What's New on the NAGRP Animal Genome Web Site
|Major updates / new additions:
|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 alone 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 many individuals and groups (see data source acknowledgement on the web page cited below) for sharing their SNP names, custom IDs 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 of 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) Official SNP, mapped: MUST have a dbSNP 'rs' number;
(2) Official SNP, un-mapped: Need BOTH 'rs' number and flanking sequences;
(3) Unofficial SNP, mapped: Need a map location on a known assembly;
(4) Unofficial SNP, un-mapped: MUST have flanking sequences.
| ||Update, Jul 03, 2021|
|Several web portal structure re-organizations were made to the Animal QTLdb with better 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|
|We have developed a new hierarchy display tool 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
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.
| ||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 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|