2025 Updates
Date | Update |
|---|---|
Feb. 11, 2026 | ENA record partially released (noncoding metadata only). Following up with ENA about the rest of the data. |
Feb. 4, 2026 | File submitted successfully to ENA. Under final review. |
Jan. 28, 2026 | ENA made requests, they are being processed. Genbank pointed out some possible fixes, will be incorporated into ENA final files. Working on JBrowse2 that will show new TAIR12 tracks. |
Jan. 21, 2026 | ENA is still trying to get the TAIR12 data through their pipeline. No further action possible or needed on our end. No estimate of completion data yet. |
Jan. 14, 2026 | No updates since the last report. We’ll post here as soon as anything changes. |
Jan. 7, 2026 | Nothing new to report. As soon as we know anything new, we’ll post here. |
Dec. 29, 2025 | Holiday break at ENA. Nothing new to report. |
Dec. 17, 2025 | Nothing new to report. Waiting for ENA to respond on remaining issues. |
Dec. 10, 2025 | Nothing new to report. |
Dec. 3, 2025 | Working with ENA for last remaining validation issues. Our data is good but their software is incorrectly flagging some cases of exon overlaps. |
Nov. 26, 2025 | Positive conference call with ENA and NCBI - submission will go to ENA and will flow into NCBI in time. webincli shows one last error that needs to be resolved by manual intervention. |
Nov. 19, 2025 | ENA and GenBank discussions in progress |
Nov. 12, 2025 | ENA submission: stalled, ENA is backed up https://www.ebi.ac.uk/ena/browser/support “Kindly note that the ENA helpdesk response time is approximately 3 weeks due to the current volume of tickets. We apologise for this delay and thank you for your patience. Due to a very high increase in recent submissions of a specific type of data to ENA in recent months we are experiencing a delay in processing and data exchange with INSDC partners. Processing and display of ENA assemblies should return to normal shortly. However we are unable to give a timeline when these will complete full exchange with INSDC partners. Thank you in advance for your patience. We will notify users again when we believe service is restored to normal.” |
Nov. 5, 2025 | ENA Submission: all files are uploaded into ENA and are being reviewed one last time by ENA’s lead bioinformatician, awaiting final feedback, release date pushed to Nov. 7. |
Oct. 29, 2025 | ENA Submission in progress: final internal validation run ongoing, minimal updates required, GFF and FASTA files to be submitted by webin-cli after clean run |
Oct. 22, 2025 | ENA Submission in progress: assembly and annotation to be uploaded in the next week with an anticipated release date of Nov. 3, 2025. |
Oct. 15, 2025 | Set up for submission of genome assembly and annotation through the European Nucleotide Archive (ENA). |
Oct. 8, 2025 | Exploring alternatives to GenBank for annotation submission. |
Oct. 1, 2025 | GenBank submission: working through last warnings of discrepancy report US government shutdown does affect the NCBI/NIH. “Because of a lapse in government funding, the information on this website may not be up to date, transactions submitted via the website may not be processed, and the agency may not be able to respond to inquiries until appropriations are enacted.” - Source: NCBI website |
Sept. 24, 2025 | GenBank submission: updated file was submitted, table2asn checking script was updated on 9/16/25, now additional errors and warnings are showing up, under evaluation |
Sept. 18, 2025 | GenBank submission: ability to upload an updated submission file added, official review of initial submission received |
Sept. 17, 2025 | GenBank submission: still in processing phase Manuscript: last trickles |
Aug. 27, 2025 | GenBank submission: slow but steady progress Manuscript: last updates trickling in |
Aug. 20, 2025 | GenBank submission: Back to work. |
Aug. 13, 2025 | GenBank submission: Still holding. (thank you for understanding) |
Aug. 6, 2025 | GenBank submission: Holding. (medical emergency) |
July 31, 2025 | Deadline: last chance to edit text and figures for manuscript. |
July 30, 2025 | Contact reestablished at NCBI! TE issue brought to light, recalculating. |
July 23, 2025 | Still waiting for response from NCBI. Reaching out to additional contact there. |
July 16, 2025 | TE minor updates incorporated into main file. Waiting for response from NCBI. |
July 9, 2025 | Update from TE team received on 7/4. Contact reestablished with NCBI. |
July 4, 2025 | Deadline: last chance for sending minor changes to GFF to Alyssa. |
July 2, 2025 | Waiting to upload next annotation file iteration to GenBank, need directory information. Waiting for last minor GFF changes. |
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 |
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April 9, 2025 |
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April 2, 2025 |
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Mar. 26, 2025 |
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Mar. 19, 2025 |
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Mar. 12, 2025 |
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Mar. 4, 2025 |
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Feb. 26, 2025 |
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February 13, 2025 | Still not there. Remaining prep of GFF file for GenBank submission:
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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. |