Annotation Conf. Call, June 28, 2011

Present: Emily, Paola, Jane, Yasmin, Becky, Julie, Ranjana, Petra, Chris, Jodie, Li, Stan, Brenley, Lakshmi, Ruth.

Ontology Development work

Paola to present the work generated from the apoptosis content meeting, held on the 1st of June, in collaboration with Apo-Sys Consortium.

• Discussion: short discussion on obsoleteion of anti-apoptosis terms.

• ACTION: Any curators wishing to join the next Apoptosis Content call on the 20th July please get in touch with Paola.

Annotation QCs

• New annotation QC checks to be added into file check script:
  • requirement for IC-evidenced annotations to have non-null WITH
  • requirement for IPI-evidenced annotations to have non-null WITH

further details available here

• ACTION: Proposed QC checks will be implemented as 'soft' rather than 'hard', as they can be seen as identifying non-ideal but not necessarily incorrect annotations. This will mean curators encouraged to improve these annotations but they will not be automatically removed from GAFs on the GOC site.

• the IPI-evidenced annotations to Biological Process terms could be due to 'guilt-by-association' assays, involving interaction with a complex, therefore no id currently available to use in the 'with'. Therefore this soft IPI check should be limited to terms from molecular function ontology

• ACTION: Suboptimal GO annotations highlighted by such soft checks should be highlighted by AmiGO, encouraging groups to correct their data. Soft QC checks will also be implemented via the web-based GAF validator demo'd by Amelia at the GOC meeting.

• The OBO file contains in the comment field: subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation"

Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC.

GO:0007610 behavior GO:0051716 cellular response to stimulus GO:0048585 negative regulation of response to stimulus GO:0048584 positive regulation of response to stimulus GO:0048583 regulation of response to stimulus GO:0009628 response to abiotic stimulus GO:0009607 response to biotic stimulus GO:0042221 response to chemical stimulus GO:0009719 response to endogenous stimulus GO:0009605 response to external stimulus GO:0050896 response to stimulus GO:0006950 response to stress

• • interest from curation tools to include this suggestion? Other terms to add to this list? Include column 16 qualifier to the annotation advise?

ACTION for Ontology Developers: Subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation". Such information should only be included in the subset field of the OBO file, not also the comment; due possible redundancy issues (Chris)

Annotation Jamboree for Transcription

• date to be decided for annotation discussion - 26th July?

- agreed.

• Ideas for the proposed transcription jamboree, to be held during the annotation call on the 26th July? Examples of issues that could be raised here

GONUTs page also now available here: http://gowiki.tamu.edu/wiki/index.php/Category:RefGenome_Electronic_Jamboree_2011-07_Txn_Factors

• Karen's transcription annotation guide: File:TxnOHreannotationGuide.xls.pdf

ACTION: Examples of issues curators have had in using transcription GO terms, from looking at specific publications, should be posted on:http://gocwiki.geneontology.org/index.php/Transcription_jamboree Examples will be circulated the week before the jamboree. Focus to be on the Reference Genome targets, however other gene products can also be included in the discussions.

Reminders of previous action items

• Call for volunteers to adopt a GO annotation guidance page

• Feedback on: http://wiki.geneontology.org/index.php/GO_annotation_fields_required_for_correct_display