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==Purpose==
= Group Leaders =
==Group Leaders==
Pascale Gaudet and Kimberly Van Auken
Rachael Huntley (GOA@UniProt) and Rama Balakrishnan (SGD) with help from Pascale (dictyBase/Ref.genome project).


==GO Annotation Meetings==
=Mission statement=
[http://gocwiki.geneontology.org/index.php/2010_GO_camp_Meeting_Logistics 2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010 ]
* 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


[[Guidelines from Annotation Camp]]
= Annotation Documentation =


[http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford Annotation Meeting Stanford, CA, Feb 2012]
[[Annotation Guidelines]]


==Migration of annotating groups to Protein2GO==
==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
|-


[[Procedure for migration of protein annotations to Protein2GO]]
|[[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
|
|}


[[Extension of Protein2GO to non-UniProtKB Identifiers - Conference Call, Monday, December 9, 2013 5pm GMT/12pm EST/9am PST]]
==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
|
|}


==Activities==
== Noctua and GO-CAM ==
{| class="wikitable"
!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-
|}


*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]
==Annotation quality control==
*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap 2011]
*[[Media:AnnotationRoadMap.pdf | RoadMap]] (PDF file - provides project goals with time line)
*Educate GOC curators about best annotation practice;
*Enforce annotation rules/policies within GOC
*Maintain the annotation/evidence code documentation
**[[Mock-ups of new GOC Annotation pages]]
*Train/assist new groups with annotations: see [[How_External_Communities_can_contribute_annotations_to_the_GO_Consortium]]
*Educate and keep all the annotating groups up-to-date with changes in GAF format


*Annotation Extensions
{| class="wikitable"
**[[Annotation Extension Relation Subsets]]
!Topic
**[[Column 16: Cell Type]]
! Status
**[[Column 16: Targets]]
! Last reviewed
**[[Issues with Annotation Extension relations]]
|-
|[[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
|}


*Keep all curators up-to-date with ontology development and how it affects annotations
==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
|}


*[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.
= Communication =
*[[Evidence Code Ontology (ECO)]] - Proposal to represent evidence in an ontology
*[[Proposal for cron tabs]] - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences
*[[Examples for phylogeny based evidence codes]]
*[[Ideas for GOC community curation tool]]
*[[Protein Complex ids as GO annotation objects]]
*[[LEGO-style annotation ideas]]
* [[Proposed Developments to the GAF annotation format]]
*[[InterPro2GO Session October 4th 2011]]
*[[MF-BP inferences]]
*[[Protein Binding clean up]]
*[[Annotation Guidance Pages]]
*[[Evidence Code proposals]]
*[[With/From field restrictions for evidence codes]]
*[[Core Consortium annotation activities]]
*[[:Category:GPAD|GPAD]]


*[[Common Annotation Framework Specification]]
== Annotation Conference Calls ==
*[[gp2protein file]]
*[[gp2rna file]]
*[[gp_unlocalized file]]
*[[mechanisms for reducing annotation redundancy]]
*[[Annotations to Cell Fraction-type terms]]
*[[TermEnrichment: Gold Standard Data Sets]]


==How To?==
=== When ===
How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?<br>
OBO-Edit can load files from the disk OR from a URL.<br>
Choose the "File -> Load..." menu option<br>
Choose the OBO File Adapter<br>
Type http://www.geneontology.org/ontology/gene_ontology.obo into the filename box<br>
(From:http://www.geneontology.org/newsletter/archive/200705.shtml#tip)


To see the has_part relationships, use this URL for the extended GO version:<br>
* 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.]


http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
=== How to Join ===


==Annotation Conference calls==
*Please consult the GO calendar for the meeting URL.


* Calls are held on the 2nd and 4th Tuesday of each month. At 4pm GMT, 8am PDT. Please add items you would like discussed into the agenda for the next call, or contact Rachael or Rama.
*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


* Past Annotation Call Minutes: [[Annotation Call 2010 Minutes | 2010]] | [[Annotation Call 2011 Minutes |2011]] | [[Annotation Call 2012 Minutes | 2012]] | [[Annotation Call 2013 Minutes | 2013]]
=== Agenda and Minutes ===


*2013
*[[Annotation Call 2022 Agenda and Minutes]]
* [[Annotation Conf. Call, January 22, 2013]]
* [[Annotation Conf. Call February 12, 2013]] Cancelled
* [[Annotation Conf. Call February 26, 2013]]
* [[Annotation Conf. Call April 23, 2013]]
* [[Annotation Conf. Call May 28, 2013]]
* [[Annotation Conf. Call June 11, 2013]]
* [[Annotation Conf. Call July 9, 2013]]
* [[Annotation Conf. Call July 23, 2013]]
* [[Annotation Conf. Call August 13, 2013]]
* [[Annotation Conf. Call August 27, 2013]]
* [[Annotation Conf. Call September 10th, 2013]]
* [[Annotation Conf. Call September 24th, 2013]]
* [[Annotation Conf. Call October 22, 2013]]
* [[Annotation Conf. Call November 26, 2013]]
* [[Annotation Conf. Call December 10, 2013]]


==Monthly Reports==
*[[Annotation Call 2021 Agenda and Minutes]]
*[[September2011_Annotation_Advocacy_Report|September 2011]]
*[[August2011_Annotation_Advocacy_Report|August 2011]]
*[[July2011_Annotation_Advocacy_Report|July 2011]]
*[[June2011_Annotation_Advocacy_Report|June 2011]]
*[[May2011_Annotation_Advocacy_Report|May 2011]]
*[[April2011_Annotation_Advocacy_Report|April 2011]]
*[[March2011_Annotation_Advocacy_Report|March 2011]]
*[[February2011_Annotation_Advocacy_Report|February 2011]]
*[[January2011_Annotation_Advocacy_Report|January 2011]]
*[[December2010_Annotation_Advocacy_Report|December 2010]]
*[[November2010_Annotation_Advocacy_Report|November 2010]]
*[[October2010_Annotation_Advocacy_Report|October 2010]]
*[[September2010_Annotation_Advocacy_Report|September 2010]]
*[[August2010_Annotation_Advocacy_Report|August 2010]]
*[[July2010_Annotation_Advocacy_Report|July 2010]]
*[[Jun2010_Annotation_Advocacy_Report|June 2010]]


==Meeting calendar==
*[[Annotation Call 2020 Agenda and Minutes]]
[[Annotation_topics for next meeting]]


[[Annotation_31Jan10]]
*Please contact Kimberly if there are items you would like to add to the agenda


[[Annotation_21Dec10]]
* 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]]


[[Annotation_19Oct10]]
== GO-CAM and Noctua Calls ==


[[Annotation_21Sept10]]
Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.


[[Annotation_17Aug10]]
We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation.


[[Annotation_04Aug10]]
=== Agenda and Minutes ===


[[Annotation_19July10]]
*[[GO-CAM and Noctua 2019 Agenda and Minutes]]


[[Annotation_22June10]]
* 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]]


[[Annotation_08June10]]
== 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]


[[Annotation_01June10]]
== 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.


[[Annotation_17May10]]
== 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].


[[Annotation_29Apr10]]
== 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].


[[Annotation_15Apr10]]
=Focused annotation projects=
* [[Kidney Development]] (2009/2010)
* [[Immunology]] (2006)


[[Annotation_08Apr10]]


[[Annotation_22Mar10]]
=PAGES TO REVIEW=


[[Annotation_15Mar10]]
==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]]


[[Annotation_10Apr10]]
==To delete, archive, or retire==
* [[Database_Objects]]
* [[GO_annotation_fields_required_for_correct_display]]


==Metrics of success==
=To review=
* [[Tools_ID_Mapping]]




* [[Annotations removed as a result of Annotation QCs]]
= History =
== [[Archived Pages]] ==


* [http://go.berkeleybop.org/news4go/node/80| Moved to GAF2.0 format on the 1st June 2010]


==Process==
[[Category: GOC Overview]]
 
[http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management Annotation Issues]
 
==Issues for the Annotation Group==
# Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)
 
[[Annotations to Catalytic activity with IPI]]
[[Annotation Quality Control Checks]]
 
[[Action items from March 2010 GOC meeting]]

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