Annotation Conf. Call 2020-01-28: Difference between revisions

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= Agenda and Minutes =
= Agenda and Minutes =
*Present:  
*Present:  
== Noctua Form 2.0 ==
*Software updates made to ensure correct environment of all components
*Additional updates:
**Entity identifiers now displayed along with labels (particularly helpful when annotating gene product isoforms)
**Causal relations decision tree (available via Connect on the Noctua form table)
*Available (SOON!) from [http://noctua.geneontology.org/ Noctua landing page] and workbenches menu on graph editor (NOW)
*[http://wiki.geneontology.org/index.php/Noctua Noctua Manual]
*[https://docs.google.com/document/d/1DZu25YKdH_D3Ics5BSmyvN8IGfGlTcCcwQ4HzviZeWM/edit#heading=h.e6msjvy4rdk9 User Guide - Google doc from Berkeley meeting, will be retired]
*ACTION: curators should try out the new form, give us feedback; we will continue to update and organize the documentation to try to help with workflow
'''*ACTION: New software updates on Noctua development site will be rolled out to production; Kimberly will email when new Noctua form is on production.


== 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
*Review retired relations:
*Relations to discuss this week:
**'has direct input' -> 'has input' for MF
**'activated by'
**'occurs at' -> 'occurs in' for MF
**'activated by' had been used to identify a chemical substance that increases the activity of the gene product.
**annotation tools need to updated
**We would like to instead model this with a 'binding activity' that 'directly positively regulates' a second, or main, molecular function enabled by the gene/gene product
 
**The aim is to capture regulatory molecules, but not things like co-factors.
'''*ACTION: Groups that have these relations in their annotation tools, should remove them.
**Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296
 
'''*ACTION: Commented on [https://github.com/oborel/obo-relations/issues/187 existing ticket in RO tracker] to obsolete 'has direct input'.





Revision as of 17:29, 27 January 2020

Agenda and Minutes

  • Present:

Annotation Relations

  • Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
  • Relations to discuss this week:
    • 'activated by'
    • 'activated by' had been used to identify a chemical substance that increases the activity of the gene product.
    • We would like to instead model this with a 'binding activity' that 'directly positively regulates' a second, or main, molecular function enabled by the gene/gene product
    • The aim is to capture regulatory molecules, but not things like co-factors.
    • Sample GO-CAM model: http://noctua.geneontology.org/editor/graph/gomodel:5db9c9a500000296