Difference between revisions of "Annotation Conf. Call 2017-08-08"

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= Minutes =
 
= Minutes =
−
*On call: David H., Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Penelope, Rob, Sabrina, Sage, Shur-Jen, Stan, Suzi, Terry, Val, Stacia
+
*On call: David H., George, Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Paul T., Penelope, Petra, Rob, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Terry, Tom, Val  
  
 
== Ontology Report ==
 
== Ontology Report ==
 +
=== Check Annotations ===
 
*SUMO protease annotations may be too generic https://github.com/geneontology/go-ontology/issues/13941
 
*SUMO protease annotations may be too generic https://github.com/geneontology/go-ontology/issues/13941
 
**Annotations to SUMO protease terms may be able to be deepened to one of the two more specific SUMO protease terms (endopeptidase or isopeptidase)
 
**Annotations to SUMO protease terms may be able to be deepened to one of the two more specific SUMO protease terms (endopeptidase or isopeptidase)
Line 36: Line 37:
 
**Mary will use her algorithmic method, but the output slim will need review from GOC member groups
 
**Mary will use her algorithmic method, but the output slim will need review from GOC member groups
 
**Val's matrix tool can be a good tool for checking redundancy in the slim
 
**Val's matrix tool can be a good tool for checking redundancy in the slim
−
***Will also address whether the chosen terms are too high level to be useful
+
***Can also help address whether the chosen terms are too high level to be useful
−
*'''AI:''' Document the methodologies used to create and analyze slims
 
−
*'''AI:''' Supply list of GO IDs used for GO slims (make new github ticket)
 
−
**Supply ID - Name pairs
 
 
*[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim]
 
*[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim]
 
**Confirm that all AGR member groups are okay with current version of GO AGR slim
 
**Confirm that all AGR member groups are okay with current version of GO AGR slim
 
**Doug had suggested including additional bins for:
 
**Doug had suggested including additional bins for:
−
***Genes not mapped to any term in the slim
+
***Genes not mapped to any term in the slim (other)
−
***Genes not annotated to any term
+
****It can be very difficult to try to map all genes to a slim term - you want to have biologically meaningful term selection without including terms that are too high level or too specific
 +
****http://pombase2.bioinformatics.nz/browse-curation/fission-yeast-go-slim-terms
 +
****For an example of how “other” bins look in ribbons see http://beta.flybase.org/reports/FBgn0011327.html
 +
***Genes not annotated to any term at all
 +
**Co-annotation can be used to capture information when a combined term in the ontology cannot be made
 +
**Analysis can help determine when there might need to be work done on the ontology (e.g. missing relations) or on the annotations (e.g. cytoplasm annotations -> cytosol annotations)
 +
**Note that in the AGR display, the labels may need to be adapted to be more biologist friendly
 +
**Can we have some outside review of the labels?
 +
 
 +
=== Action Items ===
 +
*'''AI:''' Document the methodologies used to create and analyze slims
 +
*'''AI:''' Supply list of GO ID - Name pairs used for GO slims  (new github ticket - https://github.com/geneontology/go-ontology/pull/14031)
 +
*'''AI:''' Get feedback from users on GO slim term labels
 +
**Pascale will send out the list
 +
 
 +
== Signaling Project ==
 +
*Wnt - Giulia, Helen, Kimberly
 +
**[https://docs.google.com/spreadsheets/d/1X1kfjnh_CJbqp7bfCLJuNBlRVyB3PIaLJGLaVfRID78/edit#gid=1354579580 Google spreadsheet with annotation, ontology analysis]
 +
**[https://docs.google.com/document/d/1wrPx0g4FfbV6zObVrCkGWZJvEY2SUumC1CH3soTKuGE/edit Google doc for crystallizing github tickets]
 +
**Re-opened ticket on receptor agonist activity
 +
**Consolidating other observations to create additional tickets
 +
*MAPK - David H., Sabrina
 +
**Examining genes for MAPK pathway +/- MF support
 +
**Looking at gene products potentially upstream/downstream
 +
*Ca2+ Signaling - Penelope
 +
**Still needs an ontology editor
 +
*GPCR - Pascale, Petra
 +
**Have downloaded annotations, but still need to review them
 +
**Have created a generic GO-CAM model
 +
***A few templates already existed - link to model 0000200, 0000466, 0000486
 +
***Is the heterotrimeric G protein cycle term needed?
 +
***How much detail should be included about the functions of the members of the pathway?
 +
***If there is more than one way to represent a pathway, how should we choose which way to annotate?
 +
 
  
 
[[Category: Annotation Working Group]]
 
[[Category: Annotation Working Group]]

Latest revision as of 09:05, 8 August 2017

Meeting URL

Agenda

Ontology Report

Signaling Project

  • Update on progress to date, github tickets
    • Wnt - Giulia, Helen, Kimberly
    • MAPK - David H. and Sabrina
      • Examining gene products annotated to the process with no experimental support for known MFs
      • Thinking about how to define the beginning and parts of the pathway
    • Ca2+ Signaling
      • Fertilization - Penelope
    • GPCR - Pascale, Petra
      • Some ontology tickets have been addressed
      • Needs global annotation review
      • Needs GO-CAM model
    • Reminder - discussion on specific github tickets, not on project page

Minutes

  • On call: David H., George, Harold, Helen, Kevin, Kimberly, Li, Liz, Midori, Moni, Pascale, Paul T., Penelope, Petra, Rob, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Terry, Tom, Val

Ontology Report

Check Annotations

  • SUMO protease annotations may be too generic https://github.com/geneontology/go-ontology/issues/13941
    • Annotations to SUMO protease terms may be able to be deepened to one of the two more specific SUMO protease terms (endopeptidase or isopeptidase)
    • Gene products annotated are listed on the github ticket

GO Slims

  • GOC slim ticket https://github.com/geneontology/go-ontology/issues/13996
    • Mary will use her algorithmic method, but the output slim will need review from GOC member groups
    • Val's matrix tool can be a good tool for checking redundancy in the slim
      • Can also help address whether the chosen terms are too high level to be useful
  • Modification to AGR slim
    • Confirm that all AGR member groups are okay with current version of GO AGR slim
    • Doug had suggested including additional bins for:
    • Co-annotation can be used to capture information when a combined term in the ontology cannot be made
    • Analysis can help determine when there might need to be work done on the ontology (e.g. missing relations) or on the annotations (e.g. cytoplasm annotations -> cytosol annotations)
    • Note that in the AGR display, the labels may need to be adapted to be more biologist friendly
    • Can we have some outside review of the labels?

Action Items

  • AI: Document the methodologies used to create and analyze slims
  • AI: Supply list of GO ID - Name pairs used for GO slims (new github ticket - https://github.com/geneontology/go-ontology/pull/14031)
  • AI: Get feedback from users on GO slim term labels
    • Pascale will send out the list

Signaling Project

  • Wnt - Giulia, Helen, Kimberly
  • MAPK - David H., Sabrina
    • Examining genes for MAPK pathway +/- MF support
    • Looking at gene products potentially upstream/downstream
  • Ca2+ Signaling - Penelope
    • Still needs an ontology editor
  • GPCR - Pascale, Petra
    • Have downloaded annotations, but still need to review them
    • Have created a generic GO-CAM model
      • A few templates already existed - link to model 0000200, 0000466, 0000486
      • Is the heterotrimeric G protein cycle term needed?
      • How much detail should be included about the functions of the members of the pathway?
      • If there is more than one way to represent a pathway, how should we choose which way to annotate?
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