Ontology meeting 2018-08-06

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Conference Line

Agenda

Editors Discussion

Project Update

MF Refactor Transcription Factor Branch-- https://github.com/geneontology/go-ontology/projects/7

Recent changes:

  1. Obsoleted GO:1904725 TFIIB-class transcription factor binding involved in negative regulation of transcription
  2. Restored 'transcription elongation regulator activity'
  3. Obsoleted 'transcription factor activity, protein binding' and children
    • GO:0000988 transcription factor activity, protein binding
    • GO:0000989 transcription factor activity, transcription factor binding
    • GO:0000990 transcription factor activity, core RNA polymerase binding
    • GO:0000991 'transcription factor activity, core RNA polymerase II binding
    • GO:0001076 transcription factor activity, RNA polymerase II transcription factor binding
    • GO:0001129 RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly
    • GO:0001132 RNA polymerase II transcription factor activity, TBP-class protein binding
    • GO:0001190 transcriptional activator activity, RNA polymerase II transcription factor binding
    • GO:0001191 transcriptional repressor activity, RNA polymerase II transcription factor binding
    • GO:0098811 transcriptional repressor activity, RNA polymerase II activating transcription factor binding
  4. Changed labels and improve definitions 'GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding' and children, to be consistent with GO:0003700 DNA-binding transcription factor activity.
    • For eg: GO:0000981
    • OLD LABEL: RNA polymerase II transcription factor activity, sequence-specific DNA binding
    • NEW LABEL: DNA-binding transcription factor activity, RNA polymerase II-specific
    • OLD DEF: Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    • NEW DEF: A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
  5. Change labels: 'transcription factor recruiting activity' to 'transcription regulator recruiting activity, again to be consistent with GO:0003700 DNA-binding transcription factor activity.
  6.  Fixed inconsistencies TFIIx-class transcription factor binding
  7.  Simplified labels 'ligand-dependent nuclear receptor transcription activity' and related terms
    • GO:0016922 ligand-dependent nuclear receptor binding -> nuclear receptor binding
    • GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity -> nuclear receptor coactivator activity
    • GO:2000325 regulation of ligand-dependent nuclear receptor transcription coactivator activity -> regulation of nuclear receptor transcription coactivator activity
    • GO:2000326 negative regulation of ligand-dependent nuclear receptor transcription coactivator activity -> negative regulation of nuclear receptor transcription coactivator activity
    • GO:2000327 positive regulation of ligand-dependent nuclear receptor transcription coactivator activity -> positive regulation of nuclear receptor transcription coactivator activity
  8. Improve definition of 'transcription coregulator activity' and children - again

Upcoming changes:

  1.  Merge terms transcription factor activity, RNA polymerase II distal enhancer (and proximal) sequence-specific binding and children
    • Still to be (re-)discussed with the tx group, but the rationale is that transcription factors can bind both proximal and distal regions; this is not related to their functions as tx factors. The proximal/distal binding can be captured as extensions and/or under 'DNA binding' ('RNA polymerase II distal(/proximal) enhancer sequence-specific DNA binding'
  2.  Connect transcription factor recruiting activity to preinitiation complex assembly: according to Colin, all proteins that recruit proteins to the PIC effectively are mediating the PIC assembly. He also thinks that 'PIC assembly' reflect the transient nature of the PIC (whereas 'localization' sound like a localization to a stable CC, which the PIC isn't). (Pull request waiting for feedback from Val and Karen)
  3.  The previous point indicates a need to refer to the PIC, which should perhaps be merged into 'DNA-directed RNA polymerase II, holoenzyme', see discussion here: https://github.com/geneontology/go-ontology/issues/15870
  4. Others - but these are the main ones.

Annotation reviews I created a project under the 'annotation' repo, https://github.com/geneontology/go-annotation/projects/9 Still many tickets opened


Ontology Developers' workshop possibility

  • December in Geneva? One meeting or 2? Maybe we can take a day or two to also meet with Anne and/or Alan to discuss the Rhea alignment project.


GH project link

https://github.com/geneontology/go-ontology/projects/1

Minutes

  • On call:
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