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The purpose of this working group is to outreach to potential annotating groups with a view to getting annotation of maximally feasible quality across all species. The GO endeavours to bring together information about all research species.
= Group Leaders =
Pascale Gaudet and Kimberly Van Auken


Within the GO, there are a number of excellent databases annotating model species but we need more manpower to help complete this task. There are also many species that are not being annotated at all yet and so we need to find new annotation groups to cover these species.
=Mission statement=
* Educate GOC curators about best annotation practice
* Enforce annotation rules/policies within GOC
* Maintain the annotation/evidence code documentation
* Train/assist new groups with annotations
* Educate and keep all the annotating groups up-to-date with changes in file formats
* Keep contributing groups up-to-date with ontology development and how it affects annotations


Many of these currently unannotated species are less well funded research species that are used to study unusual biological phenomena/processes. Manual annotation of such processes is essential if we are to capture the full range of gene function. This annotation will also allow us to extrapolate information back to the uncharacterised gene products of the reference genomes.
= Annotation Documentation =


''' Group Meetings'''
[[Annotation Guidelines]]


*[[Meeting Rota]]
==General Annotation Documentation==
*[[Annotation Outreach group meetings|Meeting minutes]]
{| class="wikitable"
!Topic
! Status
! Last reviewed
|-
|[http://geneontology.org/docs/go-annotations/ General introduction to GO annotation - GO website]
| Current
| 2021-01-27
|-
|[[Elements of an annotation]]
| Current
| 2019-04-11
|-
|[[Guide to GO Evidence Codes]]
| Current
| 2018-02-23
|-


|[[Tips to Produce High Quality Annotations]]
| Current
| 2019-04-11
|-
| [[Annotation Relations]]
| Draft
|
|-
! colspan="3"| Annotation Extensions
|-
|[https://docs.google.com/spreadsheets/d/1vkBVTyUg1tjipUtYGan5Ob0vE14H_j6O-PuTH9619eg/edit#gid=1456134218 Annotation Extensions - Summary]
| Current
| 2021-06-10
|-
| [[Annotation Extension | Annotation Extensions]]
| Being reviewed
|
|-
| [[Annotation Extension: Capturing cell and tissue types]]
| To be reviewed
|
|-
| [[Annotation Extension: Capturing participants]]
| To be reviewed
|
|}


'''Sections'''
==Topic-Specific Guidelines==
{| {{Prettytable}} class='sortable'
!Topic
! Status
! Last reviewed
|-
|[[Annotating from phenotypes]]
| Current
| 2018-12-18
|-
| [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual]
|
|
|-
| [[MicroRNA_GO_annotation_manual]]
| Current
| 2020-03-23
|-
| [https://docs.google.com/document/d/1bqCxx7QUblrc9q4PIynbJzoCXv248UWBxJa7fguJyXs/edit# Transcription factors annotation manual]
| Current
| 2021-06-09
|-
| [http://gocwiki.geneontology.org/index.php/Signaling Signaling]
|
|
|-
| [[Non-catalytic Molecular Functions]]
| Current
| 2022-05-19
|-
| [[Annotating binding]]
| Draft
| 2020-05-04
|-
| [[Annotating ligand-receptor pathways]]
| To be reviewed
| > 5 years old
|-
| [[Annotating regulation]]
| To be reviewed
| > 5 years old
|-
| [[Annotating downstream processes]]
| Draft
|
|-
| [[Guidelines for checkpoints]]
| To be reviewed
|
|-
| [[Response to x annotation guidelines]]
| To be reviewed
|
|-
| [[Multi-species processes]]
| To be reviewed
|
|-
| [[Experiment-Specific Annotation Guidelines]]
| Draft
|
|}


*[[Annotation Outreach group summary|Group summary]]
== Noctua and GO-CAM ==
*[[Annotation Outreach group reports|Reports]]
{| class="wikitable"
*[[Annotation Outreach group materials|Posters, talks and tutorials]]
!Topic
! Status
! Last reviewed
|-
| [[Noctua |Noctua Curation Guide]]
| Current
| 2021-
|-
| [https://docs.google.com/document/d/1Yo2O7LWj1wdRGbbOlaxX_AFDl99T-P59JOf5YoebX0Q/edit# ART Documentation]
| Current
| 2021-05-26
|-
| [[Noctua_MOD_Imports |Importing MOD annotations into Noctua]]
| Draft
| 2021-
|}


==Annotation quality control==


'''Work in Progress'''<br>
{| class="wikitable"
[[SOPs in progress]]
!Topic
! Status
! Last reviewed
|-
|[[Annotation Review Request]]
| Current
| 2022-04-22
|-
|[[Annotation maintenance]]  
| Current
| 2020-08-20
|-
|[[Proposal for Author Feedback for annotations]]
| Draft
| 2019-04-16
|-
|[[QC procedures from contributing groups]]
| Draft
| 2019-03-14
|}


==Guidelines for new Groups/new submissions ==
{| class="wikitable"
!Topic
! Status
! Last reviewed
|-
| [[General guidance to submit annotations to the GO consortium]]
| Under review
| > 5 years ago
|}


'''Outreach Practice'''
= Communication =


[[Standard letters]]
== Annotation Conference Calls ==


=== When ===


'''Outreach Records'''
* Calls are held on Tuesdays at 4:00pm GMT, 11:00am EST, 8:00am PST
* 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-consortium mailing list; [https://mailman.stanford.edu/mailman/listinfo/go-consortium sign up here.]


[[Text Version]]
=== How to Join ===
 
*Please consult the GO calendar for the meeting URL.
 
*to join via phone: enter Meeting ID found on the GO calendar after dialing in
*from US: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll)
*from UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717
*from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622
 
=== Agenda and Minutes ===
 
*[[Annotation Call 2022 Agenda and Minutes]]
 
*[[Annotation Call 2021 Agenda and Minutes]]
 
*[[Annotation Call 2020 Agenda and Minutes]]
 
*Please contact Kimberly if there are items you would like to add to the agenda
 
* Past Annotation Call Minutes: [[Annotation Call 2010 Minutes | 2010]] | [[Annotation Call 2011 Minutes |2011]] | [[Annotation Call 2012 Minutes | 2012]] | [[Annotation Call 2013 Minutes | 2013]] | [[Annotation Call 2014 Minutes | 2014]] | [[Annotation Call 2015 Minutes | 2015]] | [[Annotation Call 2016 Minutes | 2016]] | [[Annotation Call 2017 Minutes | 2017]] | [[LEGO Discussion Rota | LEGO Discussion Rota 2017]] | [[Annotation Call 2018 Agenda and Minutes | 2018]] | [[Annotation Call 2019 Agenda and Minutes | 2019]]
 
== GO-CAM and Noctua Calls ==
 
Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.
 
We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation.
 
=== Agenda and Minutes ===
 
*[[GO-CAM and Noctua 2019 Agenda and Minutes]]
 
* Past Annotation Call Minutes:  [[LEGO Annotation Calls 2015 Minutes | 2015]] | [[GO-CAM and Noctua 2016 Agenda and Minutes | 2016]] | [[GO-CAM and Noctua 2017 Agenda and Minutes | 2017]] | [[GO-CAM and Noctua 2018 Agenda and Minutes | 2018]]
 
== GO Annotation on GitHub ==
* The Gene Ontology uses an issue tracker hosted on GitHub to record and track annotation issues.
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-annotation here].
* Contact information for each group that contributes to the consortium is available [https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv here]
 
== GO Annotation on Slack ==
*The GO consortium uses [https://geneontologyworkspace.slack.com/home GO Slack] as an informal chat service.
*Curators are free to ask questions or share ideas on Slack, with issues elevated to more formal tracking (i.e. [https://github.com/geneontology/go-annotation github/go-annotation] or [[Annotation#Annotation_Documentation |wiki documentation]]), as appropriate.
 
== GO Annotation on Google Drive ==
* The Gene Ontology uses Google drive to host notes and spreadsheets for annotation review and annotation working groups.
* The GO Annotation folder on Google Drive may be accessed [https://drive.google.com/drive/folders/0B8kRPmmvPJU3fmNRM2dYTnJmVXg4bG52bTZIdk8wdU53R2F1MDlubG90Rll5LTZqbEVVN3c here].
 
== GO Consortium Mailing List ==
* Reminders about conference calls are sent to the go-consortium mailing list.
* To subscribe to the go-consortium mailing list, please click [https://mailman.stanford.edu/mailman/listinfo/go-consortium here].
 
=Focused annotation projects=
* [[Kidney Development]] (2009/2010)
* [[Immunology]] (2006)
 
 
=PAGES TO REVIEW=
 
==Intro to GO==
* [[Submit_GO_annotations]]
* [[Beginning Annotation SOP]]
* Can we use the way this is presented ?  [http://wiki.geneontology.org/images/b/b1/GOA_training_cutdown.pdf GOA Training slides]
* [[Guidelines_for_literature-based_curation]]
* [[Guidelines for electronic annotation methods]]
* MGI IEA pipeline 2008: [[Electronic - Harold and Evelyn]]
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1176400/ Clark et al., 2005]
* [[Contributing_GO_Annotations]]
* [[With_field]]
* [[Authoritative_Database_Groups]]
* Regulation [http://wiki.geneontology.org/index.php/Category:Regulation]
* https://docs.google.com/document/d/1HyOW6oYu9ZxQlHRbZqIgv73L-_fdaXmFhtZPi83DBSU/edit
* http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management
* http://wiki.geneontology.org/index.php/Annotation_Issues_and_Management
* [[GO annotation activities by central GO Consortium members]]
 
==To delete, archive, or retire==
* [[Database_Objects]]
* [[GO_annotation_fields_required_for_correct_display]]
 
=To review=
* [[Tools_ID_Mapping]]
 
 
= History =
== [[Archived Pages]] ==
 
 
[[Category: GOC Overview]]

Revision as of 05:32, 19 May 2022

Group Leaders

Pascale Gaudet and Kimberly Van Auken

Mission statement

  • Educate GOC curators about best annotation practice
  • Enforce annotation rules/policies within GOC
  • Maintain the annotation/evidence code documentation
  • Train/assist new groups with annotations
  • Educate and keep all the annotating groups up-to-date with changes in file formats
  • Keep contributing groups up-to-date with ontology development and how it affects annotations

Annotation Documentation

Annotation Guidelines

General Annotation Documentation

Topic Status Last reviewed
General introduction to GO annotation - GO website Current 2021-01-27
Elements of an annotation Current 2019-04-11
Guide to GO Evidence Codes Current 2018-02-23
Tips to Produce High Quality Annotations Current 2019-04-11
Annotation Relations Draft
Annotation Extensions
Annotation Extensions - Summary  Current 2021-06-10
Annotation Extensions Being reviewed
Annotation Extension: Capturing cell and tissue types To be reviewed
Annotation Extension: Capturing participants To be reviewed

Topic-Specific Guidelines

Topic Status Last reviewed
Annotating from phenotypes Current 2018-12-18
Apoptosis Curation Manual
MicroRNA_GO_annotation_manual Current 2020-03-23
Transcription factors annotation manual Current 2021-06-09
Signaling
Non-catalytic Molecular Functions Current 2022-05-19
Annotating binding Draft 2020-05-04
Annotating ligand-receptor pathways To be reviewed > 5 years old
Annotating regulation To be reviewed > 5 years old
Annotating downstream processes Draft
Guidelines for checkpoints To be reviewed
Response to x annotation guidelines To be reviewed
Multi-species processes To be reviewed
Experiment-Specific Annotation Guidelines Draft

Noctua and GO-CAM

Topic Status Last reviewed
Noctua Curation Guide Current 2021-
ART Documentation Current 2021-05-26
Importing MOD annotations into Noctua Draft 2021-

Annotation quality control

Topic Status Last reviewed
Annotation Review Request Current 2022-04-22
Annotation maintenance Current 2020-08-20
Proposal for Author Feedback for annotations  Draft  2019-04-16
QC procedures from contributing groups Draft 2019-03-14

Guidelines for new Groups/new submissions

Topic Status Last reviewed
General guidance to submit annotations to the GO consortium Under review > 5 years ago

Communication

Annotation Conference Calls

When

  • Calls are held on Tuesdays at 4:00pm GMT, 11:00am EST, 8:00am PST
  • 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-consortium mailing list; sign up here.

How to Join

  • Please consult the GO calendar for the meeting URL.
  • to join via phone: enter Meeting ID found on the GO calendar after dialing in
  • from US: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll)
  • from UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717
  • from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622

Agenda and Minutes

  • Please contact Kimberly if there are items you would like to add to the agenda

GO-CAM and Noctua Calls

Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.

We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation.

Agenda and Minutes

GO Annotation on GitHub

  • The Gene Ontology uses an issue tracker hosted on GitHub to record and track annotation issues.
  • The go-annotation repo on GitHub may be accessed here.
  • Contact information for each group that contributes to the consortium is available here

GO Annotation on Slack

  • The GO consortium uses GO Slack as an informal chat service.
  • Curators are free to ask questions or share ideas on Slack, with issues elevated to more formal tracking (i.e. github/go-annotation or wiki documentation), as appropriate.

GO Annotation on Google Drive

  • The Gene Ontology uses Google drive to host notes and spreadsheets for annotation review and annotation working groups.
  • The GO Annotation folder on Google Drive may be accessed here.

GO Consortium Mailing List

  • Reminders about conference calls are sent to the go-consortium mailing list.
  • To subscribe to the go-consortium mailing list, please click here.

Focused annotation projects


PAGES TO REVIEW

Intro to GO

To delete, archive, or retire

To review


History

Archived Pages