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DateUpdate
October 31, 2023Deadline secondary review.
October 17, 2023Secondary manual review begins.
September 30, 2023Deadline for primary manual review of genes.
September 21, 2023Filtered 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:

  1. Transposable element reannotation (in progress)
    1. Alex Bousios (University of Sussex)
    2. Shujun Ou (Ohio State University)
    3. Zhigui Bao (Max Planck Tübingen)
  2. integration of NOR2 and NOR4 into Col-CC (in progress)
    1. Craig Pikaard, Ramya Enganti, Dalen Fultz, Anastasia McKinlay (Indiana University)
    2. Korbinian Schneeberger, Xiao Dong, Raul Wijfjes (MPIPZ, Uni München)
  3. rDNA reannotation (in progress)
    1. Craig Pikaard, Ramya Enganti, Dalen Fultz, Anastasia McKinlay (Indiana University)
    2. Ian Henderson, Piotr Wlodzimierz (University of Cambridge)
  4. Tandem repeat reannotation (complete)
    1. Ian Henderson, Piotr Wlodzimierz (University of Cambridge)
  5. lncRNA reannotation (in progress)
    1. Andrew Nelson, Caylyn Railey, Kyle Palos (Cornell University)
    2. Michael Schon (Wageningen University & Research)
    3. Thomas Blein (Centre national de la recherche scientifique, CNRS)
    4. Aleksandra Kornienko (Gregor Mendel Institute)
    5. Selene Fernandez Valverde (UNSW Sydney)
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:

  1. RNAseq combined, coverage view - combined coverage view of ALL the 62 RNAseq tracks, partially filtered to remove alignments with extra long introns and with excessive coverage in certain regions capped to 200.
  2. RNAseq capped and merged, reads - individual reads of all files that were not able to be filtered but were individually capped at 200 and then merged.
  3. RNAseq filtered capped and merged, reads - individual reads of all files that were individually filtered, then capped at 200, and then merged.
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, 2023IMPROVED 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, 2023NEW TRACK: TranscriptomeReconstructoR models  (from Sebastian Marquardt’s group at U of Copenhagen)
July 24, 2023
  1. over 300 genes have been started, about 70 are done
  2. 4 office hours held (Wednesdays by Slack)
  3. discussions going on in Slack
    1. what to do with insertion of mt sequence in chr2 - annotate genes or not?
    2. should we have a scoring system for genes?
    3. new track suggestions
      1. PFAM domains  - community suggested, created, and loaded
      2. PANTHER families - community suggested, created, and loaded
    4. track metadata table available in Apollo Tips
July 7, 2023Gene list assignments (over 2000 genes) distributed (email and Slack)
June 29, 2023Apollo editing training session 3: 14 participants
June 28, 2023Apollo basics training session 3: 10 participants
June 8, 2023Arabidopsis Bioinformatics workshop at ICAR2023 in Chiba: Update on reannotation effort.
June 1, 2023Apollo editing training session 2: 18 participants.
May 31, 2023Apollo editing training session 1: 28 participants.
May 26, 2023Apollo basics training session 2: 25 participants from 6 countries. Now 10 countries total!
May 23, 2023Apollo basics training session 1: 35 participants from 8 countries.
May 12, 2023Apollo training dates set: May 23 (T) and May 25 (F), 7 - 8:30 am US Pacific time (UTC -7)
Apr. 27, 2023Call for community volunteers for manual review phase goes out.
Apr. 17, 2023Initial assessment of automated annotation pipeline results begins.
Apr. 11, 2023NCBI Eukaryotic Annotation automated pipeline complete.
Feb. 23, 2023NCBI Eukaryotic Annotation team begins process of running the automated annotation pipeline with several datasets suggested by the community included
Jan. 26, 2023TAIR puts out community call via social media for additional expression datasets that could be included in annotation run
Jan. 25, 2023NCBI completes review of assembly and releases to public: https://www.ncbi.nlm.nih.gov/assembly/GCA_028009825.1
Jan. 16. 2023Arabidopsis Informatics Workshop at PAG30 in San Diego: Two talks given that contained information relevant to the v12 project.
Dec. 23, 2022Schneeberger lab submits Col-CC (community consensus) assembly to NCBI
Oct. 27, 2022First community meeting
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