Annotation Conf. Call 2017-02-28

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Bluejeans URL

https://bluejeans.com/993661940

Agenda

GO Meeting Reminder

Noctua Modeling Discussion

Sabrina Toro, Zfin

Midori Harris, PomBase

  • myo2_rlc1_PMID19570908
  • Regulation of fission yeast myosin-II function and contractile ring dynamics by regulatory light-chain and heavy-chain phosphorylation.
  • In vitro and in vivo assays using nonphosphorylatable or phosphomimetic Rlc1 mutations show that Rlc1 somehow positively regulates the actin filament-based motor activity of Myo2 as part of actomyosin contractile ring contraction, in turn part of mitotic cytokinesis.
    • We were very tempted to say that Rlc1's unknown MF regulator activity directly positively regulates Myo2's microfilament motor activity because:
      • Rlc1 has previously been shown to bind Myo2;
      • The in vitro assays (Fig.1, Table 3) show an effect on Myo2 motor activity with only F-actin, Myo2, Cdc4. and Rlc1 (heavy chain, essential light chain, and regulatory light chains respectively) present.
    • The reason we didn't, and instead included the actin filament-based movement "link", is that the is_a hierarchy has motor activity as a subtype of NTPase activity:
     GO:0017111 ! nucleoside-triphosphatase activity
     -- is_a GO:0003774 ! motor activity
     ---- is_a GO:0000146 ! microfilament motor activity
 
  • From this, reasoning would infer this regulation hierarchy (whether regulation terms are instantiated or not):
     regulation of nucleoside-triphosphatase activity
     -- is_a regulation of motor activity
     ---- is_a regulation of microfilament motor activity
 
  • ... and erroneously conclude that Rlc1 does regulate Myo2's ATPase activity. The Rlc1 mutant phenotypes here say it doesn't (Fig. 76, Table 3).
  • Questions:
    • Should the MF ontology change to motor activity has_part nucleoside-triphosphatase activity?
    • Does LEGO have any way to capture when a molecular mechanism isn't known, but one possibility has been ruled out?

April Discussion

Minutes

  • On call: Barbara, David H., Edith, Giulia, Harold, Helen, Karen, Kimberly, Li, Midori, Pascale, Paul, Ruth, Sabrina, Stacia, Stan, Tanya, Terry

Noctua Modeling

  • Sabrina (Zfin) - role of TFs in neutrophil maturation
    • Two TFs, C-myb and Cebp1
    • Represent TFs with MF term for transcription factor activity, sequence-specific DNA binding
    • Indicate gene promoter bound with has_input (lyz)
    • occurs_in:
      • chromatin - based on ChIp assay
    • part_of:
      • transcription - based on direct assays and mutant phenotypes
    • transcription factor complex
      • based on co-IP of C-myb and Cebp1
    • There is no information about the precise role of lyz in neutrophil maturation
    • Transcription part_of cell maturation
      • Based on mutant phenotype
    • Neutrophil maturation didn't exist in GO
      • Created term by linking cell maturation 'results in maturation of' neutrophil
      • Evidence was direct assay based on what the authors show about this process
    • Questions:
      • Harold - transcription factor complex - why is there a separate individual for the complex as well as both each TFs separately?
        • Sabrina - this is what the data suggested
      • Karen - can use the more specific RNA polII transcription factor activity?
        • Sabrina - Yes, could do this.
      • Kimberly - Might be a nice check to have to prompt curators to use the more specific MF term when the more specific BP term is also used.
      • David - What would the reasoner give if we run it?
      • Paul T. - The coming design templates should include transcription and will give curators a standard way to annotate these things. Curators will then just need to fill in the specific entities and evidence.
      • Tried running the reasoner