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[[Category: Annotation]] [[Category:Working Groups]]
[[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)


==GO Annotation Meetings==
== Communication ==
[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]]
=== Annotation Conference Calls ===


[http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford Annotation Meeting Stanford, CA, Feb 2012]
* Calls are held on the 2nd and 4th Tuesday 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
* Recurring meeting URL: https://stanford.zoom.us/j/976175422


==Migration of annotating groups to Protein2GO==
*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)
[[Procedure for migration of protein annotations to Protein2GO]]
*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
[[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]]
 
==How To?==
====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
 
====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 2017 Minutes]]
*[[Annotation Call 2017 Minutes]]


*[[LEGO Discussion Rota]]
*[[LEGO Discussion Rota]]
* Calls are held on the 2nd and 4th Tuesday of each month. at 4pm GMT, 8am PDT.
* 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
*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


* 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]]
* 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]]
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]


==Combined GO-CAM/GPAD calls==
=== GO-CAM Calls ===
Meetings are the 2nd and 4th Wednesday of each month 11:00AM Eastern, 4:00PM Greenwich, 8:00AM Pacific
 
*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




Line 216: Line 107:
[[GO-CAM ectopic meeting July 19th 2017]]
[[GO-CAM ectopic meeting July 19th 2017]]


==Old GPAD Calls==
[[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 September 28, 2016]]
Line 223: Line 131:
[[LEGO GAF/GPAD October 5, 2016]]
[[LEGO GAF/GPAD October 5, 2016]]


=== GitHub ===


[[Category:LEGO]]
=== Gene Ontology on Google Drive ===


==Monthly Reports==
== Annotation Documentation ==
*[[GO Annotation Basics]]
*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]]
*Noctua and GO-CAM Models
*Annotation Extensions
 
== Current Working Groups and Projects ==
 
== How To? ==
====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
 
====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>
 
== 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]]
*[[September2011_Annotation_Advocacy_Report|September 2011]]
*[[August2011_Annotation_Advocacy_Report|August 2011]]
*[[August2011_Annotation_Advocacy_Report|August 2011]]
Line 244: Line 292:
*[[Jun2010_Annotation_Advocacy_Report|June 2010]]
*[[Jun2010_Annotation_Advocacy_Report|June 2010]]


==Meeting calendar==
=== Meeting calendar ===
[[Annotation_topics for next meeting]]
[[Annotation_topics for next meeting]]


Line 281: Line 329:
[[Annotation_10Apr10]]
[[Annotation_10Apr10]]


==Metrics of success==
=== Process ===
* [[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]
[http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management Annotation Issues]


==Issues for the Annotation Group==
=== Issues for the Annotation Group ===
# Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)
# Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)



Revision as of 13:14, 12 December 2017

Group Leaders

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

Communication

Annotation Conference Calls

  • Calls are held on the 2nd and 4th Tuesday 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
  • Recurring meeting URL: https://stanford.zoom.us/j/976175422
  • 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

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 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

Annotation Documentation

Current Working Groups and Projects

How To?

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.
Choose the "File -> Load..." menu option
Choose the OBO File Adapter
Type http://www.geneontology.org/ontology/gene_ontology.obo into the filename box
(From:http://www.geneontology.org/newsletter/archive/200705.shtml#tip)

To see the has_part relationships, use this URL for the extended GO version:

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.

> 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:

Now you have the necessary files to run the script in your space.

  • cd to the gene-associations/submission directory
 
>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.

Metrics of success


Archived Pages

GO Annotation Meetings

2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010

Guidelines from Annotation Camp

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

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

Monthly Reports

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

Annotation Issues

Issues for the Annotation Group

  1. 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