits correlation and heritability data. The data for downloads are, and will be, from the current database release (the immediate previous release). |
| New, Mar 17, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.6) data is released. |
| Update, Mar 16, 2022 |
| The curator tools on both QTLdb and CorrDB have been extensively re-developed in the way how "trait variants" (previously called "sibling traits") information is curated. This improvement is aimed not only to bring the erratic livestock traits curation to be practically doable, but also to gear the management of such data towards a better structure in terms of information disseminations and ontology developments. |
| New, Mar 3, 2022 |
| The NRSP8 Annual Reports from Aquaculture, Swine, and Bioinformativcs groups are posted. |
| Update, Mar 1, 2022 |
| Version 12.5 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Mar 1, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.5) data is released. |
| Update, Feb 28, 2022 |
| Version 12.4 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Feb 25, 2022 |
| Version 12.2 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Feb 24, 2022 |
| 2022 FAANG Workshop is posted. |
| New, Feb 20, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.4) data is released. |
| Update, Feb 16, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.3) data is released. |
| Update, Feb 13, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.2) data is released. |
| Update, Feb 7, 2022 |
| A new version of Livestock Breed Ontology (LBO, version 7.1) data is released. |
| Update, Feb 4, 2022 |
| The NRSP8 Pig Genome Coordinator's Report for 2021 is posted. |
| New, Jan. 11, 2022 |
| The NRSP8 Bioinformatics Coordinator's Report for 2021 is posted. |
| New, Jan. 8, 2022 |
| The NRSP8 community web site is updated to post 2022 Annual Reports (for 2021) and new leadership changes. |
| Update, Jan 5, 2022 |
| Version 12.1 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jan 7, 2022 |
| Version 3.3 of the Livestock Product Trait (LPT) ontology data is updated to the public portal. |
| Update, Jan 04, 2022 |
| What's new on the NAGRP animal genome web site (#1, 2022) |
| New, Jan 03, 2022 |
| Version 3.2 of the Livestock Product Trait (LPT) ontology data is updated to the public portal. |
| Update, Dec 02, 2021 |
| Version 11.15 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Oct 4, 2021 |
| Version 11.14 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Sep 28, 2021 |
| Version 11.13 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Sep 21, 2021 |
| Version 11.12 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Sep 17, 2021 |
| Version 3.1 of the Livestock Product Trait (LPT) ontology data is updated to the public portal. |
| Update, Sep 09, 2021 |
| Version 11.11 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Sep 8, 2021 |
| A "new updates and activities" ball icon was added to the FAANG website that automatically bullet-point new items/areas on the web site within last 30 days. |
| New, Aug 31, 2021 |
| What's new on the NAGRP animal genome web site (#3, 2021) |
| New, Aug 30, 2021 |
| A new version of Livestock Breed Ontology (LBO, version 6.7) data is released. |
| Update, Aug 26, 2021 |
| New updates on the programs are made for the upcoming VISIONS III - Star Gazing into the Galaxy of Animal Genetics and Genomics which is to be held in Ames, Iowa on Novemver 3-4, 2021. |
| Update, Aug. 22, 2021 |
| Version 11.10 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Aug 10, 2021 |
| Thanks to Guangtu Gao [guangtu.gao@usda.gov] and Yniv Palti [yniv.palti@usda.gov] for providing SNP flanking sequences that made it possible for us to use an in-house procedure to match 30,263 rainbow trout "AX-" named SNPs to their dbSNP 'rs' IDs. The new data set is added to the Livestock SNP IDs/names match repository. |
| Update, Aug 4, 2021 |
| Version 11.9 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Aug 2, 2021 |
| A new version of Livestock Breed Ontology (LBO, version 6.4) data is released. |
| Update, Jul 20, 2021 |
| A number of data portal pages on Animal CorrDB web site are reformed. These include correlartion and heritability query/browse pages and trait measurement pages. The newly added capabilities include diverse types of data filters along side of search functions, flags to show and links from traits to QTL/association data, correlations, heritability data, links to VT/LPT/CMO trait ontologies when there is a match. A featured function is to display median, interquartile ranges of heritability data when multiple measurement results exist on the same trait. |
| Update, Jul. 17, 2021 |
| Thanks to individuals and groups (see data source acknowledgement on the web page cited below) who shared their SNP names, custom IDs 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 IDs/names 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/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. |
| Update, Jul 09, 2021 |
| As a result of our continued efforts to develop tools and pipelines in order to accommodate various types of SNP information found in published data over the years, we revised our Minimum information required for Animal QTLdb data entry to reflect policy changes on accepting data for annotations where SNPs are involved:
(1) SNP in dbSNP, mapped: MUST have a dbSNP 'rs' number;
(2) SNP not in dbSNP, mapped: Need a map location on a known assembly; if on a private map, MUST have flanking sequences;
(3) SNP not in dbSNP, un-mapped: MUST have flanking sequences.
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| Update, Jul 03, 2021 |
| Some re-organizations of the Animal QTLdb web portal structure were made to improve data access routes. The goal of the improvements is to reduce/eliminate some intermediate pages for more direct access to data layers in fewer steps. |
| Update, Jun 30, 2021 |
| Version 11.8 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jun 29, 2021 |
| A new hierarchy display tool has been developed to build front-ends of Animal QTLdb web portal for data access using traits from Vertebrate Trait (VT), Livestock Product Trait (LPT) Ontology, and Clinical Measurement Ontology (CMO). Built into the display tool also included a search capability, that helps users to quickly find relavent terms in large ontologies. All species QTLdb front pages, all VT/LPT/CMP home pages are updated to include the access to this utility. |
| Update, Jun 28, 2021 |
| Version 11.7 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jun 21, 2021 |
| A new version of Livestock Breed Ontology (LBO, version 6.3) data is released. |
| Update, Jun 14, 2021 |
| Version 11.6 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jun 8, 2021 |
| What's new on the NAGRP animal genome web site (#2, 2021) |
| New, Apr 28, 2021 |
| Version 11.5 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Apr 16, 2021 |
| Complementary to our web based data upload utility in our NAGRP File Sharing Platform, a new SSH based sftp service has been worked out for NRSP8 members to upload data to AnimalGenome.ORG. The use of this service will be granted to users on case by case basis for very large data volume only. Send emails to our helpdesk to make a request. |
| New, Mar. 18, 2021 |
| A new version of Livestock Breed Ontology (LBO, version 6.2) data is released. |
| Update, Mar. 04, 2021 |
| The NRSP8 Aquaculture Genomics Annual Report for 2020 is posted. |
| Update, Feb. 26, 2021 |
| The NRSP8 Bioinformatics Coordinator's Report for 2020 is posted. |
| Update, Feb. 22, 2021 |
| The Animal CorrDB web site had a new look. The newly added section highlights the database information summary in more details. The new information include curated correlation data summary by species and by correlation types (genetic, phenotypic, environmental, and residual); curated heritability data counts by species and by traits; etc. These summary information was aided with recent addition of post-curation data processing step for improved structural data queries. |
| Update, Feb. 21, 2021 |
| Version 11.4 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Feb 16, 2021 |
| The Animal QTLdb and CorrDB are published on Figshare open access platform through the Iowa State University Library. Subsequently, now each database has an universal Digital Object Identifier (DOI), and all are covered by the Creative Commons licenses. As a result, there can be alternative ways how the users of the QTLdb or CorrDB can properly cite the use of the database resources and/or tools. Please check each database website to find more details (click on respective web page footages for copyright claims, and citation details; the same information is pre-pended to all download data files as well). |
| New, Feb. 1, 2021 |
| Version 11.2 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jan 28, 2021 |
| Version 11.1 of the Vertebrate Trait (VT) ontology data is released to the public portal. |
| Update, Jan 21, 2021 |
| Cis/Trans eQTL information are curated to the Animal QTLdb and can be seen on QTL details and data summary (by publication) pages where such data is available. |
| New, Jan 15, 2021 |
| A new version (LBO version 6.1) of Livestock Breed Ontology data is made available. |
| Update, Jan. 6, 2021 |
| What's new on the NAGRP animal genome web site (#1, 2021) |
| New, Jan 4, 2021 |
A new QTL/association data link service is added to both Animal QTLdb and Animal CorrDB. This service accepts external URL links to specific QTL ID or CorrDB for information sources across species. Such links are often used by web tools, API tools, or database dbxref references. The syntax for the URL links are https://www.animalgenome.org/QTLdb/q?id=[QTL_ID] for QTLdb and https://www.animalgenome.org/CorrDB/q?id=[CorrID] for CorrDB respectively (Replace QTL_ID or CorrID with respective actual ids, which are unique numerical identifiers for specific QTL or correlation records; Refer to QTLdb API documentations or data downloads about the IDs). |
| New, Dec 11, 2020 |
| Goat QTLdb and Goat CorrDB: Ground works are complete preparing the goat linkage maps, genome maps, SNP map data, trait management space, and other required information for both the Animal QTLdb and the CorrDB to expand to include goat as a new species for annotations of published QTL, associations, correlations, and heritability data into respective databases. |
| New, Dec 3, 2020 |
| Version 10.7 of the Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Nov 18, 2020 |
| Gene-based eQTL now is visible in the Animal QTLdb ("Gene-based eQTL" is in contrast to "trait-based eQTL"). Currently the gene-based eQTL data can be seen on the lists by publications through permanent record locator, and on individual QTL data detail tables. It will be implemented in other parts of the web site and data downloads in the coming weeks. |
| New, Oct 29, 2020 |
Two data query/annotation tools were developed and implemented in the QTLdb. The first was a SNP lookup tool based on genome coordinates from simulated GWAS analysis studies. This tool look up all SNPs in an interval, and pick the most left and the most right SNPs as flanking candidates for the given span, along with the coordinates of the SNPs for curators to compare and determine how useful the queried SNP information is in terms of being used for data annotations.
The second was a SNP names and stable 'rs' numbers match tool. The sources of various custom SNP names were mostly from the SNP discovery process, different SNP chip platforms and/or user environments. They were usually used in experiments prior to the SNP submission to dbSNP for unique identifiers. The ability to match them is critical for data annotations and comparisons.
Both of these tools were made to handle data copied from an Excel spread sheet as input, and pre-pend query results as new columns for correct data match in order to minimize the chances of errors if done by hand. In combination with out batch data curation data entry tool, this greatly accelerated the curation process and significantly reduced chances of errors compared to manual data entry.
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| New, Oct 14, 2020 |
| Web sites pages for the Vertebrate Trait (VT), 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. |
| Update, Sep 4, 2020 |
| What's new on the NAGRP animal genome web site (#3, 2020) |
| New, Aug 31, 2020 |
| The Animal QTLdb FAQ is updated with new items to address common user questions as how QTL/association data can be downloaded with specific scope on certain traits or trait classes. |
| Update, Aug 27, 2020 |
| Version 10.6 of the Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Aug 27, 2020 |
| Progress continued improving the Animal QTLdb in terms of supporting data mapping to multiple genomes. The latest outcomes included 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 lifts between genomes with the aid of SNP location coordinates information on each build. |
| Update, Aug. 08, 2020 |
| A new version (LBO version 5.5) of Livestock Breed Ontology data is available. |
| Update, Jul. 28, 2020 |
| Version 10.5 of the Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Jul 16, 2020 |
A batch SNP query tool is 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 2000 SNP IDs (dbSNP 'rs' numbers) can be posted for query. The returned results are aggregated surrounding each SNP, i.e. information are "SNP centric". The information include QTL/association genome locations, linked traits and trait ontology terms, related genes, publication references, etc on each SNP. Each of these information are further dynamicly linked to related data tools in the QTLdb. Comments are welcome to add more features and improvements for better utility.
The SNP query capability is also added to "trait search", "gene search", "location search", and "general search" tools. |
| New, Jul 9, 2020 |
| Version 10.4 of the Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, May 27, 2020 |
| A workflow and pipeline is being developed to streamline the data update and release processes for vertebrate trait (VT) ontology, livestock product (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 AnimalGenome.org databases (feeding data to QTLdb trait mappers, project web sites for data query/browse, etc). |
| Update, May 07, 2020 |
| What's new on the NAGRP animal genome web site (#2, 2020) |
| New, Apr. 29, 2020 |
| A new version (v.10.3) of Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Apr. 23, 2020 |
| A data loader is being developed to streamline the ontology data in OBO format to load to MySQL database tables serving the online ontology queries and data viewers like AmiGO. This fills a gap where the support for AmiGO and related tools were no longer available. This effort is being made in order to facilitate VT, LPT, LBO, and CMO ontology development and as a peripheral tool for Animal QTLdb/CorrDB. |
| New, Apr. 06, 2020 |
| A new version (LBO version 5.4) of Livestock Breed Ontology data is available. |
| Update, Mar. 26, 2020 |
| Improvements on the Animal CorrDB have continued. The latest changes are rephrased data categories and reformatted web page layouts for better eye catch. Internally, centralized configurations have been expanded to include the use of names and parameters for uniform web page formatting and information passage to query engines. |
| Update, Mar. 15, 2020 |
| A new version (v.10.2) of Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Mar. 04, 2020 |
| A new version (LBO version 5.3) of Livestock Breed Ontology data is available. |
| Update, Mar. 2, 2020 |
| A room-share bulletin board service is set up for the upcoming VISIONS III - Star Gazing into the Galaxy of Animal Genetics and Genomics. |
| New, Feb. 11, 2020 |
| A new version (LBO version 5.2) of Livestock Breed Ontology data is available. |
| Update, Feb. 04, 2020 |
| The NRSP8 (aka, NAGRP) 2020 leaderships name list has been updated on the 2020 PAG meeting in San Diego, CA. |
| Update, Jan. 29, 2020 |
| A new version (LBO version 5.1) of Livestock Breed Ontology data is available. |
| Update, Jan. 29, 2020 |
| The FAANG data has been processed and archived through the FAANG Data Portal. An FAQ item is developed to describe the ways how these data can be easily accessed. |
| Update, Jan. 23, 2020 |
| A new version (v.10.1) of Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Jan. 15, 2020 |
| What's new on the NAGRP animal genome web site (#1, 2020) |
| New, Jan. 3, 2020 |
| The web front of the Animal CorrDB is being improved. The latest change is a new interface to access data by species. More improvement is to come. |
| New, Dec. 31, 2019 |
| A new version of the QTL/associations enrichment analysis too is available in the Animal QTLdb. This version of the tool allows users to select traits and chromosome regions of interests for analysis of QTL/associations representations in the region versus that of the whole genome. |
| Update, Dec. 28, 2019 |
| A web site is set up for the upcoming meeting VISIONS III - Star Gazing into the Galaxy of Animal Genetics and Genomics. |
| New, Nov. 4, 2019 |
| A new version (v.9.5) of Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Nov. 1, 2019 |
| A new version (v.9.4) of Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Oct. 16, 2019 |
| A new version (v.9.3) of Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Oct. 04, 2019 |
| A new version (v.9.2) of Vertebrate Trait (VT) ontology data is updated to the public portal. |
| Update, Sep. 17, 2019 |
The DOI (Digital Object Identifier) data in the Animal QTLdb is made visible in its public portal where such data is available (for examples see the abstract view  and data summary view pages). Efforts were also made to recover 509 DOI records from PubMed Central (PMC) for data curated prior to the time when DOI was introduced in early 2018. The DOI provides direct links to the original publications on curated QTL/association data in the Animal QTLdb. |
| Update, Sep. 11, 2019 |
| What's new on the NAGRP animal genome web site (#3, 2019) |
| New, Aug. 29, 2019 |
| The FAANG web site has a new face. The new web face came with a re-structured browse mapping that puts emphasis on easy access to information for people who wish to get involved in various FAANG activities. Thanks to Peter Harrison from EBI for useful discussions and inputs. |
| Update, Aug. 20, 2019 |
| Some curated QTL/association reports in the Animal QTLdb can be related because they could be follow up studies, combined analysis of previous works, re-analysis, confirmation studies, or reports from the same experiments. Now these information are also curated in the QTLdb, and can be seen on publication information pages, for example, the abstract pages , or curated data summary page (when viewing list of QTL/associations from a publication. |
| Update, Aug. 09, 2019 |
| A new version (LBO version 4.5) of Livestock Breed Ontology data is loaded. |
| Update, Jul. 26, 2019 |
| Dynamic data download options are added to the Animal QTLdb "Trait Centric" and "Gene Centric" views (accessible through "Search and Analysis" tools ) where all data shown on a search results page can be downloaded. In this way users can relatively easily locate the data by adjusting the key words, and download what they need for further data mining/analysis. |
| New, July 15, 2019 |
| A new version (LBO version 4.4) of Livestock Breed Ontology data is loaded. |
| Update, Jun. 18, 2019 |
| "Shadow QTL", is introduced as a new data-control concept in the Animal QTLdb for curation of QTL/association locus that have been detected but its statistical tests have not reached a significant threshold. The purpose for recording such data is for the entry of significantly validated epistatic and pleiotropic data where these loci serve as anchor/target locations. |
| New, Jun 10, 2019 |
| A new version (v.9.1) of Vertebrate Trait (VT) data is loaded. |
| Update, Jun. 05, 2019 |
| The epistatic and pleiotropic data was introduced for curation into the Animal QTLdb in 2009 and 2014 respectively. Now these data can be viewed in public web portals (currently in the data summary per publications; e.g. epistatic data display ; pleiotropic data display ). More display options for epistatic and pleiotropic data will be developed. |
| Update, Jun 5, 2019 |
| A new batch upload tool is integrated into the Animal QTLdb curator/editor tools for general curators to upload pre-formatted data prepared according to the Minimum Required Information Guideline. An upload data processing pipeline is developed to allow proper data flow and jobs routing between general curators, QTLdb curators, QTLdb editors, and database administrators. |
| Update, May 9, 2019 |
| The NAGRP Data Repository is scaled down in terms of its scope accepting the types of files for deposition. In particular, we have ceased to accept supplementary data to a publications for deposition. Users are advised to use Open Science Framework (OFS, https://osf.io/) instead. |
| Update, May 8, 2019 |
| What's new on the NAGRP animal genome web site (#2, 2019) |
| New, Apr. 26, 2019 |
| An alpha test version of newly developed QTL/association entrichment tool is made available for inputs. The purpose of the new tool is for users to identify genome regions of interests where an user may find multiple traits that are enriched in close proximity, thus to facilitate further research for genetic architecture where different traits may be structurally co-located in the genome. Note that this tool is designed only to provide a gross indication, that users may need to investigate further with closer scrutiny to verify the findings. |
| Update, Apr 21, 2019 |
| The NAGRP Data Repository FAQ is updated, adding answers about NAGRP Data locators versus what some users wish to call "data accession" numbers. The update also included our forward-looking steps to safeguard the hosted data for a long term sustainability. |
| Update, Mar 16, 2019 |
| Animal QTLdb curator tools are improved to allow eQTL data entry on the curator form without requiring a trait ID in the presense of a gene ID ("trait" used to be a mandatory information). |
| Update, Mar 19, 2019 |
| The AnGenMap FAQ is updated on how to easily make long URL short in order to avoid it being truncated in email transfers. |
| Update, Feb. 15, 2019 |
| The NAGRP Data Repository at the AnimalGenome.ORG is taking forward-looking steps to safeguard the hosted data for a long term sustainability. A new message is posted on the web site to encourage users to start using Open Science Framework for their open data host options in the future. |
| New, Feb. 07, 2019 |
| A new version (LBO version 4.1) of Livestock Breed Ontology data is loaded. |
| Update, Jan. 24, 2019 |
| FAANG past meeting archives are gathered and made available. Archives from future meetings will be added to the same resource page also. |
| New, Jan. 10, 2019 |
| What's new on the NAGRP animal genome web site (#1, 2019) |
| New, Jan. 3, 2019 |
| An improved version of the QTL/association data enrichment test tool was made available recently to allow user defined sizes of chromosome regions for enrichment test. The new feature is to be presented on the upcoming Plant and Animal Genome meeting in San Diego, with a poster titled: "Implementation of a new data enrichment analysis tool in the Animal QTL Database". |
| New, Dec. 19, 2018 |
| A new version (v.8.7) of Vertebrate Trait (VT) data is loaded. |
| Update, Dec. 04, 2018 |
| A new version (LBO version 3.8) of Livestock Breed Ontology data is loaded. |
| Update, Nov. 21, 2018 |
| A new Ensembl gene models for the new cattle genome build BovARS_1.2 is added to its JBrowse tracks that align with QTL/associations, Genbank annotations, and SNP liftover locations. |
| New, Nov. 8, 2018 |
| An interactive world map showing the FAANG memberships is added to the FAANG website. |
| New, Nov. 3, 2018 |
| A world map showing the distribution of AnGenMap Members is added to the web site. |
| New, Oct. 31, 2018 |
| An automated updates of the Animal QTLdb user visit and data download activities is added to the web site (light cyan text on the right hand side below the graph column). The text is hyper-linked to a world map showing locations of unique visitors to the database, which is also made available recently. |
| New, Oct. 24, 2018 |
| September newsletter of FAANG Europe COST Action is posted on FAANG web site. |
| New, Oct. 17, 2018 |
| US Pig Genome Newsletter #126 is posted on ANGENMAP and its PDF and text versions are archived. |
| New, Oct. 11, 2018 |
| A QTL/association data enrichment test tool has been implemented in the Animal QTLdb. The tool takes a set of selected traits to perform a genome-wide data dristribution analysis with Chi-square test of a two-way contingency table (traits by chromosomes) for the most plausible locations where certain traits may be over-represented. The tool has been reported in our recent paper "Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB" published on the upcoming Nucleic Acids Research 2019 Database issue. |
| New, Oct. 10, 2018 |
| A new version (v.8.6) of Vertebrate Trait (VT) and a new version (v.2.2) of Livestock Breed Ontology data are loaded. |
| Update, Oct. 3, 2018 |
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) where all data shown on a search results page can be downloaded. In this way users can relatively easily locate the data by adjusting the key words, and download what they need for further data mining/analysis.
