Starting point for information about different JGI data stores.
GOLD
Description
metadata source for information about prokaryote and eukaryotic organisms that have been submitted to JGI. Source for biosample metadata for metagenomes.
Contact
Nikos Krypides - [email protected]
Website
https://gold.jgi.doe.gov/
Data Access
Web services available through GOLD API
Data Access API description at:
Links
GOLD project links to ITS through ITS Project Id
GOLD analysis project links to ITS though ITS analysis project id and ITS task id
GOLD links to IMG through the IMG taxon id
IMG
Description
IMG/M's Data Warehouse integrates microbial genome and microbiome datasets sequenced at JGI or provided by IMG/M's users with a comprehensive set of publicly available bacterial, archaeal, eukaryotic, and phage genomes from Genbank, as well as engineered, environmental and host associated microbiome samples. Functional characterization of genomes includes COG, KEGG, PFAM and other resources.
Contact
Amy Chen - [email protected]
Website
https://img.jgi.doe.gov/
Data Access
Website access only
Links
IMG links to GOLD with GOLD analysis project id and IMG taxon oid (id)
Phytozome
Description
Provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. Genomes have been annotated with KOG, KEGG, ENZYME, Pathway and the InterPro family of protein analysis tools.
Contact
[email protected]
Website
https://phytozome.jgi.doe.gov/pz/portal.html
Data Access
Data Access API description at:
Intermine: https://phytozome.jgi.doe.gov/phytomine/begin.do
Biomart: https://phytozome.jgi.doe.gov/biomart/
Links
Links to PMO are problematic - most data is sourced from outside and doesn’t go through PMO. Attempt to talk further with Kerrie Barry to find out more. Plant portals that were checked do not list any ITS, GOLD or IMG references.
MycoCosm
Description
Provides data access, visualization, and analysis tools for comparative genomics of fungi. Mycocosm enables users to navigate across sequenced fungal genomes, and to conduct comparative and genome-centric analyses of fungi and community annotation.
Contact
Igor Grigoriev: [email protected]
Website
https://genome.jgi.doe.gov/programs/fungi/index.jsf
Data Access
Data Access API description at:
Links
Appear to use ITS project ids
Data Warehouse
Description
Contact
Steve Wilson
Website
Data Access
Data Access API description at:
Genome Portals
Description
Provides access to JGI data sets for download and analysis.
Contact
Tatyana Smirnova
Website
https://genome.jgi.doe.gov
Data Access
Data Access API description at:
Links
IMG taxon id
ITS project id
ITS analysis project id
JAMO
Description
This a JGI data repository that stores output information from groups across JGI
Contact
Chris Beecroft: [email protected]
Website
https://sdm-dev.jgi-psf.org/doc/JAMO
Data Access
Data Access API description at:
Links
Data stored in JAMO is linked back to the parent data source through a variety of ids.
