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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) | ||
== | == 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 | |||
* | |||
* | |||
( | |||
* | |||
*[[Annotation Call 2017 Minutes]] | *[[Annotation Call 2017 Minutes]] | ||
*[[LEGO Discussion Rota]] | *[[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]] | * 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]] | ||
== | === 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 | |||
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[[GO-CAM June 28th, 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 September 28, 2016]] | ||
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[[LEGO GAF/GPAD October 5, 2016]] | [[LEGO GAF/GPAD October 5, 2016]] | ||
=== GitHub === | |||
=== Gene Ontology on Google Drive === | |||
== 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] | |||
==Monthly Reports== | >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]] | ||
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*[[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]] | ||
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[[Annotation_10Apr10]] | [[Annotation_10Apr10]] | ||
== | === 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
- Past Annotation Call Minutes: 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016
- Curation Consistency Rota: 2015 | 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
- 2015
- 2016
GO-CAM ectopic meeting July 19th 2017
Old GPAD Calls
LEGO GAF/GPAD September 28, 2016
GitHub
Gene Ontology on Google Drive
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
- Biological Process
- 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.
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
- Roadmap 2010
- Roadmap 2011
- 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
- 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
- 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
- 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
- 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
- September 2011
- August 2011
- July 2011
- June 2011
- May 2011
- April 2011
- March 2011
- February 2011
- January 2011
- December 2010
- November 2010
- October 2010
- September 2010
- August 2010
- July 2010
- June 2010
Meeting calendar
Annotation_topics for next meeting
Process
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