Annotation Conf. Call, June 28, 2011: Difference between revisions

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[[Category:Annotation Working Group]]
Present: Emily, Paola, Jane, Yasmin, Becky, Julie, Ranjana, Petra, Chris, Jodie, Li, Stan, Brenley, Lakshmi, Ruth.
Present: Emily, Paola, Jane, Yasmin, Becky, Julie, Ranjana, Petra, Chris, Jodie, Li, Stan, Brenley, Lakshmi, Ruth.


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* Discussion: short discussion on obsoleteion of anti-apoptosis terms.  
* 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.
'''* ACTION:''' Any curators wishing to join the next Apoptosis Content call on the 20th July please get in touch with Paola.


'''Annotation QCs'''
'''Annotation QCs'''
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[http://wiki.geneontology.org/index.php/Annotation_Quality_Control_Checks#Proposed_Hard_QC_checks further details available here]
[http://wiki.geneontology.org/index.php/Annotation_Quality_Control_Checks#Proposed_Hard_QC_checks further details available here]


* ACTION: Proposed QC checks will be implemented as 'soft' ones, as they can be seen as identifying sub-optimal 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.
'''* ACTION:''' Proposed QC checks will be implemented as 'soft' ones, as they can be seen as identifying sub-optimal 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
* 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.
* 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"
* The OBO file contains in the comment field: subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation"
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GO:0007610    behavior
GO:0007610    behavior
GO:0051716    cellular response to stimulus
GO:0051716    cellular response to stimulus
GO:0048585    negative regulation of response to stimulus
GO:0048585    negative regulation of response to stimulus
GO:0048584    positive regulation of response to stimulus
GO:0048584    positive regulation of response to stimulus
GO:0048583    regulation of response to stimulus
GO:0048583    regulation of response to stimulus
GO:0009628    response to abiotic stimulus
GO:0009628    response to abiotic stimulus
GO:0009607    response to biotic stimulus
GO:0009607    response to biotic stimulus
GO:0042221    response to chemical stimulus
GO:0042221    response to chemical stimulus
GO:0009719    response to endogenous stimulus
GO:0009719    response to endogenous stimulus
GO:0009605    response to external stimulus
GO:0009605    response to external stimulus
GO:0050896    response to stimulus
GO:0050896    response to stimulus
GO:0006950    response to stress
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?
** 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)
'''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'''
'''Annotation Jamboree for Transcription'''
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* date to be decided for annotation discussion - 26th July?
* date to be decided for annotation discussion - 26th July?


- agreed.
'''- 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 [http://gocwiki.geneontology.org/index.php/Transcription_jamboree  here]
* Ideas for the proposed transcription jamboree, to be held during the annotation call on the 26th July? Examples of issues that could be raised [http://gocwiki.geneontology.org/index.php/Transcription_jamboree  here]
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* Karen's transcription annotation guide: [[file:TxnOHreannotationGuide.xls.pdf]]
* Karen's transcription annotation guide: [[file:TxnOHreannotationGuide.xls.pdf]]


ACTION: Examples of issues curators have had in using transcription GO terms in annotations, from at specific experimental data publications, should be posted on:http://gocwiki.geneontology.org/index.php/Transcription_jamboree
'''ACTION:''' Examples of issues curators have had in using transcription GO terms in annotations, from at specific experimental data 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.
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'''
'''Reminders of previous action items'''

Latest revision as of 16:36, 9 April 2014

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' ones, as they can be seen as identifying sub-optimal 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

ACTION: Examples of issues curators have had in using transcription GO terms in annotations, from at specific experimental data 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