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[[Category: Annotation]] [[Category:Working Groups]]
= Group's Focus =
==Group Leaders==
* Educate GOC curators about best annotation practice
David Hill (MGI) and Kimberly Van Auken (WB)
* 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 Meetings==
= 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 =


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


==Migration of annotating groups to Protein2GO==
=== When ===


[[Procedure for migration of protein annotations to Protein2GO]]
* 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.]


[[Extension of Protein2GO to non-UniProtKB Identifiers]]
=== 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


==Activities==
=== Agenda and Minutes ===


*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]
*[[Annotation Call 2024 Agenda and Minutes]]
*[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
*Please contact Kimberly or Pascale if there are items you would like to add to the agenda
**[[Annotation Extension Relation Subsets]]
**[[Column 16: Cell Type]]
**[[Column 16: Targets]]
**[[Issues with Annotation Extension relations]]
**[[Annotation Extension Relation Documentation Jamboree]]
**[[Guidance for updating deprecated Annotation Extension Relations]]


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


*[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.
== GO Annotation on GitHub ==
*[[Evidence Code Ontology (ECO)]] - Proposal to represent evidence in an ontology
* The Gene Ontology uses an issue tracker hosted on [https://github.com/geneontology GitHub] to record and track annotation issues.
*[[Proposal for cron tabs]] - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-annotation here].
*[[Examples for phylogeny based evidence codes]]
* 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]
*[[Ideas for GOC community curation tool]]
*[[Protein Complex ids as GO annotation objects]]
** [[Annotation guidelines for annotating complexes as annotation objects]]
** [[Protein Complex Conference Call June19, 2015]]
** [[Protein Complex Conference Call July15, 2015]]
*[[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]]
== GO Annotation on Slack ==
*[[gp2protein file]]
*The GO consortium uses [https://geneontologyworkspace.slack.com/home GO Slack] as an informal chat service.
*[[gp2rna file]]
*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.
*[[gp_unlocalized file]]
*[[mechanisms for reducing annotation redundancy]]
*[[Annotations to Cell Fraction-type terms]]
*[[TermEnrichment: Gold Standard Data Sets]]
*[["Response to" terms]]
*[[GAF 2.1 specs]]


==How To?==
== GO Annotation on Google Drive ==
====How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?====
* 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.
OBO-Edit can load files from the disk OR from a URL.<br>
* The GO Annotation folder on Google Drive may be accessed [https://drive.google.com/drive/folders/1VNacKF8KZx3KSj1nLyUcxiHKP-DnHVGr here].
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>
[[Category:GOC Overview]]
 
http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
 
====How to run Mike Cherry's filtering script locally before checking the GAF into SVN?====
*You need access to SVN to run the script locally. If you don't have access please write to go-admin@genome.stanford.edu
*Familiarize yourself with SVN commands (http://geneontology.org/page/svn-help)
*You need to check out the following files from SVN. The script will fail or will give you inaccurate reports if you don't have the current version of any of the files.
 
<pre>
 
> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/ontology go/ontology
username@ext.geneontology.org's password:
[this will co the entire directory]
 
> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/gene-associations/submission go/gene-associations/submission
username@ext.geneontology.org's password:
[this will co the entire directory]
 
>svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/software/utilities go/software/utilities
username@ext.geneontology.org's password:
 
> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/doc/ go/doc
username@ext.geneontology.org's password:
 
</pre>
 
Now you have the necessary files to run the script in your space.
 
* cd to the gene-associations/submission directory
<pre>
>cd go/gene-associations/submission
>../../software/utilities/filter-gene-association.pl -e -i gene_association.sgd.gz
 
You should see the filtering script report once the script runs through the file.
</pre>
 
==Annotation Conference calls==
 
* [[Annotation Call 2016 Minutes]]
* 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.
*Recurring meeting URL: https://bluejeans.com/993661940
 
to join via phone: enter Meeting ID 993661940 after dialing in
*from US: +1.408.740.7256 or +1.888.240.2560
*from UK: +44.203.608.5256
*from Switzerland: +41.81.588.0256
 
* [[Curation Consistency Rota 2016]]
 
* 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]] | [[Curation Consistency Rota | Curation Consistency Rota 2015]]
 
==LEGO calls==
Meetings are every Monday 11:30AM Eastern, 4:30PM Greenwich, 8:30AM Pacific
 
Bluejeans recurring meeting URL: https://bluejeans.com/969313231
 
to join via phone: enter Meeting ID 969313231 after dialing in
*from US: +1.408.740.7256 or +1.888.240.2560
*from UK: +44.203.608.5256
*from Switzerland: +41.81.588.0256
 
*[[LEGO Annotation Calls 2015 Minutes | 2015]]
*2016
[[LEGO January 4, 2016]]
 
[[LEGO January 18, 2016]]
 
[[LEGO February 1, 2016]]
 
[[LEGO February 15, 2016]]
 
[[LEGO March 7, 2016]]
 
[[LEGO March 21, 2016]]
 
[[LEGO March 28, 2016]]
 
[[LEGO April 4, 2016]]
 
[[LEGO April 25, 2016]]
 
[[LEGO May 2, 2016]]
 
[[LEGO May 9, 2016]]
 
[[LEGO May 16, 2016]]
 
[[LEGO May 23, 2016]]
 
[[LEGO June 6, 2016]]
 
[[LEGO June 13, 2016]]
 
[[LEGO June 20, 2016]]
 
[[LEGO June 27, 2016]]
 
[[LEGO July 11, 2016]]
 
[[LEGO July 18, 2016]]
 
[[LEGO July 25, 2016]]
 
[[LEGO August 8, 2016]]
 
[[LEGO August 15, 2016]]
 
[[LEGO August 22, 2016]]
 
[[LEGO August 29, 2016]]
 
[[LEGO September 12, 2016]]
 
[[LEGO September 19, 2016]]
 
[[LEGO September 26, 2016]]
 
 
 
[[Category:LEGO]]
 
==Monthly Reports==
*[[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_topics for next meeting]]
 
[[Annotation_31Jan10]]
 
[[Annotation_21Dec10]]
 
[[Annotation_19Oct10]]
 
[[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]]
 
[[Annotation_10Apr10]]
 
==Metrics of success==
* [[Proposal for Author Feedback for annotations]]
 
* [[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.