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| == [[Introduction to Annotation]] == | | == [[Introduction to Annotation]] == |
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| == Ontology-Specific Guidelines == | | == Ontology-Specific Annotation Guidelines == |
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| | === [[Molecular Function]] === |
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| | === [[Cellular Component]] === |
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| === [[Biological Process]] === | | === [[Biological Process]] === |
| *Annotation Relations
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| *Term-specific Guidelines
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| === Molecular Function ===
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| *Annotation Relations
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| *Term-specific Guidelines
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| === Cellular Component ===
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| *Annotation Relations
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| *Term-specific Guidelines
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| == [[Guide to GO Evidence Codes]] == | | == [[Guide to GO Evidence Codes]] == |
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| | == [[Tips to Produce High Quality Annotations]] == |
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| == Noctua and GO-CAM Models == | | == Noctua and GO-CAM Models == |
| == Annotation Extensions == | | == [[Annotation Extensions]] == |
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| ==[[Annotation Review Request]] == | | ==[[Annotation Review Request]] == |
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| == Annotation File Pipelines == | | == [[Annotation File Pipelines]] == |
| *[[How to run Mike Cherry's filtering script locally before checking the GAF into SVN?]]
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| = Communication = | | = Communication = |
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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 |
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| * Past Annotation Call Minutes: [[LEGO Annotation Calls 2015 Minutes | 2015]] | [[GO-CAM and Noctua 2016 Agenda and Minutes | 2016]] | | * 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]] |
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| [[LEGO January 4, 2016]]
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| [[LEGO January 18, 2016]]
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| [[LEGO February 1, 2016]]
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| [[LEGO February 15, 2016]]
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| [[LEGO March 7, 2016]]
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| [[LEGO March 21, 2016]]
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| [[LEGO March 28, 2016]]
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| [[LEGO April 4, 2016]]
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| [[LEGO April 25, 2016]]
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| [[LEGO May 2, 2016]]
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| [[LEGO May 9, 2016]]
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| [[LEGO May 16, 2016]]
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| [[LEGO May 23, 2016]]
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| [[LEGO June 6, 2016]]
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| [[LEGO June 13, 2016]]
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| [[LEGO June 20, 2016]]
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| [[LEGO June 27, 2016]]
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| [[LEGO July 11, 2016]]
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| [[LEGO July 18, 2016]]
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| [[LEGO July 25, 2016]]
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| [[LEGO August 8, 2016]]
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| [[LEGO August 15, 2016]]
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| [[LEGO August 22, 2016]]
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| [[LEGO August 29, 2016]]
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| [[LEGO September 12, 2016]]
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| [[LEGO September 19, 2016]]
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| [[LEGO September 26, 2016]]
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| [[LEGO October 5, 2016]]
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| [[LEGO October 10, 2016]]
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| [[LEGO October 17, 2016]]
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| [[LEGO October 24, 2016]]
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| [[LEGO October 31, 2016]]
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| [[GO-CAM May 10th, 2016]] | |
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| [[GO-CAM May 24th, 2017]]
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| [[GO-CAM June 14th, 2017]]
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| [[GO-CAM June 28th, 2017]]
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| [[GO-CAM July 12th, 2017]]
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| [[GO-CAM ectopic meeting July 19th 2017]]
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| [[GO-CAM July 26th, 2017]]
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| [[GO-CAM August 9th, 2017]]
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| [[GO-CAM August 23, 2017]]
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| [[GO-CAM Sept 13, 2017]]
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| [[GO-CAM Sept 27, 2017]]
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| [[GO-CAM October 25th, 2017]]
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| [[GO-CAM November 8th, 2017]]
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| [[GO-CAM November 22, 2017]]
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| [[GO-CAM December 13, 2017]]
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| === Old GPAD Calls ===
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| [[LEGO GAF/GPAD September 28, 2016]]
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| [[LEGO GAF/GPAD October 5, 2016]]
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| === GitHub ===
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| === Gene Ontology on Google Drive ===
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| == Metrics of success ==
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| * [[Proposal for Author Feedback for annotations]]
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| * [[Annotations removed as a result of Annotation QCs]]
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| * [http://go.berkeleybop.org/news4go/node/80| Moved to GAF2.0 format on the 1st June 2010]
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| = Archived Pages =
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| === GO Annotation Meetings ===
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| [http://gocwiki.geneontology.org/index.php/2010_GO_camp_Meeting_Logistics 2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010 ]
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| [[Guidelines from Annotation Camp]]
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| [http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford Annotation Meeting Stanford, CA, Feb 2012]
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| === Migration of annotating groups to Protein2GO ===
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| [[Procedure for migration of protein annotations to Protein2GO]]
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| [[Extension of Protein2GO to non-UniProtKB Identifiers]]
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| === Activities ===
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| *[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]
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| *[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap 2011]
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| *[[Media:AnnotationRoadMap.pdf | RoadMap]] (PDF file - provides project goals with time line)
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| *Educate GOC curators about best annotation practice;
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| *Enforce annotation rules/policies within GOC
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| *Maintain the annotation/evidence code documentation
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| **[[Mock-ups of new GOC Annotation pages]]
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| *Train/assist new groups with annotations: see [[How_External_Communities_can_contribute_annotations_to_the_GO_Consortium]]
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| *Educate and keep all the annotating groups up-to-date with changes in GAF format
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| *Annotation Extensions
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| **[[Annotation Extension Relation Subsets]]
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| **[[Column 16: Cell Type]]
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| **[[Column 16: Targets]]
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| **[[Issues with Annotation Extension relations]]
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| **[[Annotation Extension Relation Documentation Jamboree]]
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| **[[Guidance for updating deprecated Annotation Extension Relations]]
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| *Keep all curators up-to-date with ontology development and how it affects annotations
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| *[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.
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| *[[Evidence Code Ontology (ECO)]] - Proposal to represent evidence in an ontology
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| *[[Proposal for cron tabs]] - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences
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| *[[Examples for phylogeny based evidence codes]]
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| *[[Ideas for GOC community curation tool]]
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| *[[Protein Complex ids as GO annotation objects]]
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| ** [[Annotation guidelines for annotating complexes as annotation objects]]
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| ** [[Protein Complex Conference Call June19, 2015]]
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| ** [[Protein Complex Conference Call July15, 2015]]
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| *[[LEGO-style annotation ideas]]
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| * [[Proposed Developments to the GAF annotation format]]
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| *[[InterPro2GO Session October 4th 2011]]
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| *[[MF-BP inferences]]
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| *[[Protein Binding clean up]]
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| *[[Annotation Guidance Pages]]
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| *[[Evidence Code proposals]]
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| *[[With/From field restrictions for evidence codes]]
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| *[[Core Consortium annotation activities]]
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| *[[:Category:GPAD|GPAD]]
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| *[[Common Annotation Framework Specification]]
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| *[[gp2protein file]]
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| *[[gp2rna file]]
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| *[[gp_unlocalized file]]
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| *[[mechanisms for reducing annotation redundancy]]
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| *[[Annotations to Cell Fraction-type terms]]
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| *[[TermEnrichment: Gold Standard Data Sets]]
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| *[["Response to" terms]]
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| *[[GAF 2.1 specs]]
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| === Monthly Reports ===
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| *[[September2011_Annotation_Advocacy_Report|September 2011]]
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| *[[August2011_Annotation_Advocacy_Report|August 2011]]
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| *[[July2011_Annotation_Advocacy_Report|July 2011]]
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| *[[June2011_Annotation_Advocacy_Report|June 2011]]
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| *[[May2011_Annotation_Advocacy_Report|May 2011]]
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| *[[April2011_Annotation_Advocacy_Report|April 2011]]
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| *[[March2011_Annotation_Advocacy_Report|March 2011]]
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| *[[February2011_Annotation_Advocacy_Report|February 2011]]
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| *[[January2011_Annotation_Advocacy_Report|January 2011]]
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| *[[December2010_Annotation_Advocacy_Report|December 2010]]
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| *[[November2010_Annotation_Advocacy_Report|November 2010]]
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| *[[October2010_Annotation_Advocacy_Report|October 2010]]
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| *[[September2010_Annotation_Advocacy_Report|September 2010]]
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| *[[August2010_Annotation_Advocacy_Report|August 2010]]
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| *[[July2010_Annotation_Advocacy_Report|July 2010]]
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| *[[Jun2010_Annotation_Advocacy_Report|June 2010]]
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| === Meeting calendar ===
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| [[Annotation_topics for next meeting]]
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| [[Annotation_31Jan10]]
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| [[Annotation_21Dec10]]
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| [[Annotation_19Oct10]]
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| [[Annotation_21Sept10]]
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| [[Annotation_17Aug10]]
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| [[Annotation_04Aug10]]
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| [[Annotation_19July10]]
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| [[Annotation_22June10]]
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| [[Annotation_08June10]]
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| [[Annotation_01June10]]
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| [[Annotation_17May10]]
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| [[Annotation_29Apr10]]
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| [[Annotation_15Apr10]]
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| [[Annotation_08Apr10]]
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| [[Annotation_22Mar10]]
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| [[Annotation_15Mar10]]
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| [[Annotation_10Apr10]]
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| === Process ===
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| [http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management Annotation Issues]
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| === Issues for the Annotation Group ===
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| # Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)
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| [[Annotations to Catalytic activity with IPI]]
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| [[Annotation Quality Control Checks]]
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| [[Action items from March 2010 GOC meeting]]
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| ====How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?==== | | == GO Annotation on GitHub == |
| OBO-Edit can load files from the disk OR from a URL.<br>
| | * The Gene Ontology uses an issue tracker hosted on GitHub to record and track annotation issues. |
| Choose the "File -> Load..." menu option<br>
| | * The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-annotation here]. |
| Choose the OBO File Adapter<br>
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| Type http://www.geneontology.org/ontology/gene_ontology.obo into the filename box<br>
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| (From:http://www.geneontology.org/newsletter/archive/200705.shtml#tip)
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| To see the has_part relationships, use this URL for the extended GO version:<br>
| | == 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 [https://drive.google.com/drive/folders/0B8kRPmmvPJU3fmNRM2dYTnJmVXg4bG52bTZIdk8wdU53R2F1MDlubG90Rll5LTZqbEVVN3c here]. |
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| http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
| | = History = |
| | == [[Archived Pages]] == |
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| [[Category: Annotation]] [[Category:Working Groups]] | | [[Category: Annotation]] [[Category:Working Groups]] |