Search

Your search keyword '"Dimitri Stamatis"' showing total 8 results
Start Over Author "Dimitri Stamatis"
8 results on '"Dimitri Stamatis"'

7. Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9

Author

Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A Nicolopoulos, Alessandro Favognano, I-Min A Chen, Nikos C Kyrpides, and T B K Reddy

Subjects
Genetics, Database Issue
Abstract

The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one of the flagship genomic metadata repositories of the world. The ever-increasing number of projects and metadata are freely available to the user community world-wide. GOLD’s metadata is consumed by scientists and remains an important source for large-scale comparative genomics analysis initiatives. Encouraged by this active user engagement and growth, GOLD has continued to add new components and capabilities. The new features such as a public Application Programming Interface (API) and Ecosystem landing page as well as the growth of different entities in this current GOLD v.9 edition are described in detail in this manuscript.

Published
2022

8. Genomes OnLine database (GOLD) v.7: updates and new features

Author

Alejandro Mojica, Jon Bertsch, I-Min A. Chen, Supratim Mukherjee, Dimitri Stamatis, Nikos C. Kyrpides, Hema Y Katta, Galina Ovchinnikova, and T. B. K. Reddy

Subjects
Minimum Information Standards, Context (language use), Biology, Analysis Project, World Wide Web, 03 medical and health sciences, Databases, 0302 clinical medicine, Genetic, Information and Computing Sciences, Databases, Genetic, Controlled vocabulary, Genetics, Database Issue, 030304 developmental biology, 0303 health sciences, Genomes OnLine Database, Genomics, Biological Sciences, Metadata, Gene Ontology, Metagenomics, User interface, 030217 neurology & neurosurgery, Software, Environmental Sciences, Developmental Biology
Abstract

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 33 415 Studies, 49826 Biosamples, 313324 Organisms, 215881 Sequencing Projects and 174454 Analysis Projects with a total of 541 metadata fields, of which 80 are based on controlled vocabulary (CV) terms. GOLD provides a user-friendly web interface to browse sequencing projects and launch advanced search tools across four classification levels. Users submit metadata on a wide range of Sequencing and Analysis Projects in GOLD before depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis. GOLD conforms with and supports the rules set by the Genomic Standards Consortium (GSC) Minimum Information standards. The current version of GOLD (v.7) has seen the number of projects and associated metadata increase exponentially over the years. This paper provides an update on the current status of GOLD and highlights the new features added over the last two years.

Published
2019
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results