Annotation: Difference between revisions

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==Purpose==
= Group's Focus =
==Group Leaders==
* Educate GOC curators about best annotation practice
Emily Dimmer (GOA@UniProt) and Rama Balakrishnan (SGD) with help from Pascale (dictyBase/Ref.genome project).
* 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


==GO Annotation Camp==
= Group Leaders =
[http://gocwiki.geneontology.org/index.php/2010_GO_camp_Meeting_Logistics 2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010 ]
Pascale Gaudet and Kimberly Van Auken


[[Guidelines from Annotation Camp]]
= Communication =


==Activities==
== Annotation Conference Calls ==


*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]
=== When ===
*[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
**[[Column 16: Cell Type]]
*Keep all curators up-to-date with ontology development and how it affects annotations


*[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.
* Calls are held on Tuesdays at 4:00pm GMT, 11:00am EST, 8:00am PST
*[[Evidence Code Ontology (ECO)]] - Proposal to represent evidence in an ontology
* Calls are scheduled on the GO's Google calendar.  Please request access to the calendar if you don't have it.
*[[Proposal for cron tabs]] - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences
* Reminder emails are sent out to the go-consortium mailing list; [https://mailman.stanford.edu/mailman/listinfo/go-consortium sign up here.]
*[[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]]


==How To?==
=== How to Join ===
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>
*Please consult the GO calendar for the meeting URL.


http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
*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


==Annotation Conference calls==
=== Agenda and Minutes ===


*[[Topics for annotation call | Add your topics/issues]]
*[[Annotation Call 2024 Agenda and Minutes]]


*[[Agenda for November 8th |Annotation Jamboree, Nov 8, 2010]]
*Please contact Kimberly or Pascale if there are items you would like to add to the agenda
*[[Agenda for Dec 13th | Annotation Conf. Call, Dec 13, 2010]]
*[[Annotation Conf. Call, Jan 10, 2011]]
*[[Annotation Conf. Call, Feb 22, 2011]]
*[[Annotation Conf. Call, Mar 22, 2011]]
*[[Annotation Conf. Call, June 28, 2011]]
*[[Annotation Conf. Call, July 12, 2011]]
* Annotation Conf. Call, July 26, 2011 [[Transcription jamboree]]
*[[Annotation Conf. Call, August 9, 2011]]
*[[Annotation Conf. Call, August 23, 2011]]
*[[Annotation Conf. Call, September 13, 2011]]
*[[Annotation Conf. Call, September 27, 2011]]
*[[Annotation Conf. Call, October 4, 2011]]
*[[Annotation Conf. Call, October 18, 2011]]
*[[Annotation Conf. Call, November 2, 2011]]
*[[Annotation Conf. Call, November 16, 2011]]
*[[Annotation Conf. Call, November 30, 2011]]
*[[Annotation Conf. Call, December 14, 2011]]


==Monthly Reports==
* 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]]
*[[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==
== GO Annotation on GitHub ==
[[Annotation_topics for next meeting]]
* 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].
* 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_31Jan10]]
== 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_21Dec10]]
== GO Annotation on Google Drive ==
* 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/1VNacKF8KZx3KSj1nLyUcxiHKP-DnHVGr here].


[[Annotation_19Oct10]]
[[Category:GOC Overview]]
 
[[Annotation_21Sept10]]
 
[[Annotation_17Aug10]]
 
[[Annotation_04Aug10]]
 
[[Annotation_19July10]]
 
[[Annotation_22June10]]
 
[[Annotation_08June10]]
 
[[Annotation_01June10]]
 
[[Annotation_17May10]]
 
[[Annotation_29Apr10]]
 
[[Annotation_15Apr10]]
 
[[Annotation_08Apr10]]
 
[[Annotation_22Mar10]]
 
[[Annotation_15Mar10]]
 
==Metrics of success==
 
 
* [[Annotations removed as a result of Annotation QCs]]
 
* [http://go.berkeleybop.org/news4go/node/80| Moved to GAF2.0 format on the 1st June 2010]
 
==Process==
 
[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]]

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.