JGI GOLD | News

We are very excited to share that our latest manuscript Genomes OnLine Database (GOLD) v.10: new features and updates is now available in the Database Issue of Nucleic Acids Research journal.

How-to short video series is out for you to explore. Special thanks to our talented student interns Mahathi Kandimalla and Jasmin Diaz Munoz.

GOLD and IMG group publishes review paper in the Journal of the Indian Institute of Science detailing Bioinformatics Analysis Tools for Studying Microbiomes at the DOE Joint GenomeInstitute.

Manuscript titled Standardized naming of microbiome samples in Genomes OnLine Database describing our hallmark Standardized Naming of microbiomes is published in Oxford.

Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9 is published in Nucleic Acids Research describing a host of exciting new features; includes significant contributions from three of our stellar student interns: Mahathi Kandimalla, Alessandro Favognano & Paul A Nicolopoulos.

GOLD celebrates 25 years as JGI’s flagship genomic metadata repository and is featured in JGI Science Highlights: Silver age of GOLD introduces new features.

We are very excited to share that all JGI microbiome samples submitted to NCBI now include GOLD’s five-level ecosystem classifications.

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

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.

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.

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.

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.

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.

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.

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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.

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

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

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

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.

GOLD became part of the DOE Joint Genome Institute.

Blogger added for providing information on new GOLD developments and analysis tools.

RSS Feeds added for providing information on new and updated genome projects daily.

GOLD @ Nucleic Acids Research

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

Daily updates of the dbase implemented

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)