Annotation Conf. Call 2016-08-23

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Revision as of 07:25, 23 August 2016 by Stacia (talk | contribs) (Annotation Consistency Exercise)

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Bluejeans URL: https://bluejeans.com/993661940

Agenda

Upcoming Meetings

Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Please indicate on the Meeting Logistics Page if you plan to come.
  • We are now planning a one-day Noctua/LEGO training session for the Monday (November 7th) following the general consortium meeting. Please indicate on the logistics page if you are definitely staying for that so Paul T. can arrange for a meeting room.

UK LEGO/Noctua Training

  • There will be a LEGO/Noctua training session in Hinxton, UK from Wednesday, 8/31 - Friday, 9/2.
  • Logistics
  • Agenda

Annotation Consistency Exercise

http://www.ncbi.nlm.nih.gov/pubmed/23246437

some possible items to discuss:

  1. when to include specific targets or not
  2. which qualifier/RO term to use in col16 extensions
  3. when col8 vs. col16
  4. new term chromosome_axis?
  5. do people still make TAS/NAS annotations?
  6. other topics?
Gene Name (col 2) GO ID and term name (col 5) Evidence (col 7) With/From (col 8) Annotation Extension (col 16)
SET1 GO:1990837 sequence-specific double-stranded DNA binding IMP has_direct_input SO:0000339 recombination_hotspot, happens_during GO:0051321 meiotic cell cycle
SET1 GO:0010844 recombination hotspot binding IMP has_direct_input SO:0000955 double_stranded_DNA_chromosome, happens_during GO:0051321 meiotic cell cycle
SET1 GO:0051568 histone H3-K4 methylation IDA
SET1 GO:0044648 histone H3-K4 dimethylation IMP
SET1 GO:0044648 histone H3-K4 dimethylation IMP positively_regulates GO:0042138: meiotic DNA double-strand break formation
SET1 GO:0044648 histone H3-K4 dimethylation IMP happens_during GO:0051321 meiotic cell cycle
SET1 GO:0080182 histone H3-K4 trimethylation IDA
SET1 GO:0080182 histone H3-K4 trimethylation IMP
SET1 GO:0080182 histone H3-K4 trimethylation IMP happens_during GO:0051321 meiotic cell cycle
SET1 GO:0006279 premeiotic DNA replication IMP happens_during GO:0051321 meiotic cell cycle
SET1 GO:0010780 meiotic DNA double-strand break formation IMP
SET1 GO:1903341 regulation of meiotic DNA double-strand break formation IMP
SET1 GO:1903341 regulation of meiotic DNA double-strand break formation IMP happens_during GO:0051321 meiotic cell cycle
SET1 GO:1903343 positive regulation of meiotic DNA double-strand break formation IDA
SET1 GO:1903343 positive regulation of meiotic DNA double-strand break formation IMP occurs_at CYS3, BUD23, DEP1, LSB3
SET1 GO:1903343 positive regulation of meiotic DNA double-strand break formation IGI w/HHT1, HHT2
SET1 GO:1903342 negative regulation of meiotic DNA double-strand break formation IMP occurs_at PES4, ARG3
SET1 GO:0010674 negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle IMP regulates_expression_of PES4, ARG3
SET1 GO:0071168 protein localization to chromatin IC from/ GO:0000785 chromatin, GO:1903343 positive regulation of meiotic DNA double-strand break formation has_input SPP1
SET1 GO:0071168 protein localization to chromatin IMP occurs_at SO:0000502 transcribed region, has_inut SPP1, happens_during GO:0000278 mitotic cell cycle
SET1 NTR NTR: chromosome axis IMP happens_during GO:0051321 meiotic cell cycle, conincident_with SO:0000339 recombination_hotspot
SWD3 GO:0051568 histone H3-K4 methylation IMP
SWD3 GO:0044648 histone H3-K4 dimethylation IMP
SWD3 GO:0080182 histone H3-K4 trimethylation IMP
SWD3 GO:0044648 histone H3-K4 dimethylation IMP positively_regulates GO:0042138: meiotic DNA double-strand break formation
SWD3 GO:0080182 histone H3-K4 trimethylation IMP positively_regulates GO:0042138: meiotic DNA double-strand break formation
SWD3 GO:0051569 regulation of histone H3-K4 methylation IMP
SWD3 GO:0010780 meiotic DNA double-strand break formation IMP
SWD3 GO:1903341 regulation of meiotic DNA double-strand break formation IMP
SWD3 GO:1903342 negative regulation of meiotic DNA double-strand break formation IMP occurs_at PES4, ARG3
SWD3 GO:1903343 positive regulation of meiotic DNA double-strand break formation IMP occurs_at CYS3, BUD23, DEP1, LSB3
SPP1 GO:0044648 histone H3-K4 dimethylation IMP
SPP1 GO:0080182 histone H3-K4 trimethylation IMP
SPP1 GO:0044648 histone H3-K4 dimethylation IMP positively_regulates GO:0042138: meiotic DNA double-strand break formation
SPP1 GO:0080182 histone H3-K4 trimethylation IMP positively_regulates GO:0042138: meiotic DNA double-strand break formation
SPP1 GO:0051569 regulation of histone H3-K4 methylation IMP
SPP1 GO:0051571 positive regulation of histone H3-K4 methylation IMP
SPP1 GO:1903342 negative regulation of meiotic DNA double-strand break formation IMP occurs_at PES4, ARG3
SPP1 GO:1903343 positive regulation of meiotic DNA double-strand break formation IMP occurs_at CYS3, BUD23, DEP1, LSB3
SPP1 GO:NTR chromosome axis IDA happens_during GO:0051321 meiotic cell cycle
SPP1 GO:0003682 chromatin binding IDA
SPP1 GO:0003682 chromatin binding IDA occurs_at SO:0000502 transcribed region, happens_during GO:0000278 mitotic cell cycle
SPP1 GO:0005515 protein binding IPI w/REC107 (MER2) happens_during GO:0051321 meiotic cell cycle
SPP1 GO:0005515 protein binding IDA has_input REC107 (MER2), happens_during GO:0051321 meiotic cell cycle
SPP1 GO:0005515 protein binding IPI w/REC107 (MER2) positively_regulates NTR: chromosome axis binding, happens_during GO:0051321 meiotic cell cycle
SPP1 GO:0030674 protein binding, bridging IC from GO:0005515 protein_binding, GO:0035064 methylated histone binding happens_during GO:0051321 meiotic cell cycle
SPP1 GO:0035064 methylated histone binding TAS occurs_at SO:0000170 RNA polymerase II promoter
SPP1 GO:0010780 meiotic DNA double-strand break formation IMP
SPP1 GO:1903341 regulation of meiotic DNA double-strand break formation IMP
SPP1 GO:0034613 cellular protein localization IMP has_direct_input SPO11, occurs_at GO:0035861 site of double-strand break
SPP1 GO:1990166 protein localization to site of double-strand break IMP transports_or_maintains_localization_of SPO11, happens_during GO:0051321 meiotic cell cycle
SPP1 GO:new regulation of protein localization to site of double-strand break IMP has_regulation_target SPO11
SPP1 GO:0000790 nuclear chromatin IDA coincident_with SO:0000316 CDS
SPP1 GO:0000790 nuclear chromatin IDA exists_during GO:0000278 mitotic cell cycle
SPP1 GO:0000785 chromatin IDA coincident_with RPS0A and ADH1, part_of CL:0000334 vegetative cell (sensu Fungi)
SPP1 NTR NTR: chromosome axis IDA happens_during GO:0051321 meiotic cell cycle
SPP1 GO:new chromosome axis IDA exists_during GO:0051321 meiotic cell cycle
SPP1 GO:new [condensed?] chromosome axis IDA exists_during GO:0051321 meiotic cell cycle
SPP1 NOT GO:0035861 site of double-strand break IDA
SPP1 GO:0048188 Set1C/COMPASS complex NAS
REC107 (MER2) GO:0005515 protein binding IPI w/SPP1 happens_during GO:0051321 meiotic cell cycle
REC107 (MER2) GO:0005515 protein binding IDA has_input SPP1, happens_during GO:0051321 meiotic cell cycle
REC107 (MER2) GO:0005515 protein binding IPI w/SPP1 positively_regulates NTR: chromosome axis binding, happens_during GO:0051321 meiotic cell cycle
REC107 (MER2) GO:0034613 cellular protein localization IMP happens_during GO:0051321 meiotic cell cycle, has_direct_input SPP1, occurs_at GO:NTR chromosome axis
REC107 (MER2) GO:0042138 meiotic DNA double-strand break formation IMP
REC107 (MER2) GO:new [condensed?] chromosome axis IDA exists_during GO:0051321 meiotic cell cycle
REC104 GO:0042138 meiotic DNA double-strand break formation IMP
REC102 GO:0042138 meiotic DNA double-strand break formation IMP
REC114 GO:0042138 meiotic DNA double-strand break formation IMP
MEI4 GO:0042138 meiotic DNA double-strand break formation IMP
SKI8 GO:0042138 meiotic DNA double-strand break formation IMP
SPO11 GO:0035861 site of double-strand break IDA
SPO11 GO:0035861 site of double-strand break IDA exists_during GO:0051321 meiotic cell cycle
SPO11 GO:0035861 site of double-strand break IDA happens_during GO:0051321 meiotic cell cycle

Noctua model: http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001783?barista_token=lyg8ba4blv2702bcpp9a#