Annotation Conf. Call, September 13, 2011

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Agenda

Present: SGD: Rama, Julie, Karen, Jodi
UK: Emily, Jane, Susan, Val, Midori, Paola, Rachael
WB: Kimberly
RGD: Stan, Shur-Jen
TAIR: Donghui
Berkeley: Chris, Amelia
AgBase: Lakshmi

Unpublished Reference for use with IC evidence code

We sent around an abstract for the unpublished reference for use with IC evidence code. We haven't received any comments. Is everybody okay with the text? If not, we will move this to the GO_Refs page asap. If you have more examples for use of IC in this fashion, please post them on the go-discuss mailing list. Please also see discussion on this topic from the Aug 9rd Annotation call (http://gocwiki.geneontology.org/index.php/Annotation_Conf._Call,_August_9,_2011)

GO_REF:0000036 Manual annotations that require more than one source of functional data to support the assignment of the associated GO term.  

The Gene Ontology Consortium uses the IC (Inferred by Curator) evidence code when an annotation cannot be supported by any direct evidence, 
but can be inferred by GO annotations that have been annotated to the same gene/gene product identifier in conjunction with the curator's 
knowledge of biology (supporting GO annotations must not be IC-evidenced). In many cases an IC-evidenced annotation simply applies the same 
reference that was used in the supporting GO annotation.  The use of IC evidence code in an annotation with reference GO_REF:0000036 signifies 
a curator inferred the GO term based on evidence from multiple sources of evidence/GO annotations. The 'with/from' field in these annotations 
will therefore supply >1 GO identifier, obtained from the set of supporting GO annotations assigned to the same gene/gene product identifier 
which cite publicly-available references.

Example: (from: http://wiki.geneontology.org/index.php/Transcription_jamboree)
Primary annotations to CUP9:
CUP9 GO:0000122 negative regulation of transcription from RNA polymerase II promoter IMP PMID:9427760
CUP9 GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA PMID:9427760 
CUP9 GO:0001103 RNA polymerase II repressing transcription factor binding IPI PMID:18708352 CYC8
Composite IC annotation to CUP9:
CUP9 GO:0001133 Sequence-specific transcription regulatory region DNA binding RNA 
polymerase II transcription factor recruiting transcription factor 
activity IC GO_REF:0000036  GO:0000122|GO:0000978|GO:0001103

Discussion

The IC unpublished reference is all set to go. Remember to make annotations to the granular annotations. Rama will add it to the GO_REF page and the Documentation page. We will also come up with rules for QC checks. If the annotating groups generate an internal DBID for this reference, they should make sure that ID is listed as External Accession on the GO_REF page.

Include the term 'GO:0005488; Binding' to QC Rule GO_AR:0000003

See: http://www.geneontology.org/GO.annotation_qc.shtml

GO_AR:0000003 Annotations to 'protein binding ; GO:0005515', should be made with IPI and interactor should be in the 'with' field

  • Annotations to the parent term 'binding' should also be included in this rule, as the same poor-level of information is conveyed in an annotation of gene_product 1 GO:0005488 binding IDA PMID:12345

Discussion

  • Agreed, that the upper level term should also be subjected to that rule.
  • What sorts of things can go in the 'with' column for Binding? Chebi is one example. But if you know exactly what it binds to, then pick one of the appropriate child terms.
  • We will email this QC to the GO mailing list

Use of Col-16

Midori et al (Spombe) have done lot of work in capturing data in col-16. She will go over the relationships they have used and some examples.
Relations (OBO format): http://www.geneontology.org/scratch/xps/go_annotation_extension_relations.obo
Annotation examples on the Pombase Wiki page: http://sourceforge.net/apps/trac/pombase/wiki/ListOfRelations
Examples are also available in OBO format at: http://www.geneontology.org/scratch/xps/go_annotation_extension_examples.obo

Discussion

  • Curators can refer to the pombe wiki page to see how they have used the relationships
  • if you have multiple relationships, use a comma.
  • In the future, if you need new relationships, please request them on the Ontology SF tracker.
  • How do we view these relationships? Amelia will work on a static page to view these. Obo-edit can be used too.
  • Documentation is scattered for col-16. Rama will try to clean up.
  • If your group is providing data in col-16, please post a message on the GO list saying so

Protein oligomerization SF item (Amelia, Becky)

http://sourceforge.net/tracker/?func=detail&aid=3053953&group_id=36855&atid=440764

Discussion

This will be an agenda item for the upcoming GOC meeting at UK.