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= Annotation Documentation =
= Annotation Documentation =
== [[Introduction to Annotation]] ==
== [[Introduction to Annotation]] ==
==[[Annotation conventions]]==
==[[GO Annotation Standard Operating Procedures]]==


== Ontology-Specific Guidelines ==
== Ontology-Specific Guidelines ==
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== Topic-Specific Guidelines ==
== Topic-Specific Guidelines ==
=== [[Annotating from phenotypes]]===
=== [[Annotating regulation]]===
=== [[Annotating binding]]===
=== [[When should you remove old annotations?]]===
=== [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] ===
=== [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)] ===
=== [ftp://ftp.geneontology.org/pub/go/www/txnAnnotationGuide.pdf Transcription Annotation Guide (2012)] ===
=== [[MicroRNA_GO_annotation_manual]]===
=== [[Guidelines for checkpoints]]===


== [[Guide to GO Evidence Codes]] ==
== [[Guide to GO Evidence Codes]] ==
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== Noctua and GO-CAM Models ==
== Noctua and GO-CAM Models ==
=== [http://wiki.geneontology.org/index.php/Noctua Noctua Curation Guide] ===


== [[Annotation Extensions]] ==
== [[Annotation Extensions]] ==
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== [[Annotation Quality Control]] ==
== [[Annotation Quality Control]] ==
===GO rules===
(Documentation in progress): https://github.com/geneontology/go-site/tree/master/metadata/rules
Will replace: [[Annotation Quality Control Checks]]
* '''GO rules reports'''
** Snapshot (the report groups should monitor daily or weekly): http://snapshot.geneontology.org/reports/gorule-report.html
** Latest Official Monthly Release (the errors present in our most up to date release): http://current.geneontology.org/reports/gorule-report.html
===[[Annotation Review Request]]===
How the GOC uses GitHub to request review of annotations
=== [[Proposal for Author Feedback for annotations]] ===
* To be implemented
=== [[Annotations removed as a result of Annotation QCs]] ===
*This is an old attempt at metrics for reviewed annotations.  Archive??


== [[Annotation File Pipelines]] ==
== [[Annotation File Pipelines]] ==
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=== How to Join ===
=== How to Join ===


* Recurring meeting URL: https://stanford.zoom.us/j/976175422
*Please consult the GO calendar for the meeting URL.


*to join via phone: enter Meeting ID 976175422 after dialing in
*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 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 UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717
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=== Agenda and Minutes ===
=== Agenda and Minutes ===


*[[Annotation Call 2018 Agenda and Minutes]]
*[[Annotation Call 2019 Agenda and Minutes]]


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


*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]
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=== How to Join ===
=== How to Join ===


* Recurring meeting URL: https://stanford.zoom.us/j/679970729
*Please consult the GO calendar for the meeting URL.


*to join via phone: enter Meeting ID 679970729 after dialing in
*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 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 UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717
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=== Agenda and Minutes ===
=== Agenda and Minutes ===


*[[GO-CAM and Noctua 2018 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
*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]]
* 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 ==
== GO Annotation on GitHub ==
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== GO Consortium Mailing List ==
== GO Consortium Mailing List ==
* Reminders about conference calls are sent to the go-consortium mailing list.
* Reminders about conference calls are sent to the go-consortium mailing list.
* To subscribe to the list, please click [https://mailman.stanford.edu/mailman/listinfo/go-consortium here].
* To subscribe to the go-consortium mailing list, please click [https://mailman.stanford.edu/mailman/listinfo/go-consortium here].


= History =
= History =

Revision as of 12:42, 6 February 2019

Group Leaders

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

Annotation Documentation

Introduction to Annotation

Annotation conventions

GO Annotation Standard Operating Procedures

Ontology-Specific Guidelines

Molecular Function

Cellular Component

Biological Process

Annotation Relations

Topic-Specific Guidelines

Annotating from phenotypes

Annotating regulation

Annotating binding

When should you remove old annotations?

Apoptosis Curation Manual

Transcription Annotation Guide (2018)

Transcription Annotation Guide (2012)

MicroRNA_GO_annotation_manual

Guidelines for checkpoints

Guide to GO Evidence Codes

Tips to Produce High Quality Annotations

Experiment-Specific Annotation Guidelines

Noctua and GO-CAM Models

Noctua Curation Guide

Annotation Extensions

External Mappings

Annotation Quality Control

GO rules

(Documentation in progress): https://github.com/geneontology/go-site/tree/master/metadata/rules Will replace: Annotation Quality Control Checks

Annotation Review Request

How the GOC uses GitHub to request review of annotations

Proposal for Author Feedback for annotations

  • To be implemented

Annotations removed as a result of Annotation QCs

  • This is an old attempt at metrics for reviewed annotations. Archive??

Annotation File Pipelines

Procedure for unmaintained annotations

Communication

Annotation Conference Calls

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 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

When

  • 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; 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 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 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.

History

Archived Pages