Difference between revisions of "Annotation"

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= Group Leaders =
= Group Leaders =
David Hill (MGI) and Kimberly Van Auken (WB)
Pascale Gaudet and Kimberly Van Auken


=Mission statement=
=Mission statement=
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= Annotation Documentation =
= Annotation Documentation =
== Overview of GO annotations ==
[http://geneontology.org/docs/go-annotations/ Introduction to GO annotations on the GO website]


==[[Annotation conventions]]==
[[Annotation Guidelines]]
==[[Tips to Produce High Quality Annotations]] ==
==[[GO Annotation Standard Operating Procedures]]==
==[[Annotation maintenance]]==
==[[Annotation Quality Control]]==


== Ontology-Specific Guidelines ==
==General Annotation Documentation==
{| 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
|-


=== [[Molecular Function]] ===
|[[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
|
|}


=== [[Cellular Component]] ===
==Topic-Specific Guidelines==
 
{| {{Prettytable}} class='sortable'
=== [[Biological Process]] ===
!Topic
 
! Status
=== [[Annotation Relations]] ===
! Last reviewed
 
|-
== Topic-Specific Guidelines ==
|[[Annotating from phenotypes]]
=== [[Annotating from phenotypes]]===
| Current
== Topic-Specific Guidelines under review==
| 2018-12-18
=== [[Annotating regulation]]===
|-
=== [[Annotating binding]]===
| [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual]
=== [[Annotating downstream processes]]===
|
=== [[Annotating ligand-receptor pathways]]===
|
=== [[Response to x annotation guidelines]]===
|-
=== [[Multi-species processes]]===
| [[MicroRNA_GO_annotation_manual]]
=== [http://gocwiki.geneontology.org/index.php/Signaling Signaling]===
| Current
 
| 2020-03-23
=== [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] ===
|-
=== [https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1 Transcription Annotation Guide (2018)] ===
| [https://docs.google.com/document/d/1bqCxx7QUblrc9q4PIynbJzoCXv248UWBxJa7fguJyXs/edit# Transcription factors annotation manual]
=== [ftp://ftp.geneontology.org/pub/go/www/txnAnnotationGuide.pdf Transcription Annotation Guide (2012)] ===
| Current
=== [[MicroRNA_GO_annotation_manual]]===
| 2021-06-09
=== [[Guidelines for checkpoints]]===
|-
 
| [http://gocwiki.geneontology.org/index.php/Signaling Signaling]
== [[Guide to GO Evidence Codes]] ==
|
 
|
== [[Experiment-Specific Annotation Guidelines]] - in progress ==
|-
| [[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 ==
== Noctua and GO-CAM ==
=== [http://wiki.geneontology.org/index.php/Noctua Noctua Curation Guide] ===
{| class="wikitable"
=== [http://wiki.geneontology.org/index.php/Noctua_MOD_Imports Importing MOD annotations into Noctua] ===
!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-
|}


[[Category:Annotation Working Group]]
==Annotation quality control==
[[Category:GO-CAM]]


== [[Annotation Extensions]] ==
{| class="wikitable"
!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
|}


== [[Annotation Quality Control]] ==
==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
|}


= Communication =
= Communication =
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=== When ===
=== When ===


* Calls are held on the 2nd and 4th Tuesday of each month at 4:00pm GMT, 11:00am EST, 8:00am PST  
* 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.
* 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.]
* Reminder emails are sent out to the go-consortium mailing list; [https://mailman.stanford.edu/mailman/listinfo/go-consortium sign up here.]
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=== Agenda and Minutes ===
=== Agenda and Minutes ===


*[[Annotation Call 2019 Agenda and Minutes]]
*[[Annotation Call 2022 Agenda and Minutes]]


*Please contact David and Kimberly if there are items you would like to add to the agenda
*[[Annotation Call 2021 Agenda and Minutes]]


* 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 2020 Agenda and Minutes]]


*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]
*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 ==
== GO-CAM and Noctua Calls ==


=== When ===
Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.
 
* Calls are held on the 2nd and 4th Wednesday of each month 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.]
 
=== 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
We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation.
*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 ===
=== Agenda and Minutes ===


*[[GO-CAM and Noctua 2019 Agenda and Minutes]]
*[[GO-CAM and Noctua 2019 Agenda and Minutes]]
*Please contact David and Kimberly if there are items you would like to add to the agenda


* 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]]
* 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]]
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* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-annotation here].
* 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]
* 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 ==
== GO Annotation on Google Drive ==
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* [[Submit_GO_annotations]]  
* [[Submit_GO_annotations]]  
* [[Beginning Annotation SOP]]
* [[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_literature-based_curation]]
* [[Guidelines for electronic annotation methods]]
* [[Guidelines for electronic annotation methods]]
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* https://docs.google.com/document/d/1HyOW6oYu9ZxQlHRbZqIgv73L-_fdaXmFhtZPi83DBSU/edit
* https://docs.google.com/document/d/1HyOW6oYu9ZxQlHRbZqIgv73L-_fdaXmFhtZPi83DBSU/edit
* http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management
* 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==
==To delete, archive, or retire==
* [[Database_Objects]]
* [[Database_Objects]]
* [[GO_Annotation_Usage_Guidelines]]
* [[GO_annotation_fields_required_for_correct_display]]
* [[GO_annotation_fields_required_for_correct_display]]
=To review=
* [[Tools_ID_Mapping]]


= History =
= History =
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[[Category: Annotation]]
[[Category: GOC Overview]]

Revision as of 01:54, 20 April 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
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