[IGBF-4206] Add jojoba (Simmondsia chinensis) genome to IGB - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
1.5
Epic Link:
Improve IGB for users
Sprint:
Fall 4, Fall 5

Description

Situation: Dr. Kent Chapman, a professor from the University of North Texas, attended my talk at the SS-ASPB meeting earlier this year. He's followed up with me after the conference to request that the jojoba genome be added to IGB. We recently integrated GenArk, a genome-rich datasource, with IGB, but they don't yet host this genome, either.

Task: Add the jojoba (Simmondsia chinensis) genome to IGB. Kent co-authored a paper describing this new genome assembly which I'll link below. The genome assembly and meta-data has been deposited in the Beijing Institute of Genomics (BIG) data center under the accession no. GWHAASQ00000000.

Link to the paper: https://doi.org/10.1126/sciadv.aay3240
Link to the genome/annotations: https://ngdc.cncb.ac.cn/gwh/Assembly/486/show

Attachments

Activity

Ascending order - Click to sort in descending order

Hide

Permalink

Paige Kulzer added a comment - 08/May/25 10:03 AM

Kent's email from March 30th, 2025:

Paige, Thank you again for your excellent presentation about your integrated genomics resources. If you could include jojoba (Simmondsia chinensis) in your database and web interface, that might be useful.

I think everything is referenced here in this paper and/or accessible online or through supplemental materials. If you need something else, let me know.

https://www.science.org/doi/10.1126/sciadv.aay3240

Best,
Kent

Kent D. Chapman, Ph.D.
Regents Professor of Biochemistry
Member, BioDiscovery Institute

University of North Texas
Department of Biological Sciences
1155 Union Circle #305220
Denton, TX 76203-5017
+1-940-565-2969 (office)
+1-940-300-6961 (cell)
https://bdi.unt.edu/kent-chapman

Show

Paige Kulzer added a comment - 08/May/25 10:03 AM Kent's email from March 30th, 2025: Paige, Thank you again for your excellent presentation about your integrated genomics resources. If you could include jojoba (Simmondsia chinensis) in your database and web interface, that might be useful. I think everything is referenced here in this paper and/or accessible online or through supplemental materials. If you need something else, let me know. https://www.science.org/doi/10.1126/sciadv.aay3240 Best, Kent Kent D. Chapman, Ph.D. Regents Professor of Biochemistry Member, BioDiscovery Institute University of North Texas Department of Biological Sciences 1155 Union Circle #305220 Denton, TX 76203-5017 +1-940-565-2969 (office) +1-940-300-6961 (cell) https://bdi.unt.edu/kent-chapman

4 older comments

Hide

Permalink

Paige Kulzer added a comment - 06/Oct/25 9:52 AM

I've updated the annots.xml file locally and tested that change. I'm able to load sequence in IGB now.

Ann Loraine, could you please restart the svn server? I will check in my changes once that's done.

Show

Paige Kulzer added a comment - 06/Oct/25 9:52 AM I've updated the annots.xml file locally and tested that change. I'm able to load sequence in IGB now. Ann Loraine , could you please restart the svn server? I will check in my changes once that's done.

Hide

Permalink

Paige Kulzer added a comment - 13/Oct/25 10:34 AM

The Simmondsia chinensis genome has been pushed to the SVN repo.

Ready for final review!

Show

Paige Kulzer added a comment - 13/Oct/25 10:34 AM The Simmondsia chinensis genome has been pushed to the SVN repo. Ready for final review!

Hide

Permalink

Nowlan Freese added a comment - 14/Oct/25 10:21 AM - edited

Looks good, able to load annotations and sequence. Synonyms show up correctly.

Ann Loraine - Ready for deployment to Quickload servers.

Show

Nowlan Freese added a comment - 14/Oct/25 10:21 AM - edited Looks good, able to load annotations and sequence. Synonyms show up correctly. Ann Loraine - Ready for deployment to Quickload servers.

Hide

Permalink

Ann Loraine added a comment - 23/Oct/25 2:08 PM

Updated data is deployed to Quickload servers hosted at RENCI and UNC Charlotte.
Ready for final testing.

Show

Ann Loraine added a comment - 23/Oct/25 2:08 PM Updated data is deployed to Quickload servers hosted at RENCI and UNC Charlotte. Ready for final testing.

Hide

Permalink

Nowlan Freese added a comment - 24/Oct/25 3:17 PM

Tested on IGB 10.1.0 release. Able to load annotations and sequence. Synonyms appear correctly. Linkout goes to Simmondsia chinensis quickload page.

Closing ticket.

Show

Nowlan Freese added a comment - 24/Oct/25 3:17 PM Tested on IGB 10.1.0 release. Able to load annotations and sequence. Synonyms appear correctly. Linkout goes to Simmondsia chinensis quickload page. Closing ticket.

People

Assignee:

Paige Kulzer

Reporter:

Paige Kulzer

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

08/May/25 10:01 AM

Updated:

24/Oct/25 3:17 PM

Resolved:

24/Oct/25 3:17 PM