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[[Category: Annotation]] [[Category:Working Groups]]
= Group Leaders =
= Group Leaders =
David Hill (MGI) and Kimberly Van Auken (WB)
David Hill (MGI) and Kimberly Van Auken (WB)
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== [[Introduction to Annotation]] ==
== [[Introduction to Annotation]] ==


== Ontology-Specific Guidelines ==
== Ontology-Specific Annotation Guidelines ==
 
=== [[Molecular Function]] ===
 
=== [[Cellular Component]] ===
 
=== [[Biological Process]] ===
=== [[Biological Process]] ===
*Annotation Relations
*Term-specific Guidelines
=== Molecular Function ===
*Annotation Relations
*Term-specific Guidelines
=== Cellular Component ===
*Annotation Relations
*Term-specific Guidelines


== [[Guide to GO Evidence Codes]] ==
== [[Guide to GO Evidence Codes]] ==
== [[Tips to Produce High Quality Annotations]] ==
== Noctua and GO-CAM Models ==
== Noctua and GO-CAM Models ==
== Annotation Extensions ==
== [[Annotation Extensions]] ==
 
==[[Annotation Review Request]] ==
==[[Annotation Review Request]] ==


== Annotation File Pipelines ==
== [[Annotation File Pipelines]] ==
*[[How to run Mike Cherry's filtering script locally before checking the GAF into SVN?]]


= Communication =
= Communication =


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


==== 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 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.
* Calls are scheduled on the GO's Google calendar.  Please request access to the calendar if you don't have it.


==== How to Join ====
=== How to Join ===


* Recurring meeting URL: https://stanford.zoom.us/j/976175422
* Recurring meeting URL: https://stanford.zoom.us/j/976175422
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*from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622
*from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622


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


*[[Annotation Call 2018 Minutes]]
*[[Annotation Call 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: [[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]]
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*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]


=== GO-CAM Calls ===
== GO-CAM and Noctua Calls ==


*Calls are held on the 2nd and 4th Wednesday of each month at 4:00pm GMT, 11:00am EST, 8:00am PST
=== When ===
* Please contact David and Kimberly if there are items you would like to add to the agenda


* 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.


*[[LEGO Annotation Calls 2015 Minutes | 2015]]
=== How to Join ===
*2016
[[LEGO January 4, 2016]]


[[LEGO January 18, 2016]]
* Recurring meeting URL: https://stanford.zoom.us/j/679970729


[[LEGO February 1, 2016]]
*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


[[LEGO February 15, 2016]]
=== Agenda and Minutes ===


[[LEGO March 7, 2016]]
*[[GO-CAM and Noctua 2018 Agenda and Minutes]]


[[LEGO March 21, 2016]]
*Please contact David and Kimberly if there are items you would like to add to the agenda


[[LEGO March 28, 2016]]
* 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]]


[[LEGO April 4, 2016]]
== 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 [https://github.com/geneontology/go-annotation here].


[[LEGO April 25, 2016]]
== 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 [https://drive.google.com/drive/folders/0B8kRPmmvPJU3fmNRM2dYTnJmVXg4bG52bTZIdk8wdU53R2F1MDlubG90Rll5LTZqbEVVN3c here].


[[LEGO May 2, 2016]]
= History =
== [[Archived Pages]] ==


[[LEGO May 9, 2016]]
[[Category: Annotation]] [[Category:Working Groups]]
 
[[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]]
 
[[LEGO October 5, 2016]]
 
[[LEGO October 10, 2016]]
 
[[LEGO October 17, 2016]]
 
[[LEGO October 24, 2016]]
 
[[LEGO October 31, 2016]]
 
[[GO-CAM May 10th, 2016]]
 
[[GO-CAM May 24th, 2017]]
 
[[GO-CAM June 14th, 2017]]
 
[[GO-CAM June 28th, 2017]]
 
[[GO-CAM July 12th, 2017]]
 
[[GO-CAM ectopic meeting July 19th 2017]]
 
[[GO-CAM July 26th, 2017]]
 
[[GO-CAM August 9th, 2017]]
 
[[GO-CAM August 23, 2017]]
 
[[GO-CAM Sept 13, 2017]]
 
[[GO-CAM Sept 27, 2017]]
 
[[GO-CAM October 25th, 2017]]
 
[[GO-CAM November 8th, 2017]]
 
[[GO-CAM November 22, 2017]]
 
[[GO-CAM December 13, 2017]]
 
=== Old GPAD Calls ===
 
[[LEGO GAF/GPAD September 28, 2016]]
 
[[LEGO GAF/GPAD October 5, 2016]]
 
=== GitHub ===
 
=== Gene Ontology on Google Drive ===
 
== 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]
 
= Archived Pages =
 
=== GO Annotation Meetings ===
[http://gocwiki.geneontology.org/index.php/2010_GO_camp_Meeting_Logistics 2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010 ]
 
[[Guidelines from Annotation Camp]]
 
[http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford Annotation Meeting Stanford, CA, Feb 2012]
 
=== Migration of annotating groups to Protein2GO ===
 
[[Procedure for migration of protein annotations to Protein2GO]]
 
[[Extension of Protein2GO to non-UniProtKB Identifiers]]
 
=== Activities ===
 
*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]
*[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
**[[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
 
*[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.
*[[Evidence Code Ontology (ECO)]] - Proposal to represent evidence in an ontology
*[[Proposal for cron tabs]] - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences
*[[Examples for phylogeny based evidence codes]]
*[[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]]
*[[gp2protein file]]
*[[gp2rna file]]
*[[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]]
 
=== 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]]
 
=== 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]]
 
====How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?====
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>
 
http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo

Revision as of 12:54, 19 January 2018

Group Leaders

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

Annotation Documentation

Introduction to Annotation

Ontology-Specific Annotation Guidelines

Molecular Function

Cellular Component

Biological Process

Guide to GO Evidence Codes

Tips to Produce High Quality Annotations

Noctua and GO-CAM Models

Annotation Extensions

Annotation Review Request

Annotation File Pipelines

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.

How to Join

  • to join via phone: enter Meeting ID 976175422 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.

How to Join

  • 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

  • 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.

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.

History

Archived Pages

Retrieved from "https://wiki.geneontology.org/index.php?title=Annotation&oldid=67146"