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= Annotation Documentation = | = Annotation Documentation = | ||
== Overview of GO annotations == | == Overview of GO annotations == | ||
[http://geneontology.org/docs/go-annotations/ Introduction to GO annotations on the GO website] | |||
==[[Annotation conventions]]== | ==[[Annotation conventions]]== | ||
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==[[GO Annotation Standard Operating Procedures]]== | ==[[GO Annotation Standard Operating Procedures]]== | ||
==[[Annotation maintenance]]== | ==[[Annotation maintenance]]== | ||
==[[Annotation Quality Control]]== | |||
== Ontology-Specific Guidelines == | == Ontology-Specific Guidelines == | ||
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== Topic-Specific Guidelines == | == Topic-Specific Guidelines == | ||
=== [[Annotating from phenotypes]]=== | === [[Annotating from phenotypes]]=== | ||
== Topic-Specific Guidelines under review== | |||
=== [[Annotating regulation]]=== | === [[Annotating regulation]]=== | ||
=== [[Annotating binding]]=== | === [[Annotating binding]]=== | ||
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=== [[Response to x annotation guidelines]]=== | === [[Response to x annotation guidelines]]=== | ||
=== [[Multi-species processes]]=== | === [[Multi-species processes]]=== | ||
=== [http://gocwiki.geneontology.org/index.php/Signaling Signaling]=== | |||
=== [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] === | === [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] === | ||
=== [https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1 Transcription Annotation Guide (2018)] === | === [https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1 Transcription Annotation Guide (2018)] === | ||
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== [[Guide to GO Evidence Codes]] == | == [[Guide to GO Evidence Codes]] == | ||
== [[Experiment-Specific Annotation Guidelines]] == | == [[Experiment-Specific Annotation Guidelines]] - in progress == | ||
== Noctua and GO-CAM == | == Noctua and GO-CAM == | ||
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=== [http://wiki.geneontology.org/index.php/Noctua_MOD_Imports Importing MOD annotations into Noctua] === | === [http://wiki.geneontology.org/index.php/Noctua_MOD_Imports Importing MOD annotations into Noctua] === | ||
== [[Annotation Extensions]] == | == [[Annotation Extensions]] == | ||
== [[Annotation Quality Control]] == | == [[Annotation Quality Control]] == | ||
= Communication = | = Communication = | ||
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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]] | * 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]] | ||
== GO-CAM and Noctua Calls == | == GO-CAM and Noctua Calls == | ||
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*Please contact David and Kimberly if there are items you would like to add to the agenda | *Please contact David and Kimberly if there are items you would like to add to the agenda | ||
* 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]] | | * 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]] | ||
== GO Annotation on GitHub == | == GO Annotation on GitHub == | ||
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* Reminders about conference calls are sent to the 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]. | * To subscribe to the go-consortium mailing list, please click [https://mailman.stanford.edu/mailman/listinfo/go-consortium here]. | ||
=Focused annotation projects= | |||
* [[Kidney Development]] (2009/2010) | |||
* [[Immunology]] (2006) | |||
=PAGES TO REVIEW= | =PAGES TO REVIEW= | ||
==Intro to GO== | |||
* [[Submit_GO_annotations]] | |||
* [[Beginning Annotation SOP]] | * [[Beginning Annotation SOP]] | ||
* MGI | * 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://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]] | |||
==To delete, archive, or retire== | |||
* [[Database_Objects]] | |||
* [[GO_annotation_fields_required_for_correct_display]] | |||
=To review= | |||
* [[Tools_ID_Mapping]] | |||
= History = | = History = | ||
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[[Category: | [[Category: GOC Overview]] |
Revision as of 12:12, 13 April 2019
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 (2018)
Transcription Annotation Guide (2012)
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
Annotation Quality Control
Communication
Annotation Conference Calls
When
- Calls are held on the 2nd and 4th Tuesday of each month 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
- Past Annotation Call Minutes: 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | LEGO Discussion Rota 2017 | 2018
GO-CAM and Noctua Calls
When
- Calls are held on the 2nd and 4th Wednesday of each month 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 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 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
- Kidney Development (2009/2010)
- Immunology (2006)
PAGES TO REVIEW
Intro to GO
- Submit_GO_annotations
- Beginning Annotation SOP
- Can we use the way this is presented ? GOA Training slides
- Guidelines_for_literature-based_curation
- Guidelines for electronic annotation methods
- MGI IEA pipeline 2008: Electronic - Harold and Evelyn
- Clark et al., 2005
- Contributing_GO_Annotations
- With_field
- Authoritative_Database_Groups
- Regulation [1]
- 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
To delete, archive, or retire
To review