Ontology Development: Difference between revisions

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[[Ontology_Development-v2]]
= Group's focus =
= 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.
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.
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=== When ===
=== When ===
* Calls are held weekly on Mondays, 12:00PM-1:00PM EST
* 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.
* 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
* Reminder emails are sent out to the go-ontology mailing list (see [[Internal_email_lists]] to register).


=== How to Join ===
=== How to Join ===
* Recurring meeting URL: https://stanford.zoom.us/j/828418143
* Recurring meeting URL: https://stanford.zoom.us/j/828418143
*to join via phone: enter Meeting ID 828418143# after dialing in
*to join via phone: enter Meeting ID 828418143# after dialing in
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==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]==
==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]==
==[[Installing and Using git]]==
==[[Installing and Using git]]==
==[[Ontology Editors Daily Workflow]]==
==Editing the Ontology==
==Editing the Ontology==
===[[Ontology Editors Daily Workflow]]===
===Creating and Editing Ontology Terms===
* [[Principles for creating a GO term]] - Being reviewed
* [[Guidelines for creating a GO term]]
* [[Guidelines for creating a Regulation Term]]


===[[Principles for Modifying an Existing Ontology Term]]===
To be reviewed
====[[Adding Term Comments]]====
====[[Adding a Term to a GO Subset (Slim)]]====
====[[Adding and Removing GO Subsets (Slims)]]====
====[[Adding Taxon Restrictions]]====


===[[Deleting Asserted Subclasses]]===
{| class="wikitable"
===[[Obsoleting an Existing Ontology Term]]===
!colspan="2" | [[General Gene Ontology Principles]]
===[[Merging Ontology Terms]]===
|-
!colspan="2" | New terms
|-
|rowspan="7"|[[Principles for creating a GO term]] (being reviewed)
|[[Guidelines for creating a GO term]]
|-
|[[Guidelines for creating relationships between terms]] (being reviewed)
|-
|[[Guidelines for creating disjoint terms]] (to be written)
|-
|[[Guidelines for creating a Regulation Term]]
|-
|[[Guidelines for GO textual definitions]] (being reviewed)
|-
|[[Guidelines for equivalence axioms]] (being reviewed)
|-
|[[Guidelines for new Molecular Functions]] (new)
|-
|[[Guidelines for new Biological Processes]] (new)
|-
|[[Guidelines for new Cellular Components]] (new)
|-
!colspan="2" |Modifying existing terms
|-
|rowspan="4"|[[Principles for Modifying an Existing Ontology Term]] (to be reviewed)
|[[Deleting Asserted Subclasses]]
|-
|[[Adding Term Comments]]
|-
|[[Adding a Term to a GO Subset (Slim)]]
|-
|[[Adding Taxon Restrictions]]
|-
!colspan="2" |Term obsoletion
|-
|rowspan="2" |[[Principles for term obsoletion]]
|[[Obsoleting an Existing Ontology Term]]
|-
|[[Restoring an Obsolete Ontology Term]]
|-
!colspan="2" |Term merges
|-
|[[Principles for merging terms]] (being reviewed)
|[[Merging Ontology Terms]]
|-
!colspan="2" |Subsets
|-
|Subset documentation (to add)
|[[Adding and Removing GO Subsets (Slims)]]
|-
!colspan="2" |Import Files
|-
| Principles for [[GO import files]]
|[[Adding Terms and Regenerating the Import Files]]
|}


===[[Adding Terms and Regenerating the Import Files]]===
==[[Relations]] General Relations Documentation Draft To be reviewed==


==[[General Gene Ontology Principles]]==
==[[New Ontology Editor Training]] To be reviewed==
====[[Guidelines for GO term definitions]] Being reviewed====
==[[Logical_Definitions]] To be reviewed==


===[[Editor Guide to has part]] To be reviewed===
==Website - to be moved to the wiki?==
===[[Editor Guide to Regulates]] To be reviewed===
===[[Guidelines for equivalence axioms]] To be reviewed===
===[[Curator_Guide:_Merge]] 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|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?==
*[[Editorial-type sections copied over from the GO website ontology documentation: MF]]
* [[http://www.geneontology.org/page/biological-process-ontology-guidelines  Biological-process-ontology-guidelines]]
* [[http://www.geneontology.org/page/biological-process-ontology-guidelines  Biological-process-ontology-guidelines]]


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=Other Ontology Development Group Activities=
=Other Ontology Development Group Activities=
===Complex Modeling===
*[[Regulation]]
*[[Noctua_meeting_140929|Modelling complex annotations in noctua - meeting 140929]]


[[Category:Ontology]][[Category:GO Editors]]
[[Category:Ontology]][[Category:GO Editors]]

Revision as of 11:48, 16 November 2018

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)

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-ontology mailing list (see Internal_email_lists to register).

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

Documentation

Setting up Protege for GO editors

Installing and Using git

Ontology Editors Daily Workflow

Editing the Ontology

General Gene Ontology Principles
New terms
Principles for creating a GO term (being reviewed) Guidelines for creating a GO term
Guidelines for creating relationships between terms (being reviewed)
Guidelines for creating disjoint terms (to be written)
Guidelines for creating a Regulation Term
Guidelines for GO textual definitions (being reviewed)
Guidelines for equivalence axioms (being reviewed)
Guidelines for new Molecular Functions (new)
Guidelines for new Biological Processes (new)
Guidelines for new Cellular Components (new)
Modifying existing terms
Principles for Modifying an Existing Ontology Term (to be reviewed) Deleting Asserted Subclasses
Adding Term Comments
Adding a Term to a GO Subset (Slim)
Adding Taxon Restrictions
Term obsoletion
Principles for term obsoletion Obsoleting an Existing Ontology Term
Restoring an Obsolete Ontology Term
Term merges
Principles for merging terms (being reviewed) Merging Ontology Terms
Subsets
Subset documentation (to add) Adding and Removing GO Subsets (Slims)
Import Files
Principles for GO import files Adding Terms and Regenerating the Import Files

Relations General Relations Documentation Draft To be reviewed

New Ontology Editor Training To be reviewed

Logical_Definitions 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)


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