Ontology meeting 2023-01-30

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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:


GOC consortium

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


password: goc2023

Annotation reviews at MGI

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


Editors discussion items

introduce Molecular Event class to GOPlus

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

Script to download annotations


  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"


Tickets by ontology editors