Difference between revisions of "Annotation"

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[[Category: Annotation]] [[Category:Working Groups]]
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= Group Leaders =
==Purpose==
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David Hill (MGI) and Kimberly Van Auken (WB)
==Group Leaders==
 
Rama Balakrishnan (SGD) with help from Kimberly (WormBase), David Hill (MGI)
 
  
==GO Annotation Meetings==
+
=Mission statement=
[http://gocwiki.geneontology.org/index.php/2010_GO_camp_Meeting_Logistics 2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010 ]
+
* 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
  
[[Guidelines from Annotation Camp]]
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= Annotation Documentation =
 +
== Overview of GO annotations ==
 +
[http://geneontology.org/docs/go-annotations/ Introduction to GO annotations on the GO website]
  
[http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford Annotation Meeting Stanford, CA, Feb 2012]
+
==[[Annotation conventions]]==
 +
==[[Tips to Produce High Quality Annotations]] ==
 +
==[[GO Annotation Standard Operating Procedures]]==
 +
==[[Annotation maintenance]]==
 +
==[[Annotation Quality Control]]==
  
==Migration of annotating groups to Protein2GO==
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== Ontology-Specific Guidelines ==
  
[[Procedure for migration of protein annotations to Protein2GO]]
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=== [[Molecular Function]] ===
  
[[Extension of Protein2GO to non-UniProtKB Identifiers]]
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=== [[Cellular Component]] ===
  
==Activities==
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=== [[Biological Process]] ===
  
*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]
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=== [[Annotation Relations]] ===
*[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
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== Topic-Specific Guidelines ==
**[[Annotation Extension Relation Subsets]]
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=== [[Annotating from phenotypes]]===
**[[Column 16: Cell Type]]
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== Topic-Specific Guidelines under review==
**[[Column 16: Targets]]
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=== [[Annotating regulation]]===
**[[Issues with Annotation Extension relations]]
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=== [[Annotating binding]]===
**[[Annotation Extension Relation Documentation Jamboree]]
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=== [[Annotating downstream processes]]===
 +
=== [[Annotating ligand-receptor pathways]]===
 +
=== [[Response to x annotation guidelines]]===
 +
=== [[Multi-species processes]]===
 +
=== [http://gocwiki.geneontology.org/index.php/Signaling Signaling]===
  
*Keep all curators up-to-date with ontology development and how it affects annotations
+
=== [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] ===
 +
=== [https://docs.google.com/document/d/1bqCxx7QUblrc9q4PIynbJzoCXv248UWBxJa7fguJyXs/edit# Transcription Annotation Guide (updated May 2020)] ===
 +
=== [[MicroRNA_GO_annotation_manual]]===
 +
=== [[Guidelines for checkpoints]]===
  
*[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.
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== [[Guide to GO Evidence Codes]] ==
*[[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]]
 
*[[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]]
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== [[Experiment-Specific Annotation Guidelines]] - in progress ==
*[[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]]
 
  
==How To?==
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== Noctua and GO-CAM ==
====How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?====
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=== [http://wiki.geneontology.org/index.php/Noctua Noctua Curation Guide] ===
OBO-Edit can load files from the disk OR from a URL.<br>
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=== [http://wiki.geneontology.org/index.php/Noctua_MOD_Imports Importing MOD annotations into Noctua] ===
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
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== [[Annotation Extensions]] ==
  
====How to run Mike Cherry's filtering script locally before checking the GAF into SVN?====
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= Communication =
*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>
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== Annotation Conference Calls ==
  
> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/ontology go/ontology
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=== When ===
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
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* Calls are held on Tuesdays at 4:00pm GMT, 11:00am EST, 8:00am PST
username@ext.geneontology.org's password:
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* Calls are scheduled on the GO's Google calendar.  Please request access to the calendar if you don't have it.
[this will co the entire directory]
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* Reminder emails are sent out to the go-consortium mailing list; [https://mailman.stanford.edu/mailman/listinfo/go-consortium sign up here.]
  
>svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/software/utilities go/software/utilities
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=== How to Join ===
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
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*Please consult the GO calendar for the meeting URL.
username@ext.geneontology.org's password:
 
  
</pre>
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*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
  
Now you have the necessary files to run the script in your space.
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=== Agenda and Minutes ===
  
* cd to the gene-associations/submission directory
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*[[Annotation Call 2021 Agenda and Minutes]]
<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.
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*[[Annotation Call 2020 Agenda and Minutes]]
</pre>
 
  
==Annotation Conference calls==
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*[[Annotation Call 2019 Agenda and 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, or contact Rama.
+
*Please contact David and Kimberly if there are items you would like to add to the agenda
* [[Annotation Call 2015 Minutes | 2015]]
 
* [[Curation Consistency Rota | Curation Consistency Rota 2015]]
 
  
* 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]]
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* 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]]
  
==Monthly Reports==
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== GO-CAM and Noctua Calls ==
*[[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==
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Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.
[[Annotation_topics for next meeting]]
 
  
[[Annotation_31Jan10]]
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We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation.
  
[[Annotation_21Dec10]]
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=== Agenda and Minutes ===
  
[[Annotation_19Oct10]]
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*[[GO-CAM and Noctua 2019 Agenda and Minutes]]
  
[[Annotation_21Sept10]]
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* 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-CAM and Noctua 2018 Agenda and Minutes | 2018]]
  
[[Annotation_17Aug10]]
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== 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].
 +
* 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_04Aug10]]
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== GO Annotation on gitter ==
 +
*The GO annotation group uses [https://gitter.im/geneontology/go-annotation gitter] as an informal chat service.
 +
*Curators are free to ask questions or share ideas on gitter, with issues elevated to more formal tracking (i.e. github/go-annotation or wiki documentation), as needed.
 +
*Curators can login to gitter using their github accounts.
  
[[Annotation_19July10]]
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== 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].
  
[[Annotation_22June10]]
+
== 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].
  
[[Annotation_08June10]]
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=Focused annotation projects=
 +
* [[Kidney Development]] (2009/2010)
 +
* [[Immunology]] (2006)
  
[[Annotation_01June10]]
 
  
[[Annotation_17May10]]
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=PAGES TO REVIEW=
  
[[Annotation_29Apr10]]
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==Intro to GO==
 +
* [[Submit_GO_annotations]]
 +
* [[Beginning Annotation SOP]]
 +
* Can we use the way this is presented ?  [http://wiki.geneontology.org/images/b/b1/GOA_training_cutdown.pdf GOA Training slides]
 +
* [[Guidelines_for_literature-based_curation]]
 +
* [[Guidelines for electronic annotation methods]]
 +
* MGI IEA pipeline 2008: [[Electronic - Harold and Evelyn]]
 +
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1176400/ Clark et al., 2005]
 +
* [[Contributing_GO_Annotations]]
 +
* [[With_field]]
 +
* [[Authoritative_Database_Groups]]
 +
* Regulation [http://wiki.geneontology.org/index.php/Category:Regulation]
 +
* https://docs.google.com/document/d/1HyOW6oYu9ZxQlHRbZqIgv73L-_fdaXmFhtZPi83DBSU/edit
 +
* http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management
 +
* http://wiki.geneontology.org/index.php/Annotation_Issues_and_Management
 +
* [[GO annotation activities by central GO Consortium members]]
  
[[Annotation_15Apr10]]
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==To delete, archive, or retire==
 +
* [[Database_Objects]]
 +
* [[GO_annotation_fields_required_for_correct_display]]
  
[[Annotation_08Apr10]]
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=To review=
 +
* [[Tools_ID_Mapping]]
  
[[Annotation_22Mar10]]
 
  
[[Annotation_15Mar10]]
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= History =
 +
== [[Archived Pages]] ==
  
[[Annotation_10Apr10]]
 
  
==Metrics of success==
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[[Category: GOC Overview]]
 
 
 
 
* [[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 14:26, 18 January 2021

Contents

Group Leaders

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

Mission statement

  • 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

Annotation Documentation

Overview of GO annotations

Introduction to GO annotations on the GO website

Annotation conventions

Tips to Produce High Quality Annotations

GO Annotation Standard Operating Procedures

Annotation maintenance

Annotation Quality Control

Ontology-Specific Guidelines

Molecular Function

Cellular Component

Biological Process

Annotation Relations

Topic-Specific Guidelines

Annotating from phenotypes

Topic-Specific Guidelines under review

Annotating regulation

Annotating binding

Annotating downstream processes

Annotating ligand-receptor pathways

Response to x annotation guidelines

Multi-species processes

Signaling

Apoptosis Curation Manual

Transcription Annotation Guide (updated May 2020)

MicroRNA_GO_annotation_manual

Guidelines for checkpoints

Guide to GO Evidence Codes

Experiment-Specific Annotation Guidelines - in progress

Noctua and GO-CAM

Noctua Curation Guide

Importing MOD annotations into Noctua

Annotation Extensions

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 David and Kimberly if there are items you would like to add to the agenda

GO-CAM and Noctua Calls

Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.

We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation.

Agenda and Minutes

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 gitter

  • The GO annotation group uses gitter as an informal chat service.
  • Curators are free to ask questions or share ideas on gitter, with issues elevated to more formal tracking (i.e. github/go-annotation or wiki documentation), as needed.
  • Curators can login to gitter using their github accounts.

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.

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 here.

Focused annotation projects


PAGES TO REVIEW

Intro to GO

To delete, archive, or retire

To review


History

Archived Pages