Ontology Development

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Group's focus

This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology. The group also creates rules to ensure the ontology's integrity.

Group Leader

David Hill (MGI)

Documentation

Setting up Protege for GO editors

Installing and Using git

Ontology Editing Guide

Guidelines for equivalence axioms

Curator guides

Editor_Guide

Editor_file_guide

Ontology Documentation Drafts

for working on documentation of ontology content that will become part of the web-based documentation

New Ontology Editor Training

Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity

Guidance for organizing content meetings

(old doc, but basic principles still apply)

Notes on specific terms

Website - to be moved to the wiki?

Communication

Editor's Conference calls

When

  • Calls are held weekly on Mondays, 12:00PM-1:00PM EST
  • Calls are scheduled on the GO's Google calendar. Please request access to the calendar if you don't have it.
  • Reminder emails are sent out to the go-editors mailing list

How to Join

  • Recurring meeting URL: https://stanford.zoom.us/j/828418143
  • to join via phone: enter Meeting ID 828418143# after dialing in
  • from US: +1 646 558 8656 (US Toll) or +1 408 638 0968 (US Toll)

Agenda and Minutes

Content Development

Projects

High Priority/Ongoing

  • Transcription 2018 (Pascale, Ruth, Astrid, Marcio, Paul T)
  • Cell Cycle (Val, Pombe experts, GOEds)
  • Enzymes and EC mappings
  • Synapse project (Synapse experts, DavidOS, Becky Foulger)
  • Extracellular RNA-containing vesicles (Paola, Aleks and community experts)
  • Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts)
  • Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts)

Medium Priority

Low priority

Recently completed projects

Proposed content work

A list of topics that we propose to address, but for which a timeline has not been set

Completed ontology content work

Quality Control

SPARQL checks on the ontology

[|SPARQL checks on the ontology]

Ontology release pipeline

http://wiki.geneontology.org/index.php/Release_Pipeline Errors: http://current.geneontology.org/ontology/reports/index.html

TO BE REPLACED

Other Ontology Development Group Activities

Complex Modeling