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  • GOLD News

News

     

    2020; 2019; 2017; 2016; 2015; 2014 ; 2013 ; 2011 ; 2010 ; 2009 ; 2008 ; 2007 ; 2006 ; 2005 ; 2002 ; 2001 ; 2000 ; 1999 ; 1998 ; 1997
     

     

    November, 2020
    We are very happy to report the publication of Genomes OnLine database (GOLD) v.8 paper in Nucleic Acids Research.

     

    February, 2019
    The increasing data and the availability of complex search features like Advanced Search and SRA Explorer was making it harder for users to navigate GOLD at a speed they like. To address this general deterioration in search speeds we rolled out of a new search engine, built upon Hibernate Search and Apache Lucene technologies offering improved search speeds.

     

    January, 2019
    We are very happy to report the publication of Genomes OnLine database (GOLD) v.7 paper in Nucleic Acids Research. The latest version of GOLD now includes a wide range of fields from metadata packages specifically for soil and water samples. NCBI SRA explorer, Type strain Organism tracker as well as downloadable geolocation maps were some of the additional new features that were incorporated.

     

    January, 2017
    The GOLD team is pleased to announce the release of the Genomes OnLine Database (GOLD) v.6 publication in Nucleic Acids Research describing several new features and data updates such as bifurcation of Organism and Biosample, Advanced Search capabilities, New Combined Assembly Analysis Project types and more.

     

    October, 2016
    Kaushal Sharma, a junior from Antioch High School who participated in the Biotech Partners summer internship program as a GOLD intern, was featured in the JGI Science News Blog as an author on a paper accepted for publication in Nucleic Acids Research journal. T.B.K Reddy served as his mentor.

     

    January, 2015
    We are excited to report the publication of The Genomes OnLine Database (GOLD) v.5 paper in the Nucleic Acids Research journal. The paper describes several new features including the newly designed database schema and web user interface supporting four level classification system.

     

    May 28, 2014
    We are pleased to announce the release of GOLD v.5 on May 28, 2014. The redesigned database schema and web user interface support several new features including the implementation of a four level Project organization system and a simplified intuitive web interface to access reports and launch search tools. The four level Project system is organizing genome and metagenome sequencing projects in GOLD into Studies, Biosamples, Sequencing Projects and Analysis Projects to enable their presentation and tracking in a way it was not possible before. With intuitive user interface aided with tool tips it is now easier to navigate through the GOLD data. We are currently working on extending login/edit and download capabilities from the new system.
    Report an issue or send a message to GOLD

     

    Mar 6 , 2013
    GOLD data set available for download.
    We are happy to announce that the GOLD data set is available for download once again. You can click on the link on the top left corner at www.genomesonline.org or just follow the link Excel data file.

     

    Nov 15 , 2011
    GOLD v.4 is released.
    GOLD v.4 has a brand new look and fully supports metagenomic samples.

     

    Oct 20 , 2011
    DOE JGI Microbial Genome and Metagenome Program head Nikos Kyrpides has had a microbe named for him.
    The microbe, now labeled as the type strain of a new species, Kyrpidia tusciae, was isolated from a solfatara, or natural volcanic steam vent in which sulfur gases are the dominant constituent along with hot water vapor, in a geothermal region of Tuscany, Italy. Click here to Read more

     

    March 8, 2011
    10,000 GOLD Genome Projects Mark!
    Escherichia coli O111:H8 9662 is the 10,000 GOLD genome project

     

    February 14, 2011
    We have facilitated distribution of all the data from GOLD through the excel files in order to support scientists around the world who would like to get the data and perform their own analysis and eventually publish their results. We intent to continue supporting this sort of usage by providing all the data through an excel file. However, we have recently noticed an increasing number of cases where colleagues were downloading the data in order to feed the development of systems replicating GOLD's functionality. We are putting tremenodus amount of effort to collect and curate the metadata for an increasing number of genomes and metagenomes. Funding for curation of biological data is very limited if at all available, therefore we cannot support funding of other systems based on the manual work we do. Accordingly, if you need the data in order to perform comparative analysis, leading to publication or even populate other dbases you may have we are happy to continue providing you the GOLD data through excel.

     

    2011
    GOLD became part of the DOE Joint Genome Institute.

     

    July 24, 2010
    Blogger added for providing information on new GOLD developments and analysis tools.

     

    May 10, 2010
    RSS Feeds added for providing information on new and updated genome projects daily.

     

    November 13, 2009
    GOLD @ Nucleic Acids Research

     

    October 21, 2009
    1,000 Complete Microbial Genome Projects Mark!
    Methanocaldococcus vulcanius M7, DSM 12094 is the 1,000 completely sequenced microbial genome

     

    October 21, 2009
    1,000 Complete Microbial Genome Projects Mark!
    Methanocaldococcus vulcanius M7, DSM 12094 is the 1,000 completely sequenced microbial genome

     

    October 1st, 2009
    Daily updates of the dbase implemented

     

    September 9, 2009
    GOLD v 3.0 is released.
    The new features include:

    - New improved Search Page, and Advanced Search page. Metadata search and configurable search are coming soon

    - New search result tables, with the option of re-ordering of the columns

    - New database entry point [gold.cgi page], with the addition of Google Earth map, and links to Statistics tables for Project Type, Sequencing Status and Phylogenetic distribution pages.

    Coming up soon in extended v 3.0:

    - Metadata Search and Custom (SQL) search

    - Automatically generated graphical statistics

    - Configurable search result pages

    - Graphical presentation of Metadata on search results

     

    July 20th, 2009
    GOLD reaches tracking of 5000 projects.

     

    June 15th, 2009
    New GOLD CARD pages implemented [e.g. Gc00938]

     

    June 1st, 2009
    GOLD metadata fields increase to 104. All metadata available for download.

     

    April 10, 2009
    DOE-JGI is the first sequencing center reaching 1,000 genome projects.

     

    September 14, 2008
    GOLD reaches tracking of 4000 projects.

     

    April 20, 2008
    GOLD Search page reorganization, new metadata search fields added.

     

    January 20, 2008
    GOLD Statistics page updated. Statistics data available for download.

     

    January 12, 2008
    1. New Metadata fields are available for download: oxygen requirement, cell shape, cell arrangement, motility, sporulation, energy source, temperature range, and salinity.
    2. The new Metadata fields are also added in the search page

     

    January 1, 2008
    Nucleic Acids Research 36, D475-D479

     

    October 1, 2007
    GOLD reaches tracking of 3000 projects.

     

    September 15, 2007
    Metagenome Project Classification Search function is now available in the Search Page

     

    September 1, 2007
    All Archaeal and Bacterial Genome Projects in GOLD are now also displayed on a hierarchical tree based on NCBI's taxonomy. The Archaeal and the Bacterial Trees are available on the front page of GOLD

     

    August 15, 2007
    Reorganization of all Metagenomic Projects (GOLD Metagenome Ontology document):
    1. Standardize Metagenone Project Name
    2. Implement Metagenome Project Classification (analogous to the Taxonomy of isolate Genomes)
    3. Implement Project and Sample information

     

    August 1, 2007
    New GOLD Fields are available for download: (a) pH, (b) Temperature, (c) Samples, (d) Project Status

     

    July 15, 2007

    1. New GOLD Fields are available for download: (a) Sequencing Method, (b) Sequencing depth and (c) StrainInfo.

    2. Additional fields include 5 taxonomic levels from NCBI's taxonomy (SuperKingdom, Phylum, Class, Order, Family and Genus)

    3. Mapping of GOLD_STAMPS to StrainInfo IDs added

    4. Ecotype has been renamed to Habitat in compliance with MIGS (Minimum Information About a Genome Sequence)

     

    June 15, 2007
    In the Search Page: select GEBA under Relevance to see the current status of the project.

     

    February 19, 2007
    GOLD projects connect to the Genome Catalogue (GCat_IDs).

     

    February 17, 2007
    GOLD projects connect to the Greengenes database.

     

    January 23, 2007
    Complete and Published Genomes reach 500

     

    November 9, 2006
    GOLD-STAMP Pages are generated for all projects and links to the GOLD-STAMP IDs in every project

     

    November 1, 2006
    Entrez PID is added when available, and also provided through the downloadable goldtable.txt

     

    October 25, 2006
    The field "COUNTRY" for each sequencing project is released

     

    September 25, 2006
    The new GOLD user interface is released

     

    April 1, 2006
    GOLD hits 2000 genome projects as it completes 9 years of history

     

    March 9, 2006
    All Data in GOLD can now be easily downloaded on excel spreadsheet from the front page (goldtable.txt)

     

    March 1, 2006
    In agreement with the proposal of abandoning the term "Prokaryotes" we have split what used to be Prokaryotic Ongoing projects to Archaeal and Bacterial Ongoing Projects

     

    January 1, 2006
    GOLD v2.0 @Nucleic Acids Research 34, D332-334

     

    November 25, 2005
    HOT PICKS on NetWatch @Science 310, issue 5752

     

    August 20, 2005
    GOLD v 2.0 is released, with the addition of datatypes such as Phenotypes, Ecotypes, and Project relevance

     

    August 20, 2002
    GOLD is transferred to IMBB, Greece

     

    August 15, 2002
    GOLD moves to each new location at genomesonline.org

     

    July 18, 2002
    GOLD powered by Perl CGI scripts and Postgress RDBMS (Relational Database Management System)

     

    May, 2002
    Nature Reviews Genetics 3, 324
    cover of Nature magazine

     

    January, 2002
    GOLD hits 500 Genome projects

     

    December, 2001
    Year-End Top 100 Sites @Genetic Engineering

     

    May, 2001
    Netscan Pick @ Inside-LifeScience

     

    January, 2001
    Nucleic Acids Research 29, 126-127

     

    December, 2000
    Web Alert @Current Opinions in Genetics and Developmnet

     

    July 10, 2000
    Links2Go "Key Resource" Award

     

    June 9, 2000
    HOT PICKS on NetWatch @ Science 288, 1841
    cover of Science magazine

     

    April 5, 2000
    GOLD moves to each New Location @ Integrated Genomics

     

    March 24, 2000

    ISI logo

     

    March, 2000
    Shared Computer Facility Newsletter @ The Kimmel Cancer Center, Thomas Jefferson University

     

    February 25, 2000
    Web Site of the Week @The Rowland Institute for Science

     

    February 24, 2000
    HMS logo

     

    November 9, 1999
    MolBio.org News

     

    October, 1999
    Microbial Web Sites @ORNL

     

    September, 1999
    Bioinformatics 15, 773

     

    February, 1999
    UIUC Web Sites Include Microbial Information@ORNL

     

    December, 1998
    Web alert @ Current Opinion in Genetics & Development 8, 611

     

    September, 1998
    Microbial Genomes Monitor mirrored @EBI
  • April, 1997
    Microbial Genomes Monitor web page initiates @UIUC
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