Difference between revisions of "Annotation"

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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]]==
+
==General Annotation Documentation==
==[[Tips to Produce High Quality Annotations]] ==
+
{| class="wikitable"
==[[GO Annotation Standard Operating Procedures]]==
+
!Topic
==[[Annotation maintenance]]==
+
! Status
==[[Annotation Quality Control]]==
+
! 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
 +
|-
  
== Ontology-Specific Guidelines ==
+
|[[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]]
 +
| To be reviewed
 +
|
 +
|-
 +
| [[Annotation Extension: Capturing cell and tissue types]]
 +
| To be reviewed
 +
|
 +
|-
 +
| [[Annotation Extension: Capturing participants]]
 +
| To be reviewed
 +
|
 +
|}
  
=== [[Molecular Function]] ===
+
==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]
 +
|
 +
|
 +
|-
 +
| [[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
 +
|
 +
|}
  
=== [[Cellular Component]] ===
+
== 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-
 +
|}
  
=== [[Biological Process]] ===
+
==Annotation quality control==
  
=== [[Annotation Relations]] ===
+
{| class="wikitable"
 +
!Topic
 +
! Status
 +
! Last reviewed
 +
|-
 +
|[[Annotation maintenance]]
 +
| Current
 +
| 2020-08-20
 +
|-
 +
|[[Annotation Quality Control]]
 +
| Draft
 +
| 2019-04-11
 +
|}
  
== Topic-Specific Guidelines ==
+
==Guidelines for new Groups/new submissions ==
=== [[Annotating from phenotypes]]===
+
{| class="wikitable"
== Topic-Specific Guidelines under review==
+
!Topic
=== [[Annotating regulation]]===
+
! Status
=== [[Annotating binding]]===
+
! Last reviewed
=== [[Annotating downstream processes]]===
+
|-
=== [[Annotating ligand-receptor pathways]]===
+
| [[General guidance to submit annotations to the GO consortium]]
=== [[Response to x annotation guidelines]]===
+
| Under review
=== [[Multi-species processes]]===
+
| > 5 years ago
=== [http://gocwiki.geneontology.org/index.php/Signaling Signaling]===
+
|}
 
 
=== [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] ===
 
=== [https://docs.google.com/document/d/1bqCxx7QUblrc9q4PIynbJzoCXv248UWBxJa7fguJyXs/edit# Transcription Annotation Guide (updated May 2020)] ===
 
=== [[MicroRNA_GO_annotation_manual]]===
 
=== [[Guidelines for checkpoints]]===
 
 
 
== [[Guide to GO Evidence Codes]] ==
 
 
 
== [[Experiment-Specific Annotation Guidelines]] - in progress ==
 
 
 
== Noctua and GO-CAM ==
 
=== [http://wiki.geneontology.org/index.php/Noctua Noctua Curation Guide] ===
 
=== [http://wiki.geneontology.org/index.php/Noctua_MOD_Imports Importing MOD annotations into Noctua] ===
 
 
 
 
 
== [[Annotation Extensions]] ==
 
  
 
= Communication =
 
= Communication =
Line 77: Line 183:
  
 
=== Agenda and Minutes ===
 
=== Agenda and Minutes ===
 +
 +
*[[Annotation Call 2021 Agenda and Minutes]]
  
 
*[[Annotation Call 2020 Agenda and Minutes]]
 
*[[Annotation Call 2020 Agenda and Minutes]]

Latest revision as of 06:21, 30 June 2021

Group Leaders

David Hill (MGI) and Kimberly Van Auken (WB)

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

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 To be 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 maintenance Current 2020-08-20
Annotation Quality Control Draft 2019-04-11

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 David and 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 gitter

  • The GO annotation group uses gitter as an informal chat service.
  • Curators are free to ask questions or share ideas on gitter, with issues elevated to more formal tracking (i.e. github/go-annotation or wiki documentation), as needed.
  • Curators can login to gitter using their github accounts.

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