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= Annotation Documentation = | = Annotation Documentation = | ||
== [[Introduction to Annotation]] == | == [[Introduction to Annotation]] == | ||
==[[Annotation conventions]]== | |||
==[[GO Annotation Standard Operating Procedures]]== | |||
== Ontology-Specific Guidelines == | == Ontology-Specific Guidelines == | ||
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== Topic-Specific Guidelines == | == Topic-Specific Guidelines == | ||
=== [[Annotating from phenotypes]]=== | |||
=== [[Annotating regulation]]=== | |||
=== [[Annotating binding]]=== | |||
=== [[When should you remove old annotations?]]=== | |||
=== [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)] === | ||
=== [ftp://ftp.geneontology.org/pub/go/www/txnAnnotationGuide.pdf Transcription Annotation Guide (2012)] === | === [ftp://ftp.geneontology.org/pub/go/www/txnAnnotationGuide.pdf Transcription Annotation Guide (2012)] === | ||
=== [[MicroRNA_GO_annotation_manual]]=== | |||
=== [[Guidelines for checkpoints]]=== | |||
== [[Guide to GO Evidence Codes]] == | == [[Guide to GO Evidence Codes]] == | ||
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== Noctua and GO-CAM Models == | == Noctua and GO-CAM Models == | ||
=== [http://wiki.geneontology.org/index.php/Noctua Noctua Curation Guide] === | |||
== [[Annotation Extensions]] == | == [[Annotation Extensions]] == | ||
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== [[Annotation Quality Control]] == | == [[Annotation Quality Control]] == | ||
===GO rules=== | ===GO rules=== | ||
(Documentation in progress): https://github.com/geneontology/go-site/tree/master/metadata/rules | (Documentation in progress): https://github.com/geneontology/go-site/tree/master/metadata/rules | ||
Will replace: [[Annotation Quality Control Checks]] | |||
* '''GO rules reports''' | |||
** Snapshot (the report groups should monitor daily or weekly): http://snapshot.geneontology.org/reports/gorule-report.html | |||
** Latest Official Monthly Release (the errors present in our most up to date release): http://current.geneontology.org/reports/gorule-report.html | |||
===[[Annotation Review Request]]=== | ===[[Annotation Review Request]]=== | ||
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=== How to Join === | === How to Join === | ||
* | *Please consult the GO calendar for the meeting URL. | ||
*to join via phone: enter Meeting ID | *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 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 UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717 | ||
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=== Agenda and Minutes === | === Agenda and Minutes === | ||
*[[Annotation Call | *[[Annotation Call 2019 Agenda and Minutes]] | ||
*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: [[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]] | * 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]] | ||
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]] | *Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]] | ||
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=== How to Join === | === How to Join === | ||
* | *Please consult the GO calendar for the meeting URL. | ||
*to join via phone: enter Meeting ID | *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 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 UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717 | ||
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=== Agenda and Minutes === | === Agenda and Minutes === | ||
*[[GO-CAM and Noctua | *[[GO-CAM and Noctua 2019 Agenda and Minutes]] | ||
*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 == |
Revision as of 12:42, 6 February 2019
Group Leaders
David Hill (MGI) and Kimberly Van Auken (WB)
Annotation Documentation
Introduction to Annotation
Annotation conventions
GO Annotation Standard Operating Procedures
Ontology-Specific Guidelines
Molecular Function
Cellular Component
Biological Process
Annotation Relations
Topic-Specific Guidelines
Annotating from phenotypes
Annotating regulation
Annotating binding
When should you remove old annotations?
Apoptosis Curation Manual
Transcription Annotation Guide (2018)
Transcription Annotation Guide (2012)
MicroRNA_GO_annotation_manual
Guidelines for checkpoints
Guide to GO Evidence Codes
Tips to Produce High Quality Annotations
Experiment-Specific Annotation Guidelines
Noctua and GO-CAM Models
Noctua Curation Guide
Annotation Extensions
External Mappings
Annotation Quality Control
GO rules
(Documentation in progress): https://github.com/geneontology/go-site/tree/master/metadata/rules Will replace: Annotation Quality Control Checks
- GO rules reports
- Snapshot (the report groups should monitor daily or weekly): http://snapshot.geneontology.org/reports/gorule-report.html
- Latest Official Monthly Release (the errors present in our most up to date release): http://current.geneontology.org/reports/gorule-report.html
Annotation Review Request
How the GOC uses GitHub to request review of annotations
Proposal for Author Feedback for annotations
- To be implemented
Annotations removed as a result of Annotation QCs
- This is an old attempt at metrics for reviewed annotations. Archive??
Annotation File Pipelines
Procedure for unmaintained annotations
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.