Ontology meeting 2023-01-30: Difference between revisions

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* '''Group members:''' Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
* '''Present:'''    Pascale, Harold, Raymond, Val, Edith, Jim, Tanya, Karen, Kimberly, David, Chris, Peter, Paul
* '''Regrets: '''


=Announcements=
=Announcements=
==Annotation reviews at MGI==
* Li (@LiNiMGI) will be replacing Harold for annotation tickets review.
* The group-contacts.csv file has been updated:
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv


==GOC consortium==
==GOC consortium==
Line 12: Line 11:


password: goc2023
password: goc2023
==Annotation reviews at MGI==
* Li (@LiNiMGI) will be replacing Harold for annotation tickets review.
* The group-contacts.csv file has been updated:
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv


=Editors discussion items=
=Editors discussion items=
==introduce Molecular Event class to GOPlus==
Close?
https://github.com/geneontology/go-ontology/issues/19960


=Script to download annotations=
=Script to download annotations=
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# Navigate to the [https://github.com/geneontology/simple-report-system/tree/main/reports reports] (can also go via the [https://github.com/geneontology/simple-report-system simple-report-system link] at the top  
# Navigate to the [https://github.com/geneontology/simple-report-system/tree/main/reports reports] (can also go via the [https://github.com/geneontology/simple-report-system simple-report-system link] at the top  
# Select the report that corresponds to the ticket number
# Select the report that corresponds to the ticket number
# Copy to clipboard - best to do it from "edit" mode (for Pascale - mac + firefox)
# Make a copy of the [https://docs.google.com/spreadsheets/d/1z496xuif_6RrooHLW4kKl0ob-GiZ_JPc0qd7Vv19RyE/edit#gid=0 New Annotation Review Template]
# Make a copy of the [https://docs.google.com/spreadsheets/d/1z496xuif_6RrooHLW4kKl0ob-GiZ_JPc0qd7Vv19RyE/edit#gid=0 New Annotation Review Template]
# Paste annotations
# Paste annotations
#* Results: copying from edit mode versus 'normal': https://docs.google.com/spreadsheets/d/1Tbnpc-rDzIgjacEc6vs5eHU6EU2zvQTJjilF3HstrCE/edit#gid=0
# Sort by Assigned by, then by reference
# Sort by Assigned by, then by reference
* NOTE: If you dont add the label AT ISSUE CREATION it doesnt work (to be confirmed)
* It might be nice to get another report: number of EXP, IEA, Others, for a list of GOIDs, showing 0 for terms with no annotations
==Update missing MetaCyc2GO mappings for SGD YeastPathways==
==Update missing MetaCyc2GO mappings for SGD YeastPathways==
Jim, Chris  
Jim, Chris  

Latest revision as of 09:51, 31 January 2023

  • Group members: Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
  • Present: Pascale, Harold, Raymond, Val, Edith, Jim, Tanya, Karen, Kimberly, David, Chris, Peter, Paul
  • Regrets:

Announcements

GOC consortium

  • April 27th-29th, Padua, Italy
  • If you plan to attend, please register ASAP.

geneontology.ticketleap.com/goc2023

password: goc2023

Annotation reviews at MGI

  • Li (@LiNiMGI) will be replacing Harold for annotation tickets review.
  • The group-contacts.csv file has been updated:

https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Editors discussion items

introduce Molecular Event class to GOPlus

Close? https://github.com/geneontology/go-ontology/issues/19960

Script to download annotations

https://github.com/geneontology/simple-report-system

  1. Create New issue
  2.  Paste GO term(s) (1 or many)
  3.  Select report using the labels:
    • "direct_ann_to_list_of_terms": all direct EXP annotations to the terms entered
    • "reg_ann_to_list_of_terms": all EXP annotations to the term entered, plus all children (including regulates children)
  4.  Navigate to the reports (can also go via the simple-report-system link at the top
  5.  Select the report that corresponds to the ticket number
  6.  Copy to clipboard - best to do it from "edit" mode (for Pascale - mac + firefox)
  7.  Make a copy of the New Annotation Review Template
  8.  Paste annotations
  9.  Sort by Assigned by, then by reference


  • NOTE: If you dont add the label AT ISSUE CREATION it doesnt work (to be confirmed)
  • It might be nice to get another report: number of EXP, IEA, Others, for a list of GOIDs, showing 0 for terms with no annotations

Update missing MetaCyc2GO mappings for SGD YeastPathways

Jim, Chris https://github.com/geneontology/go-ontology/issues/24597

Bulk updates

Obsoleting large sets of terms

Obsolete BPs "regulation MF"

https://github.com/geneontology/go-ontology/projects/34?add_cards_query=is%3Aopen

Tickets by ontology editors