Annotation: Difference between revisions

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= Group's Focus =
* 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
= Group Leaders =
= Group Leaders =
David Hill (MGI) and Kimberly Van Auken (WB)
Pascale Gaudet and Kimberly Van Auken
 
= 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?]]===
=== [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]] ==
 
== [[Tips to Produce High Quality Annotations]] ==
 
== [[Experiment-Specific Annotation Guidelines]] ==
 
== Noctua and GO-CAM Models ==
=== [http://wiki.geneontology.org/index.php/Noctua 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]]
* '''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]] ==
 
== [[Procedure for unmaintained annotations]] ==


= 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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=== 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 2019 Agenda and Minutes]]
*[[Annotation Call 2024 Agenda and Minutes]]


*Please contact David and Kimberly if there are items you would like to add to the agenda
*Please contact Kimberly or Pascale 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]]
* 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]] | [[LEGO Annotation Calls 2015 Minutes |  LEGO 2015]] | [[Annotation Call 2016 Minutes | 2016]] | [[GO-CAM and Noctua 2016 Agenda and Minutes | GO-CAM and Noctua 2016]] | [[Annotation Call 2017 Minutes | 2017]] | [[GO-CAM and Noctua 2017 Agenda and Minutes | GO-CAM and Noctua 2017]] | [[LEGO Discussion Rota | LEGO Discussion Rota 2017]] | [[Annotation Call 2018 Agenda and Minutes | 2018]] | [[GO-CAM and Noctua 2018 Agenda and Minutes | GO-CAM and Noctua 2018]] | [[Annotation Call 2019 Agenda and Minutes | 2019]] | [[GO-CAM and Noctua 2019 Agenda and Minutes | GO-CAM and Noctua 2019]] | [[Annotation Call 2020 Agenda and Minutes | 2020 ]] | [[Annotation Call 2021 Agenda and Minutes | 2021]] | [[Annotation Call 2022 Agenda and Minutes | 2022]] | [[Annotation Call 2023 Agenda and Minutes | 2023]]
 
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]
 
== 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; [https://mailman.stanford.edu/mailman/listinfo/go-consortium sign up here.]
 
=== How to Join ===
 
* Recurring meeting URL: https://stanford.zoom.us/j/976175422
 
*to join via phone: enter Meeting ID 679970729 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 ===
 
*[[GO-CAM and Noctua 2018 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 Annotation on GitHub ==
== GO Annotation on GitHub ==
* The Gene Ontology uses an issue tracker hosted on GitHub to record and track annotation issues.
* The Gene Ontology uses an issue tracker hosted on [https://github.com/geneontology GitHub] to record and track annotation issues.
* 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 ==
* The Gene Ontology uses Google drive to host notes and spreadsheets for annotation review and annotation working groups.
* The Gene Ontology uses [https://drive.google.com/drive/folders/0ABiscjZCrxjUUk9PVA 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].
* The GO Annotation folder on Google Drive may be accessed [https://drive.google.com/drive/folders/1VNacKF8KZx3KSj1nLyUcxiHKP-DnHVGr 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].
 
= History =
== [[Archived Pages]] ==


[[Category: Annotation]] [[Category:Working Groups]]
[[Category:GOC Overview]]

Latest revision as of 21:39, 7 January 2024

Group's Focus

  • 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

Group Leaders

Pascale Gaudet and Kimberly Van Auken

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 or Pascale 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 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.