Ontology Development

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Revision as of 04:32, 3 July 2018 by Pascale (talk | contribs) (Guidelines for GO term definitions To be reviewed)

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Contents

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. With the help of the software team the group create rules to ensure the ontology's integrity.

Group Leader

David Hill (MGI)

Documentation

Setting up Protege for GO editors

Installing and Using git

Editing the Ontology with Protégé

Ontology Editors Daily Workflow

Creating a New Ontology Term

Creating a Regulation Term

Deleting Asserted Subclasses

Obsoleting an Existing Ontology Term

Merging Ontology Terms

Adding Term Comments

Adding a Term to a GO Subset (Slim)

Adding a New GO Subset (Slim)

Adding Taxon Restrictions

Adding Terms to the Import Files

General Gene Ontology Principles

Creating new GO terms Being reviewed

Guidelines for GO term definitions Being reviewed

Editor Guide to has part To be reviewed

Editor Guide to Regulates To be reviewed

Guidelines for equivalence axioms To be reviewed

Curator Guide: Merge Split Move To be reviewed

Curator Guide: Obsoletion To be reviewed

Curator Guide: Enzymes and Reactions To be reviewed

Notes on specific terms To be reviewed

Requesting a New Complex ID from IntAct

Editor file guide To be reviewed

Ontology Documentation Drafts To be reviewed

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

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

New Ontology Editor Training To be reviewed

Website - to be moved to the wiki?

Identifiers To be reviewed

Guidance for organizing content meetings

(old doc, but basic principles still apply)


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