Annotation: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
m (Pascale moved page Annotation Group to Annotation over redirect)
 
(222 intermediate revisions by 3 users not shown)
Line 1: Line 1:
[[Category: Annotation]] [[Category:Working Groups]]
= 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 =
= Communication =
== [[Introduction to Annotation]] ==
 
== Ontology-Specific Guidelines ==
=== [[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]] ==
== Annotation Conference Calls ==
== Noctua and GO-CAM Models ==
== Annotation Extensions ==
==[[Annotation Review Request]] ==


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


= Communication =
* 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.]


=== Annotation Conference Calls ===
=== How to Join ===


* Calls are held on the 2nd and 4th Tuesday of each month at 4:00pm GMT, 11:00am EST, 8:00am PST
*Please consult the GO calendar for the meeting URL.
* Please contact David and Kimberly if there are items you would like to add to the agenda
* Recurring meeting URL: https://stanford.zoom.us/j/976175422


*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
*from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622
*from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622


*[[Annotation Call 2018 Minutes]]
=== Agenda and Minutes ===
 
*[[LEGO Discussion Rota]]
 
* 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]]
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]
 
=== GO-CAM Calls ===
 
*Calls are held on the 2nd and 4th Wednesday of each month at 4:00pm GMT, 11:00am EST, 8:00am PST
* Please contact David and Kimberly if there are items you would like to add to the agenda
 
 
*[[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]]
 
[[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]
*[[Annotation Call 2024 Agenda and Minutes]]


=== Issues for the Annotation Group ===
*Please contact Kimberly or Pascale if there are items you would like to add to the agenda
# Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)


[[Annotations to Catalytic activity with IPI]]
* 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]]
   
[[Annotation Quality Control Checks]]


[[Action items from March 2010 GOC meeting]]
== GO Annotation on GitHub ==
* 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]


====How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?====
== GO Annotation on Slack ==
OBO-Edit can load files from the disk OR from a URL.<br>
*The GO consortium uses [https://geneontologyworkspace.slack.com/home GO Slack] as an informal chat service.
Choose the "File -> Load..." menu option<br>
*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.
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>
== 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].


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