Latest updates
- Tanya Berardini
See 2025 updates for more recent news.
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January 2025 | Goal: Manuscript draft complete. | ||||||||||||||||||
January 2025 | Goal: submission to GenBank complete. | ||||||||||||||||||
Dec. 20, 2024 | All community files (manually reviewed track, TE file, lncRNA file, repeat element file, 5SrRNA file) have been integrated with the NCBI Col-CC annotation. Overlaps have been resolved. Nomenclature has been resolved, retention of old AGI identifiers and assignment of new AGI identifiers to those features that needed it. Final processing on type of entities and accessory data necessary for GenBank submission is still ongoing. | ||||||||||||||||||
October 2024 | Recognition: Deadlines have slipped. Quality control and integration of the various independent group files has proven MUCH more difficult than hoped. | ||||||||||||||||||
August 12, 2024 | More manual review was done to check differences between Araport11 proteins and draft TAIR12 proteins. Final Apollo manual review stats (as of today) Total genes reviewed: 4775 (607 more than last time)
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July 23, 2024 | GFF file status
Writing status (drafts present in shared Google Drive)
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July 17, 2024 | ICAR 2024 in San Diego, Workshop (5:30 - 6:30 pm Pacific) : Our Community Effort to Reannotate the Arabidopsis Genome | ||||||||||||||||||
July 2, 2024 | Reminder sent out for manuscript contributions | ||||||||||||||||||
June 30, 2024 | Goal: Manuscript draft complete. NOT MET | ||||||||||||||||||
June 28, 2024 | Freeze on manual edits in Apollo. Final Apollo manual review stats (as of today) Total genes reviewed: 4168
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June 13, 2024 | Apollo manual review stats (as of today)
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May 15, 2024 | Status check conference call | ||||||||||||||||||
May 1, 2024 | Apollo manual review stats (as of today)
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April 15, 2024 | Status check conference call | ||||||||||||||||||
April 12, 2024 | Apollo manual review stats (as of today)
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April 3, 2024 | Poll sent out for next status update call | ||||||||||||||||||
March 22, 2024 | Extended deadline: Final GFF2 data files from all external annotation groups to TAIR. | ||||||||||||||||||
March 21, 2024 | Apollo manual review stats (as of today)
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March 8, 2024 | Status check conference call | ||||||||||||||||||
March 4, 2024 | Doodle poll sent out for March status conference call. | ||||||||||||||||||
March 1, 2024 | Goal: Manuscript writing begins in earnest. Done: Google Drive for shared documents created. | ||||||||||||||||||
February 29, 2024 | Goals: All review, quality control, nomenclature resolution, rule-creation for annotation retention, coordinate updates for V12 should be completed by this date. Final GFF2 data files from external annotation groups to TAIR. Files expected: TEs, 5sRNAs, NOR2/NOR4, lncRNAs, TRASH pipeline results | ||||||||||||||||||
February 27, 2024 | Apollo manual review stats (as of today)
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February 20, 2024 | Apollo manual review stats (as of today)
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February 6, 2024 | Status check conference call Most of the review, quality control, nomenclature resolution, rule-creation for annotation retention, coordinate updates for V12 should be completed by this date. | ||||||||||||||||||
January 15, 2024 | PAG 2024 Arabidopsis Informatics session 12:50 - 13:00 Pacific time (some slide presentations available here) DEADLINE: sample GFF3 data files from external annotation groups to TAIR | ||||||||||||||||||
December 13, 2023 | Conference call: status update, remaining tasks, manuscript planning | ||||||||||||||||||
November 28, 2023 | Ongoing quality control of manual review, various groups finishing up their sets of annotations (TEs, lncRNAs, repeats, rDNAs). | ||||||||||||||||||
November 3, 2023 | 195/620 of secondary review left. Lots of progress made! Only 2 of 'under primary review' left. | ||||||||||||||||||
November 1, 2023 | Pikaard team paper on the sequences and functional organizations of the A. thaliana Col-0 NORs published https://www.science.org/doi/full/10.1126/sciadv.adj4509 | ||||||||||||||||||
October 31, 2023 | Deadline secondary review. | ||||||||||||||||||
October 30, 2023 | Zoom call of secondary review participants to touch on some complicated cases, decision making. | ||||||||||||||||||
October 18, 2023 | GenBank release of the Col-CC v2 https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_028009825.2/ | ||||||||||||||||||
October 17, 2023 | Secondary manual review begins. | ||||||||||||||||||
September 30, 2023 | Deadline for primary manual review of genes. (620 total marked for review) | ||||||||||||||||||
September 21, 2023 | Filtered long read coverage and read tracks finally available. These have replaced the older tracks that were cluttered with overly long introns (>12kbp). The capped and merged RNAseq read track has also been filtered and replaced. This will now be converted to bw for an even better coverage track. Track Metadata is in the Apollo Tips. | ||||||||||||||||||
August 29, 2023 | Summary of other annotation-related activities and groups:
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August 28, 2023 | NEW TRACK: RNAseq combined and recapped, coverage view - an even more reduced combined coverage view of ALL the 62 RNAseq tracks that resulted from sequential rounds of capping and merging instead of individual capping and then final merging (the scale bars will be different and more lowly expressed RNAseq reads will be more visible | ||||||||||||||||||
August 11, 2023 | NEW TRACKS:
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August 6, 2023 | Plant Biology 2023 in Savannah, GA: Plant Bioinformatics Resources for FAIR Agricultural Data Discovery and Reuse workshop (10:30 am - 12:30 pm) Update on the reannotation effort included in the TAIR presentation | ||||||||||||||||||
August 3, 2023 | IMPROVED TRACK: Protein alignments chained : We have now connected the Protein Alignments track elements so that pieces of the same protein are seen together. This is a great improvement over the isolated boxes view (which is now gone). | ||||||||||||||||||
July 27, 2023 | NEW TRACK: TranscriptomeReconstructoR models (from Sebastian Marquardt’s group at U of Copenhagen) | ||||||||||||||||||
July 24, 2023 |
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July 7, 2023 | Gene list assignments (over 2000 genes) distributed (email and Slack) | ||||||||||||||||||
June 29, 2023 | Apollo editing training session 3: 14 participants | ||||||||||||||||||
June 28, 2023 | Apollo basics training session 3: 10 participants | ||||||||||||||||||
June 8, 2023 | Arabidopsis Bioinformatics workshop at ICAR2023 in Chiba: Update on reannotation effort. | ||||||||||||||||||
June 1, 2023 | Apollo editing training session 2: 18 participants. | ||||||||||||||||||
May 31, 2023 | Apollo editing training session 1: 28 participants. | ||||||||||||||||||
May 26, 2023 | Apollo basics training session 2: 25 participants from 6 countries. Now 10 countries total! | ||||||||||||||||||
May 23, 2023 | Apollo basics training session 1: 35 participants from 8 countries. | ||||||||||||||||||
May 12, 2023 | Apollo training dates set: May 23 (T) and May 25 (F), 7 - 8:30 am US Pacific time (UTC -7) | ||||||||||||||||||
Apr. 27, 2023 | Call for community volunteers for manual review phase goes out. | ||||||||||||||||||
Apr. 17, 2023 | Initial assessment of automated annotation pipeline results begins. | ||||||||||||||||||
Apr. 11, 2023 | NCBI Eukaryotic Annotation automated pipeline complete. | ||||||||||||||||||
Feb. 23, 2023 | NCBI Eukaryotic Annotation team begins process of running the automated annotation pipeline with several datasets suggested by the community included | ||||||||||||||||||
Jan. 26, 2023 | TAIR puts out community call via social media for additional expression datasets that could be included in annotation run | ||||||||||||||||||
Jan. 25, 2023 | NCBI completes review of assembly and releases to public: https://www.ncbi.nlm.nih.gov/assembly/GCA_028009825.1 | ||||||||||||||||||
Jan. 16. 2023 | Arabidopsis Informatics Workshop at PAG30 in San Diego: Two talks given that contained information relevant to the v12 project. | ||||||||||||||||||
Dec. 23, 2022 | Schneeberger lab submits Col-CC (community consensus) assembly to NCBI | ||||||||||||||||||
Oct. 27, 2022 | First community meeting |