Highlighting the latest interactive version of the JGI’s plant data portal.
On August 6, 2021, version 12 of Phytozome will be retired, and version 13 will become the current, and only, version of Phytozome accessible as an interactive website. Since May 2019, v12 has not had any additional genomes added to it, nor had any feature updates. Phytozome v13, which now hosts upwards of 250 plant genomes and has been under active development for over 5 years, provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on from Phytozome, with a more intuitive interface, deployed on much more maintainable software and hardware infrastructure. Phytozome v13 has been accessible to users since 2019.
We have attempted to make sure users will continue to have straightforward access to all the data in Phytozome v12, and that most bookmarked v12 links (e.g., to gene reports and organism information pages) will be seamlessly forwarded to Phytozome v13.
Below are some answers to Frequently Asked Questions about the transition from Phytozome v12 to v13.
Why is it necessary to retire Phytozome v12?
David Goodstein
The codebase for Phytozome v12 was first deployed (as the foundation for Phytozome v10) back in 2014. Several components of that codebase are no longer supported, and there are now much more powerful and flexible tools available for building high performance user interfaces and backend data systems. Trying to maintain v12’s codebase and legacy data resources and hardware, while also developing a modern and maintainable version of Phytozome, is not prudent nor possible given the finite staff available to the Phytozome project.
What will happen to Phytozome v12 URLs after August 6th?
All URLs with a domain of https://phytozome.jgi.doe.gov will be forwarded (where possible) to their corresponding pages at https://phytozome-next.jgi.doe.gov.
- If a genome from v12 is present in v13, the organism info page will be forwarded (e.g., https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa will be forwarded to https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v3_0 .
- Gene pages will also be forwarded (e.g., Gene Potri.006G034600 on v12 will be forwarded to Gene Report: Potri.006G034600 on v13)
- Gene Family pages are treated differently, because the active gene family version in v13 is different from the one in v12. v12 Family pages will be forwarded to the v13 BioMart data warehouse with filters preset to select that family.
- JBrowse, keyword search, and BLAST result links will NOT be forwarded. You can find the v13 JBrowsers corresponding to many of the v12 genome versions at https://phytozome-next.jgi.doe.gov/jbrowse/index.html
How can I access the genome data that was formerly at Phytozome v12?
All genome data released in Phytozome v12 (and version 13 and, in fact, all versions of Phytozome), can always be access in one of two ways:
- From the BioMart Genome Archive data warehouse. Got to https://phytozome-next.jgi.doe.gov/biomart and select “Genome Archive – All data” as the database, and choose the genome you’re after as the dataset.
- From the (new and improved JGI Data Portal). Go to https://data.jgi.doe.gov/refine-download/phytozome and use the Search input box to find the organism and genome version you’re after. You can even grab genomes based on which version of Phytozome (e.g., 9, 10, 11, 12) they were first released in.
Are any genomes from v12 NOT available (via URL forwarding) in v13?
- A total of 7 genomes present in v12 are not available interactively in v13. They are:
- Vvinifera_Genoscope.12
- Crubella_v1.0
- Mdomestica_v1.0
- Fvesca_v1.1
- Pvirgatum_v1.1
- Zmays_6a
- Ahypochondriacus_v1.0.
Gene report links from Phytozome v12 for these organisms will be forwarded to BioMart with the filters preset for the gene in question, so you can download sequences, annotations, and gene structures. These genomes’ organism info pages will not be forwarded, as they don’t have an analogous page in v13. As noted above, you can also access all data for these genomes via our BioMart Genome Archive data warehouse, or the JGI Data portal.
Are any v12 features NOT present in v13?
We’ve delayed the migration of several legacy v12 features to v13 based on staffing constraints. We hope to add several of them soon, but don’t yet have a timeline for their restoration. They include
- Jalview (for viewing and modifying multiple sequence alignments).
- Variation view on individual gene pages
- The ability to construct composite custom gene families
- The ability to user query sequences to gene families
What about PhytoMine?
PhytoMine, the Phytozome implementation of the InterMine data warehouse, is still available in v13. However, the genomes included in PhytoMine will typically lag the full set of released genomes available in Phytozome (and in the BioMart data warehouse). We are still working out the best protocols to allow us to update PhytoMine and keep it current given the accelerated rate of new genome releases in Phytozome v13. If the genome(s) you’re interested in working with are in the PhytoMine set, great, please continue to use that data warehouse. If not, you can use the BioMart warehouse, which is always up to date with the set of released genomes in Phytozome.
The Phytozome team is committed to helping users make a successful transition from v12 to v13. As always, please contact the team at [email protected] with any questions or concerns you may have.
-David Goodstein and the Phytozome Team