Annotation Conf. Call 2020-02-04: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(Created page with "= Agenda and Minutes = *Present: Bob, Chris, David, Edith, Giulia, Harold, Helen, Karen, Kimberly, Laurent-Philippe, Li, Midori, Pascale, Penelope, Sabrina, Seth, Stacia, Stan...")
 
Line 1: Line 1:
= Agenda and Minutes =
= Agenda and Minutes =
*Present: Bob, Chris, David, Edith, Giulia, Harold, Helen, Karen, Kimberly, Laurent-Philippe, Li, Midori, Pascale, Penelope, Sabrina, Seth, Stacia, Stan, Suzi, Tanya
*Present:  


==Annotation Calls==
==Annotation Calls==
Line 7: Line 7:


==Noctua==
==Noctua==
*Noctua will be updated later today to make the new Noctua form the default version of the form.
*Noctua is now updated to make the new Noctua form the default version of the form.
*Please let us know if you experience any trouble with Noctua after the update, or have questions on how to use the form.
*Please let us know if you experience any trouble with Noctua after the update, or have questions on how to use the form.
*Documentation is here:  http://wiki.geneontology.org/index.php/Noctua
*Documentation is here:  http://wiki.geneontology.org/index.php/Noctua
*Thank you to the MGI curators and to Sabrina for their feedback


== Annotation Relations ==
== Annotation Relations ==
*Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
*Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
*Relation to discuss this week:
*Relation discussed this week:
**'activated by'
**'activated by'
**https://github.com/geneontology/go-annotation/issues/2718
**https://github.com/geneontology/go-annotation/issues/2718
**'activated by' had been defined as a relation used to identify a chemical substance that increases the activity of the gene product
**'activated by' had been defined as a relation used to identify a chemical substance that increases the activity of the gene product
**Going forward, though, the aims are to:
 
***model regulatory events in terms of activities enabled by gene products (this implies that we have some knowledge of the regulatory mechanism)
===Follow-Up Discussion with Ontology Editors===
***capture bona fide regulatory molecules (what is being 'sensed'), but not cofactors such as ions or coenzymes
===Chemical Entity Binding Terms===
****experiments that determine an enzyme's ion specificity, for example, would not be annotated
*Question from last week's call: should curators request new pre-composed binding terms for binding chemical entities, or should they use 'binding' has_input 'ChEBI term'?
**For standard annotation, an example is:
*Ontology editors discussed this on their weekly call yesterday and the decision is:
***GeneProduct 1 'enables' small molecule binding (GO:0036094) 'has_input' (some chemical), 'directly_positively_regulates' molecular function
**Going forward, curators are asked to annotate to 'binding' and use the 'has input' extension to capture the chemical entity
***GeneProduct 1 'enables' molecular function
**Future work will evaluate existing 'binding' terms in the ontology and decide which should stay and also the criteria for instantiating new 'binding' terms
**Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296
**As an annotation group, we will also continue to evaluate what 'binding' annotations are appropriate for GO and why
**Note that, in some cases, we have MF terms that capture what curators may have been trying to capture with 'activated by', e.g. calcium-activated potassium channel activity (GO:0015269)
**Most groups can make annotation extensions in their current tools; if not, Noctua is available for groups to use partially or fully
***Ontology editors could discuss these types of terms and making sure we are consistent with term creation and labels
===Molecular Function Regulators===
*One of the inferred annotations generated from the proposed nuclear receptor model was that of molecular function regulator (GO:0098772)
*Molecular function regulator
**Textual definition: A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
**Logical definition: molecular function AND ('directly regulates' some molecular function)
**''Any'' upstream MF that directly regulates a downstream MF will be inferred to be a 'molecular function regulator' by the reasoner
**Two issues from last week's call:
***Was the model of nuclear receptor activity correct?  
****The idea was to try to model cases where curators used the 'activated by' extension relation, but in the case of nuclear receptors the premise that the ligand binding 'activates' the transcription factor activity may not actually be the correct way to think about this compound function
 
***directly = direct physical interaction
***reasoning rule behind-the-scenes that generates that resulting 'protein binding' annotation




[[Category: Annotation Working Group]]
[[Category: Annotation Working Group]]

Revision as of 17:03, 3 February 2020

Agenda and Minutes

  • Present:

Annotation Calls

  • We will meet weekly on Tuesdays at 8am PST.
  • Will no longer make the distinction between annotation and GO-CAM/Noctua calls.

Noctua

  • Noctua is now updated to make the new Noctua form the default version of the form.
  • Please let us know if you experience any trouble with Noctua after the update, or have questions on how to use the form.
  • Documentation is here: http://wiki.geneontology.org/index.php/Noctua
  • Thank you to the MGI curators and to Sabrina for their feedback

Annotation Relations

  • Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
  • Relation discussed this week:

Follow-Up Discussion with Ontology Editors

Chemical Entity Binding Terms

  • Question from last week's call: should curators request new pre-composed binding terms for binding chemical entities, or should they use 'binding' has_input 'ChEBI term'?
  • Ontology editors discussed this on their weekly call yesterday and the decision is:
    • Going forward, curators are asked to annotate to 'binding' and use the 'has input' extension to capture the chemical entity
    • Future work will evaluate existing 'binding' terms in the ontology and decide which should stay and also the criteria for instantiating new 'binding' terms
    • As an annotation group, we will also continue to evaluate what 'binding' annotations are appropriate for GO and why
    • Most groups can make annotation extensions in their current tools; if not, Noctua is available for groups to use partially or fully

Molecular Function Regulators

  • One of the inferred annotations generated from the proposed nuclear receptor model was that of molecular function regulator (GO:0098772)
  • Molecular function regulator
    • Textual definition: A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
    • Logical definition: molecular function AND ('directly regulates' some molecular function)
    • Any upstream MF that directly regulates a downstream MF will be inferred to be a 'molecular function regulator' by the reasoner
    • Two issues from last week's call:
      • Was the model of nuclear receptor activity correct?
        • The idea was to try to model cases where curators used the 'activated by' extension relation, but in the case of nuclear receptors the premise that the ligand binding 'activates' the transcription factor activity may not actually be the correct way to think about this compound function
      • directly = direct physical interaction
      • reasoning rule behind-the-scenes that generates that resulting 'protein binding' annotation