Repository details

Phytozome

Name of repository
Phytozome
Additional name(s)
  • The JGI Comparative Plant Genomics Portal
Repository URL
https://phytozome-next.jgi.doe.gov/
Subject(s)
Description
Phytozome is the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute. Families of related genes representing the modern descendants of ancestral genes are constructed at key phylogenetic nodes. These families allow easy access to clade-specific orthology/paralogy relationships as well as insights into clade-specific novelties and expansions.
Contact(s)
  • administrative: phytozome@jgi-psf.org
Content type(s)
Keyword(s)
Persistent identifier(s) of the repository
Repository size
411 assembled and annotated genomes, from 174 Archaeplastida species; 54 Brachypodium distachyon lines from the BrachyPan pan-genome study; 20 species included in the Brassicales Map Alignment Project; 8 cowpea (Vigna unguiculata) genomes included in the CowpeaPan pan-genome project
Repository type(s)
  • disciplinary
Research data repository language(s)
  • English
Data and/or service provider
  • dataProvider

Institutions (2)

Institution
United States Department of Energy, Office of Science, Joint Genome Institute
Additional name(s)
  • JGI
Institution
Country
United States
Type(s) of responsibility
  • general
Type of institution
non-profit
Institution
University of California
Institution
Country
United States
Type(s) of responsibility
  • technical
Type of institution
non-profit

Policies (2)

Policy Name
NHGRI Policies and Guidelines
Policy Name
Genomic Data Sharing Policies and Expectations

Database access

Type of access to research data repository
open

Data access (1)

Type of access to data
restricted
Data access restriction type(s)
  • registration

Data licenses (2)

DataLicense
Public Domain
DataLicense
Copyrights

Data upload (1)

Type of data upload
restricted
Data upload restriction type(s)
  • registration
Persistent identifier system(s)
  • none
Versioning
yes
Data citation guideline
https://mycocosm.jgi.doe.gov/pages/citeUs.jsf
Enhanced Publication
yes

Application programming interfaces (1)

Type
REST
Url
https://phytozome-next.jgi.doe.gov/phytomine/api.do

Remarks

Remarks
Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable.
Entry date
2014-07-14
Last update
2024-11-15
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Cite this re3data.org record:

re3data.org: Phytozome; editing status 2024-11-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2025-04-26