Annotation Conf. Call 2016-08-23

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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#

Minutes

  • On call: Alice, Barbara, David H., David OS, Edith, Elena, George, Giulia, Helen, Kimberly, Li, Melanie, Moni, Paola, Penelope, Petra, Ruth, Sage, Shur-Jen, Stacia, Tanya

Upcoming Meetings

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

  • Please add your name to the attendees list on the logistics wiki page
  • Please also indicate if you are planning to stay for the Noctua/LEGO training session on Monday, 11/7, the day after the consortium meeting ends

UK LEGO/Noctua Training

  • Need full list of attendees on the logistics page - DONE
  • Off-site people need to make sure that Claire has given your name to EBI security

Annotation Consistency Exercise

Overall Consistency

  • Generally our annotations of the biology were consistent, but there are still issues with annotating to the process term or regulation of that process - this goes back to the perennial issue of defining when a process begins and ends

LEGO Modeling and Use of Regulates Relations

  • There is a LEGO model in progress for this paper (see link above)
  • Note that when annotating in LEGO, regulation (usually known to be positive or negative) is captured as a relation between the MF and the BP - curators would not enter a regulation BP term as the process
    • How will the correct annotations to 'regulation of BP' be output in the legacy GAF/GPAD files then?
    • The reasoner that is used to generate the GAF/GPAD files would be used to make the correct BP annotations using the existing relations

Including Targets as Annotation Extensions

  • There was also some discussion on when to include targets of a process - no clear decision or guideline there yet

Protein Binding - IPI and With/From or IDA and Annotation Extensions?

  • Another big issue of discussion was how to represent protein binding - Col. 8 (With/From) vs Col. 16 (Annotation Extension)
    • Historically, we have used the IPI evidence code and Col. 8 to capture the identifier of the interacting gene product, but LEGO handles this is a different way, by using the IDA evidence code and 'has_input' relation which is translated into a Col. 16 annotation
    • Using Col. 16 to capture protein binding interactors is not a new idea; Emily proposed this several years ago
    • Protein binding assays are direct assays, so that is not inconsistent with using that evidence code, which we already use when the exact identifier of the interacting partner is not known (e.g. actin)
    • Using Col. 16 might allow us to more readily create 'x protein family binding' terms
    • Ruth pointed out, though, that there are downstream implications to making this change that need to be sorted out first
      • First, no system currently exists for automatically creating these 'x protein family binding' terms, so that is not an issue at this point
      • Second, we would need a system in place to handle the transition for existing annotations BEFORE we make this switch
        • This system would need to handle cross-species experiments (we should review these types of experiments in LEGO, too)
      • This, Tony S. and Ruth worked on a project that would translate GO's protein binding IPI annotations into a Cytoscape view of protein binding networks; this would need to be changed to accommodate the new representation
  • For now, though, we will continue to use IPI and the With/From column if the identifier is known, and IDA with nothing in the With/From column if the identifier is not known
  • AI: Assess necessary steps to make the change from With/From to AEs for protein binding

New CC Term - Chromosome Axis

  • One of the reasons Stacia picked this paper was to explore the idea of creating a new CC term: 'chromosome axis'
  • Is this a real CC? If so, how would it be defined?
  • The chromosome axis appears to be part of a temporary arrangement of the meiotic chromosome
    • Does the impermanent nature of this structure make it unsuitable for a GO CC term?
  • The concept of the chromosome axis does appear important for understanding the biology of meiotic recombination, though
  • AI: Attempt a definition of chromosome axis term and consult with authors of this paper or other experts in the field for feedback on term, definition, and ontology placemnt

Clarification on Pipes and Commas in Annotation Extensions

  • Just a note - targets captured in annotation extensions should be separated with a pipe if they are acted upon individually
  • The use of a comma in the table for this exercise is just an artifact of wiki formatting that creates a new cell in the wiki table