Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1.5
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Epic Link:
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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
Updated data is deployed to Quickload servers hosted at RENCI and UNC Charlotte.
Ready for final testing.
Looks good, able to load annotations and sequence. Synonyms show up correctly.
Ann Loraine - Ready for deployment to Quickload servers.
The Simmondsia chinensis genome has been pushed to the SVN repo.
Ready for final review!
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.
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,
KentKent D. Chapman, Ph.D.
Regents Professor of Biochemistry
Member, BioDiscovery InstituteUniversity 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
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.