Difference between revisions of "Annotation Advocacy progress report for 2015"

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(GAF 2.1)
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The new version of the GAF format was released. GAF 2.1 allows the use of pipes (|) and comma (,) in column 8 (with/from column) compared to GAF 2.0 which allows the use of pipes only. Pipe will indicate 'OR' and Comma will indicate 'AND'. <br>
 
The new version of the GAF format was released. GAF 2.1 allows the use of pipes (|) and comma (,) in column 8 (with/from column) compared to GAF 2.0 which allows the use of pipes only. Pipe will indicate 'OR' and Comma will indicate 'AND'. <br>
 
http://geneontology.org/page/go-annotation-file-gaf-format-21
 
http://geneontology.org/page/go-annotation-file-gaf-format-21
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 +
===Plans for 2016===
 +
# Continue with the consistency exercises
 +
# consolidate QC checks (integrate QC checks from GOA and Mike's filtering script with Jenkins)
 +
# Document guidelines for annotating complexes on the GOC website

Revision as of 08:56, 15 October 2015

Management

Rama Balakrishnan (SGD)

Annotation Consistency

Annotation calls

We continue to discuss annotation issues on our biweekly annotation calls. Subjects can be anything from new annotation guidelines, Annotation Extension guidelines, quality control checks, ontology or evidence code-related discussions, tool development or updates from annotating groups.

Some of the discussion we have had this year include:

  1. Mechanics of these annotation calls, how to make them productive, effective. We switched to using Bluejeans. We also decided to have a annotation consistency exercise every month
  2. ECO presentation by Marcus Chibucos
  3. Jenkins GAF reports
  4. Availability of RNAcentral IDs for annotating RNA gene products
  5. Behind the scenes of how data/GO annotations (GAF) are received, processed and disseminated, how to run the GAF filtering script
  6. Transferring col-16 data while doing an ISS annotation
  7. Ontology issues with ion channels (specific vs non-specific)
  8. new guidelines for creating complexes in GO to be in sync with IntAct
  9. moving SourceForge ontology tracker to github
  10. GAF 2.1 release (in this release, the with/from column can handle pipe or comma)
  11. changing the term string for transcription terms so they are more readable
  12. No more merges in the Ontology.
  13. report on how cell lines are handled by MGI
  14. review of Obsolete relations in col-16 and rehousing existing annotations
  15. New ECO term for inter-ontology inferencing pipeline
  16. update on new TermGenie templates
  17. miRNA guideline
  18. how to annotate regulation of activity (unresolved)
  19. review of col-16 documentation on github (https://github.com/geneontology/annotation_extensions)
  20. What IDs should be allowed in col-16 and column-8 (with/from)?
  21. When to tag a term with the Do Not Automatically annotate tag

New Datasets

  • Synapse group from BROAD
  • MaizeDB has submitted annotations
  • Received annotations for lncRNAs from the community

Annotation to complexes as Objects

A working group was formed to come up with guidelines for annotating complexes as objects. Minutes from these working group discussions are available:
http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015 http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_July15,_2015

GO Help desk

The Annotation Advocacy group manages the GOhelp desk with help from various consortium members. The GO help desk receives at least one email a day.

GAF 2.1

The new version of the GAF format was released. GAF 2.1 allows the use of pipes (|) and comma (,) in column 8 (with/from column) compared to GAF 2.0 which allows the use of pipes only. Pipe will indicate 'OR' and Comma will indicate 'AND'.
http://geneontology.org/page/go-annotation-file-gaf-format-21

Plans for 2016

  1. Continue with the consistency exercises
  2. consolidate QC checks (integrate QC checks from GOA and Mike's filtering script with Jenkins)
  3. Document guidelines for annotating complexes on the GOC website