Annotation Conf. Call 2019-11-19: Difference between revisions

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=== 'activated by' and 'inhibited by' ===
=== 'activated by' and 'inhibited by' ===
*If the chemical or molecular entity performing the activation or inhibition acts directly on the gene product by binding to it and is believed to be an endogenous regulator:
*If the chemical or molecular entity performing the activation or inhibition acts directly on the gene product by binding to it and is believed to be an endogenous regulator:
**remove the 'activated by' or 'inhibited by' annotation extension
**remove the ''activated by'' or ''inhibited by'' annotation extension
**create a new 'binding' annotation with an annotation extension of: 'directly positively regulates' or 'directly negatively regulates' the regulated activity of the gene product
**create a new 'binding' annotation with an annotation extension of: ''directly positively regulates'' or ''directly negatively regulates'' the regulated activity of the gene product
*If the annotation is to a binding term, and the extension is 'activated by' the chemical or molecular entity bound:
**Example:
**remove the 'activated by' annotation extension and replace with 'has input'
***GP ''enables''
**the annotations will be used in the future to create or check the logical definitions in the ontology
*If the annotation is to a binding term, and the extension is ''activated by'' the chemical or molecular entity bound:
**remove the ''activated by'' annotation extension and replace with ''has input''
**Example:
***GP ''enables'' '(1->3)-beta-D-glucan binding' ''has input'' '(1->3)-beta-D-glucan'
**the annotations can be used in the future to create or check term logical definitions in the ontology
*If the inhibitor acts by competitively binding to an entity required for the activity of another gene product:
*If the inhibitor acts by competitively binding to an entity required for the activity of another gene product:
**proposal: the activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the downstream gene product
**The activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the next (downstream) gene product
**Examples (with standard annotations):
**Examples (with standard annotations):
***Two DNA-binding transcription factors that compete for overlapping regulatory sequences
***Two DNA-binding transcription factors that compete for overlapping regulatory sequences
****TF-A ''enables'' 'regulatory region binding' directly negatively regulates 'regulatory region binding'
****TF-A ''enables'' 'RNA polymerase II regulatory region sequence-specific DNA binding' ''directly negatively regulates'' 'RNA polymerase II regulatory region sequence-specific DNA binding'
***A gene product that binds and sequesters an enzyme substrate
***A gene product that binds and sequesters an enzyme's substrate
***Inhibitor A 'enables' 'substrate binding' directly negatively regulates 'catalytic activity'
***Inhibitor ''enables'' 'protein binding' ''directly negatively regulates'' 'catalytic activity'
***A decoy receptor that binds and sequesters a ligand
***A decoy receptor that binds and sequesters a ligand
****decoy receptor 'enables' ligand binding directly negatively regulates 'receptor activity'
****Decoy receptor ''enables'' 'protein binding' ''directly negatively regulates'' 'receptor activity'
****secreted frizzled-related proteins
*****secreted frizzled-related proteins


* Spreadsheet for activated_by: https://docs.google.com/spreadsheets/d/1bUQ7uSHaLbr8uvYu04Jbmr76bn-ja01hJxbcGnx-U6I/edit#gid=0
* Spreadsheet for activated_by: https://docs.google.com/spreadsheets/d/1bUQ7uSHaLbr8uvYu04Jbmr76bn-ja01hJxbcGnx-U6I/edit#gid=0

Revision as of 11:00, 19 November 2019

Agenda

Progress Reports

  • Reminder: due mid-December
  • Annotation Group Template
  • GO will generate annotation stats

Annotation Extension Relations

'activated by' and 'inhibited by'

  • If the chemical or molecular entity performing the activation or inhibition acts directly on the gene product by binding to it and is believed to be an endogenous regulator:
    • remove the activated by or inhibited by annotation extension
    • create a new 'binding' annotation with an annotation extension of: directly positively regulates or directly negatively regulates the regulated activity of the gene product
    • Example:
      • GP enables
  • If the annotation is to a binding term, and the extension is activated by the chemical or molecular entity bound:
    • remove the activated by annotation extension and replace with has input
    • Example:
      • GP enables '(1->3)-beta-D-glucan binding' has input '(1->3)-beta-D-glucan'
    • the annotations can be used in the future to create or check term logical definitions in the ontology
  • If the inhibitor acts by competitively binding to an entity required for the activity of another gene product:
    • The activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the next (downstream) gene product
    • Examples (with standard annotations):
      • Two DNA-binding transcription factors that compete for overlapping regulatory sequences
        • TF-A enables 'RNA polymerase II regulatory region sequence-specific DNA binding' directly negatively regulates 'RNA polymerase II regulatory region sequence-specific DNA binding'
      • A gene product that binds and sequesters an enzyme's substrate
      • Inhibitor enables 'protein binding' directly negatively regulates 'catalytic activity'
      • A decoy receptor that binds and sequesters a ligand
        • Decoy receptor enables 'protein binding' directly negatively regulates 'receptor activity'
          • secreted frizzled-related proteins

Noctua Form 2.0 Demo

Minutes

  • Present:
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