Difference between revisions of "Annotation"

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[[Category: Annotation]] [[Category:Working Groups]]
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= Group Leaders =
==Group Leaders==
 
 
David Hill (MGI) and Kimberly Van Auken (WB)
 
David Hill (MGI) and Kimberly Van Auken (WB)
  
==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]]
+
= 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==
+
== Ontology-Specific Guidelines ==
  
[[Procedure for migration of protein annotations to Protein2GO]]
+
=== [[Molecular Function]] ===
  
[[Extension of Protein2GO to non-UniProtKB Identifiers]]
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=== [[Cellular Component]] ===
  
 +
=== [[Biological Process]] ===
  
 +
=== [[Annotation Relations]] ===
  
==Activities==
+
== 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]]===
 +
=== [http://gocwiki.geneontology.org/index.php/Signaling Signaling]===
  
*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]
+
=== [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] ===
*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap 2011]
+
=== [https://docs.google.com/document/d/1bqCxx7QUblrc9q4PIynbJzoCXv248UWBxJa7fguJyXs/edit# Transcription Annotation Guide (updated May 2020)] ===
*[[Media:AnnotationRoadMap.pdf | RoadMap]] (PDF file - provides project goals with time line)
+
=== [[MicroRNA_GO_annotation_manual]]===
*Educate GOC curators about best annotation practice;
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=== [[Guidelines for checkpoints]]===
*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
+
== [[Guide to GO Evidence Codes]] ==
**[[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
+
== [[Experiment-Specific Annotation Guidelines]] - in progress ==
  
*[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.
+
== Noctua and GO-CAM ==
*[[Evidence Code Ontology (ECO)]] - Proposal to represent evidence in an ontology
+
=== [http://wiki.geneontology.org/index.php/Noctua Noctua Curation Guide] ===
*[[Proposal for cron tabs]] - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences
+
=== [http://wiki.geneontology.org/index.php/Noctua_MOD_Imports Importing MOD annotations into Noctua] ===
*[[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]]
 
  
==How To?==
+
== [[Annotation Extensions]] ==
====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>
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= Communication =
  
http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
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== Annotation Conference Calls ==
  
====How to run Mike Cherry's filtering script locally before checking the GAF into SVN?====
+
=== When ===
*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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* 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.]
  
> 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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=== How to Join ===
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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*Please consult the GO calendar for the meeting URL.
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
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*to join via phone: enter Meeting ID found on the GO calendar after dialing in
username@ext.geneontology.org's password:
+
*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
  
> 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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=== Agenda and Minutes ===
username@ext.geneontology.org's password:
 
  
</pre>
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*[[Annotation Call 2021 Agenda and Minutes]]
  
Now you have the necessary files to run the script in your space.
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*[[Annotation Call 2020 Agenda and Minutes]]
  
* cd to the gene-associations/submission directory
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*[[Annotation Call 2019 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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*Please contact David and Kimberly if there are items you would like to add to the agenda
</pre>
 
  
==Annotation Conference calls==
+
* 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]]
  
* [[Annotation Call 2016 Minutes]]
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== GO-CAM and Noctua Calls ==
* 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
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Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.
*from US: +1.408.740.7256 or +1.888.240.2560
 
*from UK: +44.203.608.5256
 
  
* [[Curation Consistency Rota 2016]]
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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.
  
* 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]]
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=== Agenda and Minutes ===
  
==LEGO calls==
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*[[GO-CAM and Noctua 2019 Agenda and Minutes]]
Meetings are every Monday 11:30AM Eastern, 4:30PM Greenwich, 8:30AM Pacific
 
  
Bluejeans recurring meeting URL: https://bluejeans.com/969313231
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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]]
  
to join via phone: enter Meeting ID 969313231 after dialing in
+
== GO Annotation on GitHub ==
*from US: +1.408.740.7256 or +1.888.240.2560
+
* The Gene Ontology uses an issue tracker hosted on GitHub to record and track annotation issues.
*from UK: +44.203.608.5256
+
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-annotation here].
*from Switzerland: +41.81.588.0256
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* 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]
  
*[[LEGO Annotation Calls 2015 Minutes | 2015]]
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== GO Annotation on gitter ==
*2016
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*The GO annotation group uses [https://gitter.im/geneontology/go-annotation gitter] as an informal chat service.
[[LEGO January 4, 2016]]
+
*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.
  
[[LEGO January 18, 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 February 1, 2016]]
+
== 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].
  
[[LEGO February 15, 2016]]
+
=Focused annotation projects=
 +
* [[Kidney Development]] (2009/2010)
 +
* [[Immunology]] (2006)
  
[[LEGO March 7, 2016]]
 
  
[[LEGO March 21, 2016]]
+
=PAGES TO REVIEW=
  
[[LEGO March 28, 2016]]
+
==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]]
  
[[LEGO April 4, 2016]]
+
==To delete, archive, or retire==
 +
* [[Database_Objects]]
 +
* [[GO_annotation_fields_required_for_correct_display]]
  
[[LEGO April 25, 2016]]
+
=To review=
 +
* [[Tools_ID_Mapping]]
  
[[LEGO May 2, 2016]]
 
  
[[LEGO May 9, 2016]]
+
= History =
 +
== [[Archived Pages]] ==
  
[[LEGO May 16, 2016]]
 
  
[[LEGO May 23, 2016]]
+
[[Category: GOC Overview]]
 
 
[[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]]
 
 
 
 
 
 
 
[[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 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