Annotation: Difference between revisions
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==Purpose== | |||
==Group Leaders== | |||
Emily Dimmer (GOA@UniProt) and Rama Balakrishnan (SGD) with help from Pascale (dictyBase/Ref.genome project). | |||
==GO Annotation Camp== | |||
[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]] | |||
==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 | |||
**[[Column 16: Cell Type]] | |||
*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]] | |||
==How To?== | |||
How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?<br> | |||
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 | |||
==Annotation Conference calls== | |||
*[[Topics for annotation call | Add your topics/issues]] | |||
*[[Agenda for November 8th |Annotation Jamboree, Nov 8, 2010]] | |||
*[[Agenda for Dec 13th | Annotation Conf. Call, Dec 13, 2010]] | |||
*[[Annotation Conf. Call, Jan 10, 2011]] | |||
*[[Annotation Conf. Call, Feb 22, 2011]] | |||
*[[Annotation Conf. Call, Mar 22, 2011]] | |||
*[[Annotation Conf. Call, June 28, 2011]] | |||
*[[Annotation Conf. Call, July 12, 2011]] | |||
* Annotation Conf. Call, July 26, 2011 [[Transcription jamboree]] | |||
*[[Annotation Conf. Call, August 9, 2011]] | |||
*[[Annotation Conf. Call, August 23, 2011]] | |||
*[[Annotation Conf. Call, September 13, 2011]] | |||
*[[Annotation Conf. Call, September 27, 2011]] | |||
*[[Annotation Conf. Call, October 4, 2011]] | |||
*[[Annotation Conf. Call, October 18, 2011]] | |||
*[[Annotation Conf. Call, November 2, 2011]] | |||
*[[Annotation Conf. Call, November 16, 2011]] | |||
*[[Annotation Conf. Call, November 30, 2011]] | |||
*[[Annotation Conf. Call, December 14, 2011]] | |||
==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]] | |||
==Metrics of success== | |||
* [[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]] |
Revision as of 04:28, 26 September 2011
Purpose
Group Leaders
Emily Dimmer (GOA@UniProt) and Rama Balakrishnan (SGD) with help from Pascale (dictyBase/Ref.genome project).
GO Annotation Camp
2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010
Guidelines from Annotation Camp
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
- 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
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
Annotation Conference calls
- Annotation Jamboree, Nov 8, 2010
- Annotation Conf. Call, Dec 13, 2010
- Annotation Conf. Call, Jan 10, 2011
- Annotation Conf. Call, Feb 22, 2011
- Annotation Conf. Call, Mar 22, 2011
- Annotation Conf. Call, June 28, 2011
- Annotation Conf. Call, July 12, 2011
- Annotation Conf. Call, July 26, 2011 Transcription jamboree
- Annotation Conf. Call, August 9, 2011
- Annotation Conf. Call, August 23, 2011
- Annotation Conf. Call, September 13, 2011
- Annotation Conf. Call, September 27, 2011
- Annotation Conf. Call, October 4, 2011
- Annotation Conf. Call, October 18, 2011
- Annotation Conf. Call, November 2, 2011
- Annotation Conf. Call, November 16, 2011
- Annotation Conf. Call, November 30, 2011
- Annotation Conf. Call, December 14, 2011
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
Metrics of success
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