UPCOMING July 31, 2025
Deadline: last chance to edit text and figures for manuscript.
UPCOMING July 4, 2025
Deadline: last chance for sending minor
July 2, 2025
Waiting to upload next annotation file iteration to GenBank, need directory information. Waiting for last minor
June 27, 2025
Manuscript finalization call.
Decision: release TAIR12 via GenBank as soon as all quality control checks have passed.
June 19, 2025
Arabidopsis Informatics workshop at ICAR2025
June 18, 2025
Still waiting for NCBI staff member to return to office and respond. Will shift to secondary contact.
June 17-20, 2025
ICAR2025 in Ghent, Belgium - looking forward to seeing people there.
June 11, 2025
Most Genbank issues resolved, waiting for NCBI staff member to return to office.
June 4, 2025
Still working through Genbank submission issues, mostly have to do with ncRNA formatting.
May 22, 2025
Working on addressing issues with GenBank submission. Various groups working on their parts of the manuscript: text and figures.
May 14, 2025
Call planned for end of June to finalize manuscript. Collection of final figures and text in the time between now and then.
May 8, 2025
Follow up and clarification email sent to GenBank. The staff member assisting us is out of office until May 14, 2025.
May 7, 2025
Initial comments received. No blocking errors. Warnings have been prioritized. Remediation in progress.
May 2, 2025
Reminder email sent out to all groups contributing to the manuscript.
April 28, 2025
Annotation submitted to GenBank. Finally. Now, we await review and acceptance.
April 23, 2025
Two ERRORS left to clear: cDNA/mRNA mismatch and one small intron
Will submit to portal after these are cleared and see what next steps are.
April 17, 2025
IN PROGRESS submission to GenBank, under review with NCBI staff
minor issues all addressed, waiting for reply fromGenBank on rRNA formatting
April 9, 2025
IN PROGRESS submission to GenBank, under review with NCBI staff
current validation run shows single digits of errors per chromosome for most categories
April 2, 2025
IN PROGRESS submission to GenBank, under review with NCBI staff
table2asn errors cleaned up significantly
Mar. 26, 2025
DONE Adjust FASTA headers for protein submission
I DONE Run checks to make sure there are no duplicate features or other strange formatting in col9
DONE iterative local runs of table2asn, review and addressing of errors
IN PROGRESS submission to GenBank, under review with NCBI staff - 12 categories detected by manual inspection
Mar. 19, 2025
IN PROGRESS Adjust FASTA headers for protein submission
IN PROGRESS Run checks to make sure there are no duplicate features or other strange formatting in col9
DONE parent feature for TE mobile elements
IN PROGRESS iterative local runs of table2asn, review and addressing of errors
No more outside requests for changes
Scheduled for March 24 submission to GenBank
Mar. 12, 2025
DONE duplicate '/product information from the mRNA to the matching CDS lines
DONE verify all col3 features
DONE miRNA annotations: deconvolute pre-miRNA, miRNA_primary_transcript, miRNA
NOT YET STARTED Adjust FASTA headers for protein submission
DONE Fix several cases of exons extending past parent feature
IN PROGRESS Run a check to make sure there are no duplicate features in col9
IN PROGRESS: Should be done by the end of this week parent feature for TE mobile elements
Mar. 4, 2025
DONE duplicate '/product information from the mRNA to the matching CDS lines
DONE verify all col3 features
IN PROGRESS: ‘derives from’ feature being added : miRNA annotations: deconvolute pre-miRNA, miRNA_primary_transcript, miRNA
NOT YET STARTED Adjust FASTA headers for protein submission
DONE Fix several cases of exons extending past parent feature
IN PROGRESS Run a check to make sure there are no duplicate features in col9
IN PROGRESS: New file incorporated, final check on numbering left to do parent feature for TE mobile elements
Feb. 26, 2025
DONE duplicate '/product information from the mRNA to the matching CDS lines
DONE verify all col3 features
IN PROGRESS: New rules developed based on discussion with lncRNA group : miRNA annotations: deconvolute pre-miRNA, miRNA_primary_transcript, miRNA
NOT YET STARTED Adjust FASTA headers for protein submission
DONE Fix several cases of exons extending past parent feature
IN PROGRESS Run a check to make sure there are no duplicate features in col9
IN PROGRESS: New file provided by TE group needs evaluation (Pseudo code, but have not implemented) parent feature for TE mobile elements
February 13, 2025
Still not there.
Remaining prep of GFF file for GenBank submission:
duplicate '/product information from the mRNA to the matching CDS lines
verify all col3 features
miRNA annotations: deconvolute pre-miRNA, miRNA_primary_transcript, miRNA
Adjust FASTA headers for protein submission
Fix several cases of exons extending past parent feature
Run a check to make sure there are no duplicate features in col9
(Pseudo code, but have not implemented) parent feature for TE mobile elements
January 2025
Goal: Manuscript draft complete.
January 2025
Goal: submission to GenBank complete.
January 13, 2025
TAIR talk at Arabidopsis Informatics session at PAG32, with section on TAIR12
Slides available
January 6, 2025
GFF3 files sent out to annotation teams for final review.